Patent Publication Number: US-2021189365-A1

Title: Engineered acid alpha-glucosidase variants

Description:
The present application claims priority to US Prov. Appln. Ser. No. 62/951,625, filed Dec. 20, 2019, hereby incorporated by reference in its entirety for all purposes. 
    
    
     FIELD OF THE INVENTION 
     The present invention provides engineered acid alpha-glucosidase (GAA) polypeptides and compositions thereof. In some embodiments, the engineered GAA polypeptides have been optimized to provide increased expression, stability at neutral and acidic pH, increased uptake into cells, and activity in cell lysates. the invention also provides methods for utilization of the compositions comprising the engineered GAA polypeptides for therapeutic and other purposes. 
     REFERENCE TO SEQUENCE LISTING, TABLE OR COMPUTER PROGRAM 
     The official copy of the Sequence Listing is submitted concurrently with the specification as an ASCII formatted text file via EFS-Web, with a file name of “CX7-199US2_ST25.txt”, a creation date of Dec. 17, 2020, and a size of 18.2 megabytes. The Sequence Listing filed via EFS-Web is part of the specification and is incorporated in its entirety by reference herein. 
     BACKGROUND OF THE INVENTION 
     Pompe disease is an autosomal recessive lysosomal storage disorder that is caused by mutations in the gene encoding acid alpha-glucosidase. This genetic defect leads to reduction of or absence of GAA in the body tissues. The resulting accumulation of glycogen in the lysosomes results in lysosomal swelling and rupture, which can lead to cell damage, organelle dysfunction, and other cellular defects. There are two forms of Pompe disease, including the classical infantile form and late-onset (childhood or adulthood) form. Disease severity is related to the amount of enzyme activity present in the cells of affected individuals. The infantile form is the most severe and rapidly progressive form, typically with GAA activity that is less than 1%, resulting in marked accumulation of glycogen in skeletal muscle, as well as heart and other tissues (See e.g., Hahn and Schänzer, Ann. Transl. Med., 7:283 [2019]). In these patients, there is multi-system storage of accumulated lysosomal and non-lysosomal bound-glycogen in the heart, skeletal muscle, and brain tissue (See, Schoser, Ann. Transl. Med., 7:292 [2019]). Patients present with elevated creatinine kinase levels, hypertrophic cardiomyopathy, failure to thrive, muscular hypotonia, and axial muscle weakness. If untreated, patients typically die within the first year of life due to cardiorespiratory insufficiency. Survival beyond 18 months of age is exceptional. This form is distinguished from non-classic or late-infantile Pompe disease, in which patients present with much less severe cardiac hypertrophy. Patients with late-onset Pompe disease typically experience progressive limb-girdle myopathy and respiratory dysfunction. These patients present with predominant, but not exclusive, muscle involvement. The patients eventually become wheelchair and/or ventilator-dependent. Respiratory insufficiency is the leading cause of death in these patients. Some patients may synthesize a non-functional form of GAA, but others are incapable of producing any type of native enzyme. The human GAA gene encoding GAA has been localized to chromosome 17q25.2-q25.3 and has been cloned and sequenced (See, Peruzzo et all, Ann. Transl. Med., 7:278-287 [2019]; and Martiniuk et al., DNA Cell. Biol., 10:283-292 [1991]). Although numerous mutations in the gene have been reported, the pathological mechanisms that lead to the wide range of phenotypes observed in affected patients remains unknown. Despite the availability of enzyme replacement therapy (ERT) utilizing recombinant GAA, there remains the need for better treatment and management options for affected patients. 
     SUMMARY OF THE INVENTION 
     The present invention provides engineered acid alpha-glucosidase (GAA) polypeptides and compositions thereof. In some embodiments, the engineered GAA polypeptides have been optimized to provide increased expression, stability at neutral and acidic pH, increased uptake into cells, and activity in cell lysates. The invention also provides methods for utilization of the compositions comprising the engineered GAA polypeptides for therapeutic and other purposes. 
     In some embodiments, the present invention provides engineered GAA polypeptides (also referred to herein as “recombinant GAA polypeptides”) and biologically active fragments and analogs thereof having improved properties when compared to a wild-type GAA enzyme and/or a reference GAA polypeptide under essentially the same conditions. The invention is further directed to methods of using the engineered GAA polypeptides and biologically active fragments and analogs thereof in therapeutic and/or other compositions. 
     The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. In some embodiments, the present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. In some embodiments, the present invention also provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. In some embodiments, the present invention further provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence consisting of SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. In some embodiments, the recombinant acid alpha-glucosidase sequences include a signal peptide sequence (e.g., SEQ ID NO: 3382 or 3384) encoded by the polynucleotides set forth in SEQ ID NO: 3381 and 3383, respectively. In some embodiments, the recombinant polynucleotides encoding the recombinant acid alpha-glucosidases of the present invention comprise a 57 base pair sequence that encodes a signal peptide. In some embodiments, the polypeptides of the recombinant acid alpha-glucosidases of the present invention comprise a 19 amino acid signal peptide. In some alternative embodiments, the recombinant polynucleotides encoding recombinant acid alpha-glucosidases do not include a sequence encoding a signal peptide. In some additional embodiments, the recombinant polypeptides comprising recombinant acid alpha-glucosidases do not include a signal peptide. It is not intended that the present invention be limited to recombinant acid alpha-glucosidase polynucleotide or polypeptide sequences comprising the signal peptide nucleotide or polypeptide sequence. It is also not intended that the present invention be limited to recombinant acid alpha-glucosidase polynucleotide or polypeptide sequences that do not comprise a signal peptide nucleotide or polypeptide sequence. 
     The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 2. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 27, 27/944, 28, 29/478, 30, 88, 107, 109, 109/842, 110, 113, 135, 137, 138, 148, 150, 247, 274, 276, 278, 375, 403, 414, 418, 418/499, 421, 426, 437, 444, 455, 463, 471, 471/478, 476, 489, 527, 547, 581, 610, 642, 668, 670, 692, 725/732, 750, 753, 786, 820, 862, 871, 895, 897, 930, 934, and 944, wherein the positions are numbered with reference to SEQ ID NO: 2. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from 27P, 27P/944W, 27R, 28P, 28R, 28S, 29T/478T, 30G, 30K, 30T, 88G, 88S, 107G, 107P, 109G/842E, 109P, 110G, 110L, 113S, 135A, 135Q, 137P, 138A, 148G, 148Y, 150G, 247R, 274G, 276F, 276Y, 278A, 278G, 375E, 403W, 414P, 418E/499R, 418R, 421S, 426R, 437S, 444T, 455V, 463A, 471Q/478S, 471S, 476A, 476H, 489R, 527R, 547G, 581G, 581T, 610A, 610G, 610S, 642M, 642Q, 642S, 668H, 670N, 692Q, 725N/732I, 750P, 753T, 786P, 786Y, 820E, 862G, 871E, 895R, 897V, 930R, 934R, 944G, and 944R, wherein the positions are numbered with reference to SEQ ID NO: 2. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from F27P, F27P/C944W, F27R, L28P, L28R, L285, L29T/A478T, V30G, V30K, V30T, K88G, K885, Q107G, Q107P, L109G/G842E, L109P, Q110G, Q110L, Q113S, S135A, S135Q, E137P, M138A, T148G, T148Y, T150G, Q247R, D274G, A276F, A276Y, T278A, T278G, I375E, R403W, R414P, A418E/H499R, A418R, Q421S, G426R, A437S, A444T, R455V, E463A, K471Q/A478S, K471S, S476A, S476H, A489R, N527R, A547G, K581G, K581T, W610A, W610G, W610S, L642M, L642Q, L642S, S668H, L670N, T692Q, K725N/V732I, A750P, A753T, R786P, R786Y, G820E, R862G, 1,871E, K895R, T897V, C930R, L934R, C944G, and C944R, wherein the positions are numbered with reference to SEQ ID NO: 2. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 29/218/240/668/700/744/869, 29/218/240/700/869, 29/240/596/668/700/744/869, 29/240/596/668/869, 36/106/150/218/527/750/883/894, 106/112/150/218/414/527/793/883, 106/150/169/218/414/486/527/750/894, 106/150/169/218/414/486/527/894, 106/150/169/218/414/486/749/793/883/894, 106/150/169/218/414/486/750/793/883/894, 106/150/169/218/414/486/793/883,106/150/169/218/414/486/894, 106/150/169/218/414/749/750/793/883, 106/150/169/218/414/749/793, 106/150/169/218/414/749/793/883, 106/150/169/218/486/527/749/793/894, 106/150/169/218/486/749/883, 106/150/169/218/486/883, 106/150/169/218/749/800, 106/150/169/414/486/749/750/883, 106/150/169/527/749/793/883, 106/150/169/749/793/883/894, 106/150/218/3311/414/486/527/733/749/793, 106/150/218/414/486/642/750/793/883, 106/150/218/414/486/750/793/894, 106/150/218/414/527/749/750/883, 106/150/218/414/527/749/793/883/894, 106/150/218/414/749/750/793/883/894, 106/150/218/414/749/793/883, 106/150/218/486/527/749/894, 106/150/218/486/793/883, 106/150/218/527/749/750/793, 106/150/218/527/793/894, 106/150/218/749/750/793, 106/150/218/793, 106/150/218/793/894, 106/150/245/793/883/894, 106/150/414/749/750/793/894, 106/150/414/749/793/894, 106/150/486/527/750/793, 106/150/486/749/793/883/894, 106/150/749/793/883, 106/169/185/218/414/749/750/793, 106/191/280/402/414/444/727, 106/191/414/444/522/928/944, 106/191/414/489/928/944, 106/280/402/414/444/489/727/944, 150/169/218/414/527/793, 150/218/414/486/749/750, 150/218/414/486/750/793, 150/218/414/486/750/793/883, 150/218/414/749/750/793/894, 150/218/414/749/793, 150/218/527/749/793, 150/218/749/750/793, 150/218/749/793, 150/414/486/527/750/894, 150/414/486/749/750/793, 150/486/750/883/894, 169/486/750/793/883, 180/275/402/518/547/610/638/669/671, 180/402/431/507/547/610/669/671/793, 180/402/507/547/610/671, 191/280/402/414/444/465/842/928, 191/280/402/414/444/489/500/944, 191/280/414/444/489/500/522/842/928/944, 191/280/414/444/489/522/727/944, 191/280/414/489/842/928/944, 191/280/414/944, 191/414/522/842/944, 196/402/431/547/610/638, 218/668/700/869, 224/402/507/518/547/638/668, 269/275/431/518/547/638/668/669, 275/281/402/431/507/518/610/668, 275/281/402/431/518/547/610/669/671, 275/281/402/507/518/547/638/669/671, 275/281/402/518/547/610/638/671, 275/281/402/518/547/610/668/669/887, 275/281/402/547/610/638/669/671, 275/281/431/518/547/638/669/671, 275/281/507/547/669/671, 275/281/610/638/668/669, 275/281/671, 275/377/402/507/518/669/671/715, 275/402/431/507/547/671, 275/402/431/518/610/638/669/671/922, 275/402/507/547/610/638/668/669, 275/402/507/547/610/638/669/671, 275/402/507/547/610/671, 275/402/547/610/638/669/671, 275/402/547/638/669/671, 275/402/638/669/671, 275/431/507/518/547/668/669/671, 275/431/507/518/610/669/671, 275/431/507/547/610/638/671, 275/431/518/547/638/668, 275/431/518/610/638/669/671, 275/431/638, 275/507/518/547/610/638/668/669, 275/507/518/547/638/669/671, 275/507/547/610/638/669/671, 275/507/547/668/669/671, 275/518/671, 280/402/536/928, 281/402/507/518/547/610/638/669/671, 281/402/507/547/638/669/671, 281/402/518/547/610/638/668/669, 281/402/518/547/668, 281/431/507/518/547/610/638/668, 402/431/518/547/610/668, 402/431/518/547/671, 402/431/518/610, 402/431/547/638/671, 431/507/518/541/547/638/669/671, 431/507/518/669/671, 507/547/610, 507/547/638/669/671, 547/610/638/671, and 547/638/668, wherein the positions are numbered with reference to SEQ ID NO: 2, In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from 29Q/218S/240I/668D/700F/744V/869L, 29Q/240I/596P/668D/869L, 29Q/240I/596S/668D/700F/744V/869T, 29V/218S/240I/700F/869T, 36R/106P/150S/218S/527D/750P/883H/894R, 106P/112S/150S/218S/414G/527D/793K/883H, 106P/150S/169S/218S/414G/486E/527D/750P/894R, 106P/150S/169S/218S/414G/486E/527D/894R, 106P/150S/169S/218S/414G/486E/749E/793K/883H/894R, 106P/150S/169S/218S/414G/486E/750P/793K/883H/894R, 106P/150S/169S/218S/414G/486E/793K/883H, 106P/150S/169S/218S/414G/486E/894R, 106P/150S/169S/218S/414G/749E/750P/793K/883H, 106P/150S/169S/218S/414G/749E/793K, 106P/150S/169S/218S/414G/749E/793K/883H, 106P/150S/169S/218S/486E/527D/749E/793K/894R, 106P/150S/169S/218S/486E/749E/883H, 106P/150S/169S/218S/486E/883H, 106P/150S/169S/218S/749E/800A, 106P/150S/169S/414G/486E/749E/750P/883H, 106P/150S/169S/527D/749E/793K/883H, 106P/150S/169S/749E/793K/883H/894R, 106P/150S/218 S/331A/414G/486E/527D/733E/749E/793K, 106P/150S/218S/414G/486E/642F/750P/793K/883H, 106P/150S/218S/414G/486E/750P/793K/894R, 106P/150S/218S/414G/527D/749E/750P/883H, 106P/150S/218S/414G/527D/749E/793K/883H/894G, 106P/150S/218S/414G/749E/750P/793K/883H/894R, 106P/150S/218S/414G/749E/793K/883H, 106P/150S/218S/486E/527D/749E/894R, 106P/150S/218S/486E/793K/883H, 106P/150S/218S/527D/749E1750P/793K, 106P/150S/218S/527D/793K/894G, 106P/150S/218S/749E/750P/793K, 106P/150S/218S/793K, 106P/150S/218S/793K/894R, 106P/150S/245S/793K/883H/894R, 106P/150S/414G/749E/750P/793K/894R, 106P/150S/414G/749E/793K/894R, 106P/150S/486E/527D/750P/793K, 106P/150S/486E/749E/793K/883H/894G, 106P/150S/749E/793K/883H, 106P/169S/185G/218S/414G/749E/750P/793K, 106P/191R/280D/402A/414G/444P/727P, 106P/191R/414G/444P/522V/928T/944S, 106P/191R/414G/489D/928T/944S, 106P/280D/402A/414G/444P/489D/727P/944S, 150S/169S/218S/414G/527D/793K, 150S/218S/414G/486A/750P/793K, 150S/218S/414G/486E/749E/750P, 150S/218S/414G/486E/750P/793K/883H, 150S/218S/414G/749E/750P/793K/894R, 150S/218S/414G/749E/793K, 150S/218S/527D/749E/793K, 150S/218S/749E/750P/793K, 150S/218S/749E/793K, 150S/414G/486E/527D/750P/894R, 150S/414G/486E/749E/750P/793K, 150S/486E/750P/883H/894G, 169S/486E/750P/793K/883H, 180H/275M/402A/518V/547G/610R/638I/669H/671N, 180H/402A/431V/507L/547G/610R/669H/671N/793G, 180H/402A/507L/547G/610R/671N, 191R/280D/402A/414G/444P/465E/842S/928T, 191R/280D/402A/414G/444P/489D/500A/944S, 191R/280D/414G/444P/489D/500A/522V/842S/928T/944S, 191R/280D/414G/444P/489D/522V/727P/944S, 191R/280D/414G/489D/842S/928T/944S, 191R/280D/414G/944S, 191R/414G/522V/842S/944S, 196V/402A/431V/547G/61.0R/638I, 218S/668D/700F/869T, 224F/402A/507L/518V/547G/638I/668D, 269N/275M/431V/518V/547G/638I/668D/669H, 275M/281V/402A/431V/507/518V/610R/668D, 275M/281V/402A/507L/518 V/547G/638I/669H/671N, 275M/281V/402A/518V/547G/610R/638I/671N, 275 M/281V/402A/518V/547G/610R/668D/669H/887D, 275M/281V/402A/547G/610R/638I/669H/671N, 275M/281V/507L/547G/669H/671N, 275M/28IV/610R/638I/668D/669H, 275M/402A/431V/507L/547G/671N, 275M/402A/507L/547G/610R/671N, 275M/402A/547G/638/669H/671N, 275M/431V/518V/547G/638I/668D, 275M/431V/518V/610R/638I/669H/671N, 275M/431V/638I, 275M/507L/547G/668D/669H/671N, 275V/281V/402A/431V/518V/547G/610R/669H/671N, 275V/281V/431V/518V/547G/638I/669H/671N, 275V/281V/671N, 275V/377K/402A/507L/518V/669H/671N/715G, 275 V/402A/431V/518V/610R/638I/669H/671N/922L, 275V402A/507L/547G/610R/638I/668D/669H, 275 V/402A/507L/547G/610R/638I/669H/671N, 275V/402A/547G/610R/638I/669H/671N, 275V/402A/638I/669H/671N, 275 V/431V/507L/518V/547G/668D/669H/671N, 275V/431V/507L/518V/610R/669H/671N, 275 V/431V/507L/547G/610R/638I/671N, 275V/507L/518V/547G/610R/638I/668D/669H, 275V/507L/518V/547G/638I/669H/671N/275 V/507L/547G/610R/638I/669H/671N, 275V/518V/671N, 280D/402A/536I/928T, 281V/402A/507L/518V/547G/610R/638I/669H/671N, 281V/402A/507L/547G/638I/669H/671N, 281V/402A/518V/547G/610R/638I/668D/669H, 281V/402A/518V/547G/668D, 281V/431V/507L/518V/547G/610R/638/668D, 402A/431V/518V/547G/610R/668D, 402A/431V/518V/547G/671N, 402A/431V/518V/610R, 402A/431V/547G/638I/671N, 431V/507L/518V/541E/547G/638I/669H/671N, 431V/507L/518V/669H/671N, 507L/547G/610R, 507L/547G/638I/669H/671N, 547G/610R/638I/671N, and 547G/638I/668D, wherein the positions are numbered with reference to SEQ ID NO: 2. In sonic embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from L29Q/L218S/240I/668D/H700F/I744V/I869L, L29Q/L240I/A596P/S668D/I869L, L29Q/L240I/A596S/S668D/H700F/I744V/I869T, L29V/L218S/L240I/H700F/I869T, G36R/K106P/T150S/L218S/N527D/A750P/R883H/Q894R, K106P/A112S/T150S/L218S/R414G/N527D/E793K/R883H, K106P/T150S/N169S/L218S/R414G/T486E/N527D/A750P/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/N527D/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/Q749E/E793K/R883H/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/A750WE793K/R883H/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/E793K/R883H, K106P/T150S/N169S/L218S/R414G/T486E/Q894R, K106P/T150S/N169S/L218S/R414G/Q749E/A750P/E793K/R883H, K106P/T150S/N169S/L218S/R414G/Q749E/E793K, K106P/T150S/N169/L218S/R414G/Q749E/E793K/R883H, K106P/T150S/N169S/L218S/T486E/N527D/Q749E/E793K1Q894R, K106P/T150S/N169S/L218S/T486E/Q749E/R883H, K106/T150S/N169S/L218S/T486E/R883H, K106P/T150S/N169S/L218S/Q749E/P800A, K106P/T150S/N169S/R414G/T486E/Q749E/A750P/R883H, K106P/T150S/N169S/N527D/Q749E/E793K/R883H, K106P/T150S/N169S/Q749E/E793K/R883H/Q894R, K106P/T150S/L218S/V331A/R414G/T486E/N527D/D733E/Q749E/E793K, K106P/T150S/L218S/R414G/T486E/L642F/A750P/E793K/R883H, K106P/T150S/L218S/R414G/T486E/A750P/E793K/Q894R, K106P/T150S/L218S/R414G/N527D/Q749E/A750P/R883H, K106P/T150S/L218S/R414G/N527D/Q749E/E793K/R883H/Q894G, K106P/T150S/L218S/R414G/Q749E/A750P/E793K/R883H/Q894R, K106P/T150S/L218S/R414G/Q749E/E793K/R883H, K106P/T150S/L218S/T486E/N527D/Q749E/Q894R, K106P/T150S/L218S/T486E/E793K/R883H, K106P/T150S/L218S/N527D/Q749E/A750P/E793K, K106P/T150S/L218S/N527D/E793K/Q894G, K106P/T150S/L218S/Q749E/A750P/E793K, K106P/T150S/L218S/E793K, K106P/T150S/L218S/E793K/Q894R, K106P/T150S/P245S/E793K/R883H/Q894R, K106P/T150S/R414G/Q749E/A750P/E793K/Q894R, K106P/T150S/R414G/Q749E/E793K/Q894R, K106P/T150S/T486E/N527D/A750P/E793K, K106P/T150S/T486E/Q749E/E793K/R883H/Q894G, K106P/T150S/Q749E/E793K/R883H, K106P/N169S/V185G/L218S/R414G/Q749E/A750P/E793K, K106P/H191R/G280D/S402A/R414G/A444P/S727P, K106P/H191R/R414G/A444P/E522V/D928T/C944S, K106P/H191 R414G/A489D/D928T/C944S, K106P/G280D/S402A/R4141G/A444P/A489D/S727P/C944S, T150S/N1.69S/L218S/R414G/N527D/E793K, T150S/L218S/R414G/T486A/A750P/E793K, T150S/L218S/R414G/T486E/Q749E/A750P, T150S/L218S/R414G/T486E/A750P/E793K/R883H, T150S/L218S/R414G/Q749E/A750P/E793K/Q894R, T10S/L218S/R414G/Q749E/E793K, T150S/L21S/N527D/Q749E/E793K, T150S/L218S/Q749E/A750P/E793K, T10S/L218S/Q749E/E793K, T150S/R414G/T486E/N527D/A750P/Q894R, T150S/R414G/T486E/Q749E/A750P/E793K, T150/T486E/A750P/R883H/Q894G, N169S/T486E/A750P/E793K/R883H, N180H/L275M/S402A/I518V/A547G/W610R/V638I/L669H/S671N, N180H/S402A/M431V/M507L/A547G/W610R/L669H/S671N/E793G, N180H/S402A/M507L/A547G/W610R/S671N, H191R/G280D/S402A/R414G/A444P/G465E/G842S/D928T, H191R/G280D/S402A/R414G/A444P/A489D/D500A/C944S, H19 R/G280D/R414G/A444P/A489D/D500A/E522V/G842S/D928T/C944S, H191R/G280D/R414G/A444P/A489D/E522V/S727P/C944S, H191R/G280D/R414G/A489D/G842S/D928T/C944S, H191R/G280D/R414G/C944S, H191R/R414G/E522V/G842S/C944S, A196V/S402A/M431V/A547G/W610R/V638I, L218S/S668D/H700F/I869T, L224F/S402A/M507L/I518V/A547G/V638I/S668D, T269N/L275M/M431V/I518V/A547G/V638I/S668D/L669H, L275M/A281V/S402A/M431V/M507L/I518V/W610P/S668D, L275M/A281V/S402A/M507L/I518V/A547G/V638I/L669H/S671N, L275M/A281V/S402A/I518V/A547G/W610R/V638I/S671N, L275M/A281V/S402A/I518V/A547G/W610R/S668D/L669H/E887D, L275M/A281V/S402A/A547G/W610R/V638I/L669H/S671N, L275M/A281V/M507L/A547G/L669H/S671N, L275M/A281V/V610R/V638I/S668D/L669H, L275M/S402A/M431V/M507L/A547G/S671N, L275M/S402A/M507L/A547G/W610R/S671N, L275M/S402A/A547G/V638I/L669H/S671N, L275M/M431V/I518V/A547G/V638I/S668D, L275M/M431V/I518V/W610R/V638I/L669H/S671N, L275M/M431V/V638I, L275M/M507L/A547G/S668D/L669H/S671N, L275 V/A281V/S402A/M431V/I518V/A547G/W610R/L669H/S671N, L275V/A281I V/M431V/I518 V/A547G/V638/L669H/S671N, L275V/A281V/S671N, L275V/R377K/S402A/M507L/I518V/L669H/S671N/V715G, L275 V/S402A/M431V/I518V/W610R/V638I/L669H/S671N/P922L, L275V/S402A/M507L/A547G/W610R/V638I/S668D/L669H, L275 V/S402A/M507L/A547G/W610R/V638I/L669H/S671N, L275V/S402A/A547G/W610R/V638I/L669H/S671N, L275V/S402A/V638I/L669H/S671N, L275V/M431V/M507L/I518V/A547G/S668D/L669H/S671N, L275V/M431V/M507L/I518V/W610R/L669H/S671N, L275 V/M431V/M507L/A547G/W610R/V638I/S671N, L275V/M507L/I518V/A547G/W610R/V638I/S668D/L669H, L275V/M507L/I518V/A547G/V638I/L669H/S671N, L275V/M507L/A547G/W610R/V638I/L669H/S671N, L275V/I518V/S671N, G280D/S402A/V536I/D928T, A281V/S402A/M507L/I518V/A547G/W610R/V638I/L669H/S671N, A281V/S402A/M507L/A547G/V638I/L669H/S671N, A281V/S402A/I518V/A547G/W610R/V638I/S668D/L669H, A281V/S402A/I518V/A547G/S668D, A281V/M431V/M507L/I518V/A547G/W610R/V638I/S668D, S402A/M431V/I518V/A547G/W610R/S668D, S402A/M431V/I518V/A547G/S671N, S402A/M431V/I518V/W610R, S402A/M431V/A547G/V638I/S671N, M431V/M507L/I518V/G541E/A547G/V638I/L669H/S671N, M431V/M507L/I518V/L669H/S671N, M507L/A547G/W610R, M507L/A547G/V638I/L669H/S671N, A547G/W610R/V638I/S671N, and A547G/V638I/S668D, wherein the positions are numbered with reference to SEQ ID NO: 2. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from 27, 27/944, 28, 29/218/240/668/700/744/869, 29/218/240/700/869, 29/240/596/668/700/744/869, 29/240/596/668/869, 29/478, 30, 36/106/150/218/527/750/883/894, 106/112/150/218/414/527/793/883, 106/150/169/218/414/486/527/750/894, 106/150/169/218/414/486/527/894, 106/150/169/218/414/486/749/793/883/894, 106/150/169/218/414/486/750/793/883/894, 106/150/169/218/414/486/793/883, 106/150/169/218/414/486/894, 106/150/169/218/414/749/750/793/883, 106/150/169/218/414/749/793, 106/150/169/218/414/749/793/883, 106/150/169/218/486/749/883, 106/150/169/218/486/883, 106/150/169/414/486/749/750/883, 106/150/169/527/749/793/883, 106/150/169/749/793/883/894, 106/150/218/331/414/486/527/733/749/793, 106/150/218/414/486/642/750/793/883, 106/150/218/414/486/750/793/894, 106/150/218/414/527/749/750/883, 106/150/218/414/527/749/793/883/894, 106/150/218/414/749/750/793/883/894, 106/150/218/414/749/793/883, 106/150/218/486/527/749/894, 106/150/218/486/793/883, 106/150/218/527/793/894, 106/150/245/793/883/894, 106/150/414/749/750/793/894, 106/150/414/749/793/894, 106/150/486/527/750/793, 106/150/486/749/793/883/894, 106/150/749/793/883, 106/169/185/218/414/749/750/793, 106/191/280/402/414/444/727, 106/280/402/414/444/489/727/944, 107, 109, 109/842, 110, 135, 138, 148, 150, 150/218/414/486/749/750, 150/218/414/486/750/793, 150/218/414/486/750/793/883, 150/218/414/749/750/793/894, 150/218/414/749/793, 150/414/486/527/750/894, 150/414/486/749/750/793, 150/486/750/883/894, 169/486/750/793/883, 180/275/402/518/547/610/638/669/671, 180/402/431/507/547/610/669/671/793, 180/402/507/547/610/671, 191/280/402/414/444/489/500/944, 191/280/414/444/489/522/727/944, 191/280/414/944, 191/414/522/842/944, 196/402/431/547/610/638, 218/668/700/869, 224/402/507/518/547/638/668, 269/275/431/518/547/638/668/669, 274, 275/281/402/431/507/518/610/668, 275/281/402/431/518/547/610/669/671, 275/281/402/507/518/547/638/669/671, 275/281/402/518/547/610/638/671, 275/281/402/518/547/610/668/669/887, 275/281/402/547/610/638/669/671, 275/281/431/518/547/638/669/671, 275/281/507/547/669/671, 275/281/610/638/668/669, 275/377/402/507/518/669/671/715, 275/402/431/507/547/671, 275/402/431/518/610/638/669/671/922, 275/402/507/547/610/638/668/669, 275/402/507/547/610/638/669/671, 275/402/507/547/610/671, 275/402/547/610/638/669/671, 275/402/547/638/669/671, 275/402/638/669/671, 275/431/507/518/547/668/669/671, 275/431/507/518/610/669/671, 275/431/507/547/610/638/671, 275/431/518/547/638/668, 275/431/518/610/638/669/671, 275/431/638, 275/507/518/547/610/638/668/669, 275/507/518/547/638/669/671, 275/507/547/610/638/669/671, 275/507/547/668/669/671, 276, 281/402/507/518/547/610/638/669/671, 281/402/507/547/638/669/671, 281/402/518/547/610/638/668/669, 281/402/518/547/668, 281/431/507/518/547/610/638/668, 375, 402/431/518/547/610/668, 402/431/518/547/671, 402/431/518/610, 402/431/547/638/671, 403, 414, 418/499, 431/507/518/541/547/638/669/671, 431/507/518/669/671, 437, 471/478, 507/547/610, 507/547/638/669/671, 547, 547/610/638/671, 547/638/668, 581, 642, 670, 692, 750, 753, 820, 871, and 944, wherein the positions are numbered with reference to SEQ ID NO: 2. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from 27P, 27P/944W, 27R, 28P, 28S, 29Q/218S/240I/668D/700F/744V/869L, 29Q/240I/596P/668D/869L, 29Q/240I/596S/668D/700F/744V/869T, 29T/478T, 29V/218S/240I/700F/869T, 30G, 30K, 30T, 36R/106P/150S/218S/527D/750P/883H/894R, 106P/112S/150S/218S/414G/527D/793K/883H, 106P/150S/169S/218S/414G/486E/527D/750P/894R, 106P/150S/169S/218S/414G/486E/527D/894R, 106P/150S/169S/218S/414G/486E/749E/793K/883H/894R, 106P/150S/169S/218S/414G/486E/750P/793K/883H/894R, 106P/150S/169S/218S/414G/486E/793K/883H, 106P/150S/169S/218S/414G/486E/894R, 106P/150S/169S/218S/414G/749E/750P/793K/883H, 106P/150S/169S/218S/414G/749E/793K, 106P/150S/169S/218S/414G/749E/793K/883H, 106P/150S/169S/218S/486E/749E/883H, 106P/150S/169S/218S/486E/883H, 106P/150S/169S/414G/486E/749E/750P/883H, 106P/150S/169S/527D/749E/793K/883H, 106P/150S/169S/749E/793K/883H/894R, 106P/150S/218S/331A/414G/486E/527D/733E/749E/793K, 106P/150S/218S/414G/486E/642F/750P/793K/883H, 106P/150S/218S/414G/486E/750P/793K/894R, 106P/150S/218S/414G/527D/749E/750P/883H, 106P/150S/218S/414G/527D/749E/793K/883H/894G, 106P/150S/218S/414G/749E/750P/793K/883H/894R, 106P/150S/218S/414G/749E/793K/883H, 106P/150S/218S/486E/527D/749E/894R, 106P/150S/218S/486E/793K/883H, 106P/150S/218S/527D/793K/894G, 106P/150S/245S/793K/883H/894R, 106P/150S/414G/749E/750P/793K/894R, 106P/150S/414G/749E/793K/894R, 106P/150S/486E/527D/750P/793K, 106P/150S/486E/749E/793K/883H/894G, 106P/150S/749E/793K/883H, 106P/169S/185G/218S/414G/749E/750P/793K, 106P/191R/280D/402A/414G/444P/727P, 106P/280D/402A/414G/444P/489D/727P/944S, 107G, 109G/842E, 109P, 110G, 110L, 135Q, 138A, 148G, 148Y, 150G, 150S/218S/414G/486A/750P/793K, 150S/218S/414G/486E/749E/750P, 150S/218S/414G/486E/750P/793K/883H, 150/218S/414G/749E/750P/793K/894R, 150S/218S/414G/749E/793K, 150S/414G/486E/527D/750P/894R, 150S/414G/486E/749E/750P/793K, 150S/486E/750P/883H/894G, 169S/486E/750P/793K/883H, 180H/275M/402A/518V/547G/610R/638I/669H/671N, 180H/402A/431V/507L/547G/610R/669H/671N/793G, 180H/402A/507L/547G/610R/671N, 191R/280D/402A/414G/444P/489D/500A/944S, 191R/280D/414G/444P/489D/522V/727P/944S, 191R/280D/414G/944S, 191R/414G/522V/842S/944S, 196V/402A/431V/547G/610R/638I, 218S/668D/700F/869T, 224F/402A/507L/518V/547G/638I/668D, 269N/275M/431V/518V/547G/638I/668D/669H, 274G, 275M/281V/402A/431V/507L/518V/610R/668D, 275M/281V/402A/507L/518V/547G/638I/669H/671N, 275M/281V/402A/518V/547G/610R/638I/671N, 275M/281V/402A/518V/547G/610R/668D/669H/887D, 275M/281V/402A/547G/610R/638I/669H/671N, 275M/281V/507L/547G/669H/671N, 275M/281V/610R/638I/668D/669H, 275M/402A/431V/507L/547G/671N, 275M/402A/507L/547G/610R/671N, 275M/402A/547G/638I/669H/671N, 275M/431V/518V/547G/638/668D, 275M/431V/518V/610R/638I/669H/671N, 275M/431V/638I, 275M/507L/547G/668D/669H/671N, 275V/281V/402A/431V/518V/547G/610R/669H/671N, 275V/281V/431V/518V/547G/638I/669H/671N, 275V/377K/402A/507L/518V/669H/671N/715G, 275V/402A/431V/518V/610R/638I/669H/671N/922L, 275V/402A/507L/547G/610R/638I/668D/669H, 275V/402A/507L/547G/610R/638I/669H/671N, 275V/402A/547G/610R/638I/669H/671N, 275V/402A/638I/669H/671N, 275V/431V/507L/518V/547G/668D/669H/671N, 275V/431V/507L/518V/610R/669H/671N, 275V/431V/507L/547G/610R/638I/671N, 275V/507L/518V/547G/610R/638I/668D/669H, 275V/507L/518V/547G/638I/669H/671N, 275V/507L/547G/610R/638I/669H/671N, 276Y, 281V/402A/507L/518V/547G/610R/638I/669H/671N, 281V/402A/507L/547G/638I/669H/671N, 281V/402A/518V/547G/610R/638I/668D/669H, 281V/402A/518V/547G/668D, 281V/431V/507L/518V/547G/610R/638I/668D, 375E, 402A/431V/518V/547G/610R/668D, 402A/431V/518V/547G/671N, 402A/431V/518V/610R, 402A/431V/547G/638I/671N, 403W, 414P, 418E/499R, 431V/507L/518V/541E/547G/638I/669H/671N, 431V/507L/518V/669H/671N, 437S, 471Q/478S, 507L/547G/610R, 507L/547G/638I/669H/671N, 547G, 547G/610R/638I/671N, 547G/638I/668D, 581G, 581T, 642Q, 642S, 670N, 692Q, 750P, 753T, 820E, 871E, and 944G, wherein the positions are numbered with reference to SEQ ID NO: 2. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from F27P, F27P/C944W, F27R, L28P, L28S, L29Q/L218S/L240I/S668D/H700F/I744V/I869L, L29Q/L240I/A596P/S668D/I869L, L29Q/L240I/A596S/S668D/H700F/I744V/I869T, L29T/A478T, L29V/L218S/L240I/H700F/I869T, V30G, V30K, V30T, G36R/K106P/T150S/L218S/N527D/A750P/R883H/Q894R, K106P/A112S/T150S/L218S/R414G/N527D/E793K/R883H, K106P/T150S/N169S/L218S/R414G/T486E/N527D/A750P/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/N527D/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/Q749E/E793K/R883H/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/A750P/E793K/R883H/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/E793K/R883H, K106P/T150S/N169S/L218S/R414G/T486E/Q894R, K106P/T150S/N169S/L218S/R414G/Q749E/A750P/E793K/R883H, K106P/T150S/N169S/L218S/R414G/Q749E/E793K, K106P/T150S/N169S/L218S/R414G/Q749E/E793K/R883H, K106P/T150S/N169S/L218S/T486E/Q749E/R883H, K106P/T150S/N169S/L218S/T486E/R883H, K106P/T1505/N169S/R414G/T486E/Q749E/A750P/R883H, K106P/T1505/N169S/N527D/Q749E/E793K/R883H, K106P/T150S/N169S/Q749E/E793K/R883H/Q894R, K106P/T150S/L218S/V331A/R414G/T486E/N527D/D733E/Q749E/E793K, K106P/T150S/L218S/R414G/T486E/L642F/A750P/E793K/R883H, K106P/T150S/L218S/R414G/T486E/A750P/E793K/Q894R, K106P/T150S/L218S/R414G/N527D/Q749E/A750P/R883H, K106P/T150S/L218S/R414G/N527D/Q749E/E793K/R883H/Q894G, K106P/T150S/L218S/R414G/Q749E/A750P/E793K/R883H/Q894R, K106P/T150S/L218S/R414G/Q749E/E793K/R883H, K106P/T150S/L218S/T486E/N527D/Q749E/Q894R, K106P/T150S/L218S/T486E/E793K/R883H, K106P/T150S/L218S/N527D/E793K/Q894G, K106P/T150S/P245S/E793K/R883H/Q894R, K106P/T150S/R414G/Q749E/A750P/E793K/Q894R, K106P/T150S/R414G/Q749E/E793K/Q894R, K106P/T150S/T486E/N527D/A750P/E793K, K106P/T150S/T486E/Q749E/E793K/R883H/Q894G, K106P/T150S/Q749E/E793K/R883H, K106P/N169S/V185G/L218S/R414G/Q749E/A750P/E793K, K106P/H191R/G280D/S402A/R414G/A444P/S727P, K106P/G280D/S402A/R414G/A444P/A489D/S727P/C944S, Q107G, L109G/G842E, L109P, Q110G, Q110L, S135Q, M138A, T148G, T148Y, T150G, T150S/L218S/R414G/T486A/A750P/E793K, T150S/L218S/R414G/T486E/Q749E/A750P, T150S/L218S/R414G/T486E/A750P/E793K/R883H, T150S/L218S/R414G/Q749E/A750P/E793K/Q894R, T150S/L218S/R414G/Q749E/E793K, T150S/R414G/T486E/N527D/A750P/Q894R, T150S/R414G/T486E/Q749E/A750P/E793K, T150S/T486E/A750P/R883H/Q894G, N169S/T486E/A750P/E793K/R883H, N180H/L275M/S402A/I518V/A547G/W610R/V6381/L669H/S671N, N180H/S402A/M431V/M507L/A547G/W610R/L669H/S671N/E793G, N180H/S402A/M507L/A547G/W610R/S671N, H191R/G280D/S402A/R414G/A444P/A489D/D500A/C944S, H191R/G280D/R414G/A444P/A489D/E522V/S727P/C944S, H191R/G280D/R414G/C944S, H191R/R414G/E522V/G842S/C944S, A196V/S402A/M431V/A547G/W610R/V638I, L218S/S668D/H700F/I869T, L224F/S402A/M507L/I518V/A547G/V6381/S668D, T269N/L275M/M431V/I518V/A547G/V638I/S668D/L669H, D274G, L275M/A281V/S402A/M431V/M507L/I518V/W610R/S668D, L275M/A281V/S402A/M507L/I518V/A547G/V638I/L669H/S671N, L275M/A281V/S402A/I518V/A547G/W610R/V6381/S671N, L275M/A281V/S402A/I518V/A547G/W610R/S668D/L669H/E887D, L275M/A281V/S402A/A547G/W610R/V638I/L669H/S671N, L275M/A281V/M507L/A547G/L669H/S671N, L275M/A281V/W610R/V638I/S668D/L669H, L275M/S402A/M431V/M507L/A547G/S671N, L275M/S402A/M507L/A547G/W610R/S671N, L275M/S402A/A547G/V638I/L669H/S671N, L275M/M431V/I518V/A547G/V638I/S668D, L275M/M431V/I518V/W610R/V638I/L669H/S671N, L275M/M431V/V638I, L275M/M507L/A547G/S668D/L669H/S671N, L275V/A281V/S402A/M431V/I518V/A547G/W610R/L669H/S671N, L275V/A281V/M431V/I518V/A547G/V638I/L669H/S671N, L275V/R377K/S402A/M507L/I518V/L669H/S671N/V715G, L275 V/S402A/M431V/I518V/W610R/V638I/L669H/S671N/P922L, L275 V/S402A/M507L/A547G/W610R/V638I/S668D/L669H, L275 V/S402A/M507L/A547G/W610R/V638I/L669H/S671N, L275V/S402A/A547G/W610R/V638I/L669H/S671N, L275V/S402A/V638I/L669H/S671N, L275V/M431V/M507L/I518V/A547G/S668D/L669H/S671N, L275V/M431V/M507L/I518V/W610R/L669H/S671N, L275V/M431V/M507L/A547G/W610R/V6381/S671N, L275V/M507L/I518V/A547G/W610R/V6381/S668D/L669H, L275 V/M507L/I518V/A547G/V638I/L669H/S671N, L275V/M507L/A547G/W610R/V638I/L669H/S671N, A276Y, A281V/S402A/M507L/I518V/A547G/W610R/V638I/L669H/S671N, A281V/S402A/M507L/A547G/V6381/L669H/S671N, A281V/S402A/I518V/A547G/W610R/V638I/S668D/L669H, A281V/S402A/I518V/A547G/S668D, A281V/M431V/M507L/I518V/A547G/W610R/V6381/S668D, I375E, S402A/M431V/I518V/A547G/W610R/S668D, S402A/M431V/I518V/A547G/S671N, S402A/M431V/I518V/W610R, S402A/M431V/A547G/V638I/S671N, R403W, R414P, A418E/H499R, M431V/M507L/I518V/G541E/A547G/V638I/L669H/S671N, M431V/M507L/I518V/L669H/S671N, A437S, K471Q/A478S, M507L/A547G/W610R, M507L/A547G/V638I/L669H/S671N, A547G, A547G/W610R/V638I/S671N, A547G/V638I/S668D, K581G, K581T, L642Q, L642S, L670N, T692Q, A750P, A753T, G820E, L871E, and C944G, wherein the positions are numbered with reference to SEQ ID NO: 2. 
     The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 6. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 27, 27/944, 28, 29/218/240/668/700/744/869, 29/218/240/700/869, 29/240/596/668/700/744/869, 29/240/596/668/869, 29/478, 30, 36/106/150/218/527/750/883/894, 88, 106/112/150/218/414/527/793/883, 106/150/169/218/414/486/527/750/894, 106/150/169/218/414/486/527/894, 106/150/169/218/414/486/749/793/883/894, 106/150/169/218/414/486/750/793/883/894, 106/150/169/218/414/486/793/883, 106/150/169/218/414/486/894, 106/150/169/218/414/749/750/793/883, 106/150/169/218/414/749/793, 106/150/169/218/414/749/793/883, 106/150/169/218/486/527/749/793/894, 106/150/169/218/486/749/883, 106/150/169/218/486/883, 106/150/169/218/749/800, 106/150/169/414/486/749/750/883, 106/150/169/527/749/793/883, 106/150/169/749/793/883/894, 106/150/218/331/414/486/527/733/749/793, 106/150/218/414/486/642/750/793/883, 106/150/218/414/486/750/793/894, 106/150/218/414/527/749/750/883, 106/150/218/414/527/749/793/883/894, 106/150/218/414/749/750/793/883/894, 106/150/218/414/749/793/883, 106/150/218/486/527/749/894, 106/150/218/486/793/883, 106/150/218/527/749/750/793, 106/150/218/527/793/894, 106/150/218/749/750/793, 106/150/218/793, 106/150/218/793/894, 106/150/245/793/883/894, 106/150/414/749/750/793/894, 106/150/414/749/793/894, 106/150/486/527/750/793, 106/150/486/749/793/883/894, 106/150/749/793/883, 106/169/185/218/414/749/750/793, 106/191/280/402/414/444/727, 106/191/414/444/522/928/944, 106/191/414/489/928/944, 106/280/402/414/444/489/727/944, 107, 109, 109/842, 110, 113, 135, 137, 138, 148, 150, 150/169/218/414/527/793, 150/218/414/486/749/750, 150/218/414/486/750/793, 150/218/414/486/750/793/883, 150/218/414/749/750/793/894, 150/218/414/749/793, 150/218/527/749/793, 150/218/749/750/793, 150/218/749/793, 150/414/486/527/750/894, 150/414/486/749/750/793, 150/486/750/883/894, 169/486/750/793/883, 180/275/402/518/547/610/638/669/671, 180/402/431/507/547/610/669/671/793, 180/402/507/547/610/671, 191/280/402/414/444/465/842/928, 191/280/402/414/444/489/500/944, 191/280/414/444/489/500/522/842/928/944, 191/280/414/444/489/522/727/944, 191/280/414/489/842/928/944, 191/280/414/944, 191/414/522/842/944, 196/402/431/547/610/638, 218/668/700/869, 224/402/507/518/547/638/668, 247, 269/275/431/518/547/638/668/669, 274, 275/281/402/431/507/518/610/668, 275/281/402/431/518/547/610/669/671, 275/281/402/507/518/547/638/669/671, 275/281/402/518/547/610/638/671, 275/281/402/518/547/610/668/669/887, 275/281/402/547/610/638/669/671, 275/281/431/518/547/638/669/671, 275/281/507/547/669/671, 275/281/610/638/668/669, 275/281/671, 275/377/402/507/518/669/671/715, 275/402/431/507/547/671, 275/402/431/518/610/638/669/671/922, 275/402/507/547/610/638/668/669, 275/402/507/547/610/638/669/671, 275/402/507/547/610/671, 275/402/547/610/638/669/671, 275/402/547/638/669/671, 275/402/638/669/671, 275/431/507/518/547/668/669/671, 275/431/507/518/610/669/671, 275/431/507/547/610/638/671, 275/431/518/547/638/668, 275/431/518/610/638/669/671, 275/431/638, 275/507/518/547/610/638/668/669, 275/507/518/547/638/669/671, 275/507/547/610/638/669/671, 275/507/547/668/669/671, 275/518/671, 276, 278, 280/402/536/928, 281/402/507/518/547/610/638/669/671, 281/402/507/547/638/669/671, 281/402/518/547/610/638/668/669, 281/402/518/547/668, 281/431/507/518/547/610/638/668, 375, 402/431/518/547/610/668, 402/431/518/547/671, 402/431/518/610, 402/431/547/638/671, 403, 414, 418, 418/499, 421, 426, 431/507/518/541/547/638/669/671, 431/507/518/669/671, 437, 444, 455, 463, 471, 471/478, 476, 489, 507/547/610, 507/547/638/669/671, 527, 547, 547/610/638/671, 547/638/668, 581, 610, 642, 668, 670, 692, 725/732, 750, 753, 786, 820, 862, 871, 895, 897, 934, and 944, wherein the positions are numbered with reference to SEQ ID NO: 6. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 27P, 27P/944W, 27R, 28P, 28R, 28S, 29Q/218S/240I/668D/700F/744V/869L, 29Q/240I/596P/668D/869L, 29Q/240I/596S/668D/700F/744V/869T, 29T/478T, 29V/218S/240I/700F/869T, 30G, 30K, 30T, 36R/106P/150S/218S/527D/750P/883H/894R, 88G, 88S, 106P/112S/150S/218S/414G/527D/793K/883H, 106P/150S/169S/218S/414G/486E/527D/750P/894R, 106P/150S/169S/218S/414G/486E/527D/894R, 106P/150S/169S/218S/414G/486E/749E/793K/883H/894R, 106P/150S/169S/218S/414G/486E/750P/793K/883H/894R, 106P/150S/169S/218S/414G/486E/793K/883H, 106P/150S/169S/218S/414G/486E/894R, 106P/150S/169S/218S/414G/749E/750P/793K/883H, 106P/150S/169S/218S/414G/749E/793K, 106P/150S/169S/218S/414G/749E/793K/883H, 106P/150S/169S/218S/486E/527D/749E/793K/894R, 106P/150S/169S/218S/486E/749E/883H, 106P/150S/169S/218S/486E/883H, 106P/150S/169S/218S/749E/800A, 106P/150S/169S/414G/486E/749E/750P/883H, 106P/150S/169S/527D/749E/793K/883H, 106P/150S/169S/749E/793K/883H/894R, 106P/150S/218S/331A/414G/486E/527D/733E/749E/793K, 106P/150S/218S/414G/486E/642F/750P/793K/883H, 106P/150S/218S/414G/486E/750P/793K/894R, 106P/150S/218S/414G/527D/749E/750P/883H, 106P/150S/218S/414G/527D/749E/793K/883H/894G, 106P/150S/218S/414G/749E/750P/793K/883H/894R, 106P/150S/218S/414G/749E/793K/883H, 106P/150S/218S/486E/527D/749E/894R, 106P/150S/218S/486E/793K/883H, 106P/150S/218S/527D/749E/750P/793K, 106P/150S/218S/527D/793K/894G, 106P/150S/218S/749E/750P/793K, 106P/150S/218S/793K, 106P/150S/218S/793K/894R, 106P/150S/245S/793K/883H/894R, 106P/150S/414G/749E/750P/793K/894R, 106P/150S/414G/749E/793K/894R, 106P/150S/486E/527D/750P/793K, 106P/150S/486E/749E/793K/883H/894G, 106P/150S/749E/793K/883H, 106P/169S/185G/218S/414G/749E/750P/793K, 106P/191R/280D/402A/414G/444P/727P, 106P/191R/414G/444P/522V/928T/944S, 106P/191R/414G/489D/928T/944S, 106P/280D/402A/414G/444P/489D/727P/944S, 107G, 107P, 109G/842E, 109P, 110G, 110L, 113S, 135A, 135Q, 137P, 138A, 148G, 148Y, 150G, 150S/169S/218S/414G/527D/793K, 150S/218S/414G/486A/750P/793K, 150S/218S/414G/486E/749E/750P, 150S/218S/414G/486E/750P/793K/883H, 150S/218S/414G/749E/750P/793K/894R, 150S/218S/414G/749E/793K, 150S/218S/527D/749E/793K, 150S/218S/749E/750P/793K, 150S/218S/749E/793K, 150S/414G/486E/527D/750P/894R, 150S/414G/486E/749E/750P/793K, 150S/486E/750P/883H/894G, 169S/486E/750P/793K/883H, 180H/275M/402A/518V/547G/610R/6381/669H/671N, 180H/402A/431V/507L/547G/610R/669H/671N/793G, 180H/402A/507L/547G/610R/671N, 191R/280D/402A/414G/444P/465E/842S/928T, 191R/280D/402A/414G/444P/489D/500A/944S, 191R/280D/414G/444P/489D/500A/522V/842S/928T/944S, 191R/280D/414G/444P/489D/522V/727P/944S, 191R/280D/414G/489D/842S/928T/944S, 191R/280D/414G/944S, 191R/414G/522V/842S/944S, 196V/402A/431V/547G/610R/638I, 218S/668D/700F/869T, 224F/402A/507L/518V/547G/638I/668D, 247R, 269N/275M/431V/518V/547G/6381/668D/669H, 274G, 275M/281V/402A/431V/507L/518V/610R/668D, 275M/281V/402A/507L/518V/547G/6381/669H/671N, 275M/281V/402A/518V/547G/610R/638I/671N, 275M/281V/402A/518V/547G/610R/668D/669H/887D, 275M/281V/402A/547G/610R/638I/669H/671N, 275M/281V/507L/547G/669H/671N, 275M/281V/610R/638I/668D/669H, 275M/402A/431V/507L/547G/671N, 275M/402A/507L/547G/610R/671N, 275M/402A/547G/638I/669H/671N, 275M/431V/518V/547G/638I/668D, 275M/431V/518V/610R/638I/669H/671N, 275M/431V/638I, 275M/507L/547G/668D/669H/671N, 275V/281V/402A/431V/518V/547G/610R/669H/671N, 275V/281V/431V/518V/547G/638I/669H/671N, 275V/281V/671N, 275V/377K/402A/507L/518V/669H/671N/715G, 275V/402A/431V/518V/610R/638I/669H/671N/922L, 275V/402A/507L/547G/610R/638I/668D/669H, 275V/402A/507L/547G/610R/638I/669H/671N, 275V/402A/547G/610R/638I/669H/671N, 275V/402A/638I/669H/671N, 275V/431V/507L/518V/547G/668D/669H/671N, 275V/431V/507L/518V/610R/669H/671N, 275V/431V/507L/547G/610R/638I/671N, 275V/507L/518V/547G/610R/638I/668D/669H, 275V/507L/518V/547G/638I/669H/671N, 275V/507L/547G/610R/638S/669H/671N, 275V/518V/671N, 276F, 276Y, 278A, 278G, 280D/402A/536I/928T, 281V/402A/507L/518V/547G/610R/638I/669H/671N, 281V/402A/507L/547G/638I/669H/671N, 281V/402A/518V/547G/610R/638I/668D/669H, 281V/402A/518V/547G/668D, 281V/431V/507L/518V/547G/610R/638I/668D, 375E, 402A/431V/518V/547G/610R/668D, 402A/431V/518V/547G/671N, 402A/431V/518V/610R, 402A/431V/547G/638I/671N, 403W, 414P, 418E/499R, 418R, 421S, 426R, 431V/507L/518V/541E/547G/638I/669H/671N, 431V/507L/518V/669H/671N, 437S, 444T, 455V, 463A, 471Q/478S, 471S, 476A, 476H, 489R, 507L/547G/610R, 507L/547G/638I/669H/671N, 527R, 547G, 547G/610R/638I/671N, 547G/638I/668D, 581G, 581T, 610A, 610G, 610S, 642M, 642Q, 642S, 668H, 670N, 692Q, 725N/7321, 750P, 753T, 786P, 786Y, 820E, 862G, 871E, 895R, 897V, 934R, 944G, and 944R, wherein the positions are numbered with reference to SEQ ID NO: 6. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from F27P, F27P/C944W, F27R, L28P, L28R, L28S, L29Q/L218S/L240I/S668D/H700F/1744V/I869L, L29Q/L2401/A596P/S668D/I869L, L29Q/L240I/A596S/S668D/H700F/I744V/I869T, L29T/A478T, L29V/L218S/L240I/H700F/I869T, V30G, V30K, V30T, G36R/K106P/T150S/L218S/N527D/A750P/R883H/Q894R, K88G, K88S, K106P/A112S/T150S/L218S/R414G/N527D/E793K/R883H, K106P/T150S/N169S/L218S/R414G/T486E/N527D/A750P/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/N527D/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/Q749E/E793K/R883H/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/A750P/E793K/R883H/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/E793K/R883H, K106P/T1505/N169S/L218S/R414G/T486E/Q894R, K106P/T1505/N169S/L218S/R414G/Q749E/A750P/E793K/R883H, K106P/T150S/N169S/L218S/R414G/Q749E/E793K, K106P/T150S/N169S/L218S/R414G/Q749E/E793K/R883H, K106P/T1505/N169S/L218S/T486E/N527D/Q749E/E793K/Q894R, K106P/T150S/N169S/L218S/T486E/Q749E/R883H, K106P/T150S/N169S/L218S/T486E/R883H, K106P/T150S/N169S/L218S/Q749E/P800A, K106P/T150S/N169S/R414G/T486E/Q749E/A750P/R883H, K106P/T1505/N169S/N527D/Q749E/E793K/R883H, K106P/T150S/N169S/Q749E/E793K/R883H/Q894R, K106P/T150S/L218S/V331A/R414G/T486E/N527D/D733E/Q749E/E793K, K106P/T150S/L218S/R414G/T486E/L642F/A750P/E793K/R883H, K106P/T150S/L218S/R414G/T486E/A750P/E793K/Q894R, K106P/T150S/L218S/R414G/N527D/Q749E/A750P/R883H, K106P/T150S/L218S/R414G/N527D/Q749E/E793K/R883H/Q894G, K106P/T150S/L218S/R414G/Q749E/A750P/E793K/R883H/Q894R, K106P/T150S/L218S/R414G/Q749E/E793K/R883H, K106P/T150S/L218S/T486E/N527D/Q749E/Q894R, K106P/T150S/L218S/T486E/E793K/R883H, K106P/T150S/L218S/N527D/Q749E/A750P/E793K, K106P/T150S/L218S/N527D/E793K/Q894G, K106P/T150S/L218S/Q749E/A750P/E793K, K106P/T150S/L218S/E793K, K106P/T150S/L218S/E793K/Q894R, K106P/T150S/P245S/E793K/R883H/Q894R, K106P/T150S/R414G/Q749E/A750P/E793K/Q894R, K106P/T150S/R414G/Q749E/E793K/Q894R, K106P/T150S/T486E/N527D/A750P/E793K, K106P/T150S/T486E/Q749E/E793K/R883H/Q894G, K106P/T150S/Q749E/E793K/R883H, K106P/N169S/V185G/L218S/R414G/Q749E/A750P/E793K, K106P/H191R/G280D/S402A/R414G/A444P/S727P, K106P/H191R/R414G/A444P/E522V/D928T/C944S, K106P/H191R/R414G/A489D/D928T/C944S, K106P/G280D/S402A/R414G/A444P/A489D/S727P/C944S, Q107G, Q107P, L109G/G842E, L109P, Q110G, Q110L, Q113S, S135A, S135Q, E137P, M138A, T148G, T148Y, T150G, T150S/N169S/L218S/R414G/N527D/E793K, T150S/L218S/R414G/T486A/A750P/E793K, T150S/L218S/R414G/T486E/Q749E/A750P, T150S/L218S/R414G/T486E/A750P/E793K/R883H, T150S/L218S/R414G/Q749E/A750P/E793K/Q894R, T150S/L218S/R414G/Q749E/E793K, T150S/L218S/N527D/Q749E/E793K, T150S/L218S/Q749E/A750P/E793K, T150S/L218S/Q749E/E793K, T150S/R414G/T486E/N527D/A750P/Q894R, T150S/R414G/T486E/Q749E/A750P/E793K, T150S/T486E/A750P/R883H/Q894G, N169S/T486E/A750P/E793K/R883H, N180H/L275M/S402A/1518V/A547G/W610R/V638I/L669H/S671N, N180H/S402A/M431V/M507L/A547G/W610R/L669H/S671N/E793G, N180H/S402A/M507L/A547G/W610R/S671N, H191R/G280D/S402A/R414G/A444P/G465E/G842S/D928T, H191R/G280D/S402A/R414G/A444P/A489D/D500A/C944S, H191R/G280D/R414G/A444P/A489D/D500A/E522V/G842S/D928T/C944S, H191R/G280D/R414G/A444P/A489D/E522V/S727P/C944S, H191R/G280D/R414G/A489D/G842S/D928T/C944S, H191R/G280D/R414G/C944S, H191R/R414G/E522V/G842S/C944S, A196V/S402A/M431V/A547G/W610R/V638I, L218S/S668D/H700F/I869T, L224F/S402A/M507L/I518V/A547G/V6381/S668D, Q247R, T269N/L275M/M431V/I518V/A547G/V638I/S668D/L669H, D274G, L275M/A281V/S402A/M431V/M507L/I518V/W610R/S668D, L275M/A281V/S402A/M507L/I518V/A547G/V638I/L669H/S671N, L275M/A281V/S402A/I518V/A547G/W610R/V6381/S671N, L275M/A281V/S402A/I518V/A547G/W610R/S668D/L669H/E887D, L275M/A281V/S402A/A547G/W610R/V638I/L669H/S671N, L275M/A281V/M507L/A547G/L669H/S671N, L275M/A281V/W610R/V638I/S668D/L669H, L275M/S402A/M431V/M507L/A547G/S671N, L275M/S402A/M507L/A547G/W610R/S671N, L275M/S402A/A547G/V638I/L669H/S671N, L275M/M431V/I518V/A547G/V638I/S668D, L275M/M431V/I518V/W610R/V638I/L669H/S671N, L275M/M431V/V638I, L275M/M507L/A547G/S668D/L669H/S671N, L275V/A281V/S402A/M431V/I518V/A547G/W610R/L669H/S671N, L275V/A281V/M431V/I518V/A547G/V638I/L669H/S671N, L275V/A281V/S671N, L275V/R377K/S402A/M507L/I518V/L669H/S671N/V715G, L275V/S402A/M431V/I518V/W610R/V638I/L669H/S671N/P922L, L275V/S402A/M507L/A547G/W610R/V6381/S668D/L669H, L275V/S402A/M507L/A547G/W610R/V638I/L669H/S671N, L275V/S402A/A547G/W610R/V638I/L669H/S671N, L275V/S402A/V638I/L669H/S671N, L275V/M431V/M507L/I518V/A547G/S668D/L669H/S671N, L275V/M431V/M507L/I518V/W610R/L669H/S671N, L275V/M431V/M507L/A547G/W610R/V6381/S671N, L275V/M507L/I518V/A547G/W610R/V6381/S668D/L669H, L275V/M507L/I518V/A547G/V6381/L669H/S671N, L275V/M507L/A547G/W610R/V638I/L669H/S671N, L275V/I518V/S671N, A276F, A276Y, T278A, T278G, G280D/S402A/V536I/D928T, A281V/S402A/M507L/I518V/A547G/W610R/V638I/L669H/S671N, A281V/S402A/M507L/A547G/V6381/L669H/S671N, A281V/S402A/I518V/A547G/W610R/V638I/S668D/L669H, A281V/S402A/I518V/A547G/S668D, A281V/M431V/M507L/I518V/A547G/W610R/V638I/S668D, I375E, S402A/M431V/I518V/A547G/W610R/S668D, S402A/M431V/I518V/A547G/S671N, S402A/M431V/I518V/W610R, S402A/M431V/A547G/V638I/S671N, R403W, R414P, A418E/H499R, A418R, Q421S, G426R, M431V/M507L/I518V/G541E/A547G/V638I/L669H/S671N, M431V/M507L/I518V/L669H/S671N, A437S, A444T, R455V, E463A, K471Q/A478S, K471S, S476A, S476H, A489R, M507L/A547G/W610R, M507L/A547G/V638I/L669H/S671N, N527R, A547G, A547G/W610R/V638I/S671N, A547G/V638I/S668D, K581G, K581T, W610A, W610G, W610S, L642M, L642Q, L642S, S668H, L670N, T692Q, K725N/V7321, A750P, A753T, R786P, R786Y, G820E, R862G, L871E, K895R, T897V, L934R, C944G, and C944R, wherein the positions are numbered with reference to SEQ ID NO: 6. 100101 The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 8. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 4, 27, 27/28/489, 27/418/478, 28, 28/29, 28/29/113/135/138, 28/29/113/135/418, 28/29/135, 28/29/418, 29/113/126/135/193, 29/113/135, 29/113/135/455, 29/113/138, 29/148, 29/478, 106, 106/138/218/431/671/749, 106/218/281, 106/218/455, 106/218/455/507/749, 106/489/671, 106/638, 106/671/934, 113, 113/135/418, 113/418/455/478/581, 113/418/478/489/581, 135, 135/148/150/418, 135/478/489/581, 135/489, 135/944, 138/218/668/671, 138/218/749/934, 138/671/749/934, 157, 218, 218/281, 218/281/431, 218/281/671, 218/431, 218/431/489/507/749/934, 218/455, 218/507/749, 218/507/934, 218/638/671, 218/749, 281/431/489/668, 345/934, 418, 418/489, 431/668/671, 489/638/934, 489/671/934, 489/749, 489/934, 507/668, 507/671/934, 671/749, 671/934, and 749/784, wherein the positions are numbered with reference to SEQ ID NO: 8. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from 4H, 27P/28S/489R, 27P/418E/4781, 27R, 28S, 28S/29T, 28S/29T/113S/135Q/138A, 28S/29T/113S/135Q/418E, 28S/29T/135Q, 28S/29T/418E, 29T/113S/126Q/135Q/193Q, 29T/113S/135Q, 29T/113S/135Q/455V, 29T/113S/138A, 29T/148G, 29T/478T, 106P, 106P/138A/218S/431V/671N/749E, 106P/218S/281V, 106P/218S/455V, 106P/218S/455V/507L/749E, 106P/489R/671N, 106P/638I, 106P/671N/934R, 113S, 113S/135Q/418E, 113S/418E/455V/478T/581T, 113S/418E/478T/489R/581T, 135P/944Y, 135Q, 135Q/148G/150G/418E, 135Q/478T/489R/581T, 135Q/489R, 138A/218S/668D/671N, 138A/218S/749E/934R, 138A/671N/749E/934R, 157M, 218S, 218S/281V, 218S/281V/431V, 218S/281V/671N, 218S/431V, 218S/431V/489R/507L749E/934R, 218S/455 V, 218S/507L/749E, 218S/507L/934R, 218S/638I/671N, 218S/749E, 281V/431V/489R/668D, 345K/934R, 418E, 418E/489R, 431V/668D/671N, 489R/638I/934R, 489R/671N/934R, 489R/749E, 489R/934R, 507L/668D, 507L/671N/934R, 671N/749E, 671N/934R, and 749E/784T, wherein the positions are numbered with reference to SEQ ID NO: 8. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from P4H, F27P/L28S/A489R, F27P/A418E/A478T, F27R, L285, L28S/L29T, L28S/L29T/Q113S/S135Q/M138A, L28S/L29T/Q113S/S135Q/A418E, L28S/L29T/S135Q, L28S/L29T/A418E, L29T/Q113S/P126Q/S135Q/H193Q, L29T/Q113S/S135Q, L29T/Q113S/S135Q/R455V, L29T/Q113/M138A, L29T/T148G, L29T/A478T, K106P, K106P/M 138A/L218S/M431V/S671N/Q749E, K106P/L218S/A281V, K106P/L218S/R455V, K106P/L218S/R455V/M507L/Q749E, K106P/A489R/671N, K106P/V638I, K106P/S671N/L934R, Q113S, Q113S/S135Q/A418E, Q113S/A418E/R455V/A478T/K581T, Q113S/A418E/A478T/A489R/K581T, S135P/C944Y, S135Q, S135Q/T148G/S150G/A418E, S135Q/A478T/A489R/K581T, S135Q/A489R, M138A/L218S/S668D/S671N, M138A/L218S/Q749E/L934R, M138A/S671N/Q749E/L934R, L157M, L218S, L218S/A281V , L218S/A281V/M431V, L218S/A281V/S671N, L218S/M431V, L218S/M431V/A489R/M507L/Q749E/L934R, L218S/R455V, L218S/M507L/Q749E, L218S/M507L/L934R, L218S/V638I/S671N, L218S/Q749E, A281V/M431V/A489R/S668D, Q345/L934R, A418E, A418E/A489R, M431V/S668D/S671N, A489R/V638I/L934R, A489R/S671N/L934R, A489R/Q749E, A489R/L934R, M507L/S668D, M507L/S671N/L934R, S671N/Q749E, S671N/L934R, and Q749E/A784, wherein the positions are numbered with reference to SEQ ID NO: 8. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from 27, 27/418/478, 28, 28/29, 28/29/113/135/138, 28/29/113/135/418, 28/29/135, 28/29/418, 29/113/126/135/193, 29/113/135, 29/113/135/455, 29/113/138, 29/148, 29/478, 106, 106/138/218/431/671/749, 106/489/671, 106/638, 113/135/418, 113/418/455/478/581, 113/418/478/489/581, 135, 135/148/150/418, 135/478/489/581, 135/944, 138/218/668/671, 157, 218/638/671, 418, 418/489, 431/668/671, 507/668, and 671/749, wherein the positions are numbered with reference to SEQ ID NO: 8. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from 27P/418E/478T, 27R, 28S, 28S/29T, 28S/29T/113S/135Q/138A, 28S/29T/113S/135Q/418E, 28S/29T/135Q, 28S/29T/418E, 29T/113S/126Q/135Q/193Q, 29T/113S/135Q, 29T/113S/135Q/455V, 29T/113S/138A, 29T/148G, 29T/478T, 106P, 106P/138A/218S/431V/671N/749E, 106P/489R/671N, 106P/638I, 113S/135Q/418E, 113S/418E/455V/478T/581T, 113S/418E/478T/489R/581T, 135P/944Y, 135Q, 135Q/148G/150G/418E, 135Q/478T/489R/581T, 138A/218S/668D/671N, 157M, 218S/638I/671N, 418E, 418E/489R, 431V/668D/671N, 507L/668D, and 671N/749E, wherein the positions are numbered with reference to SEQ ID NO: 8. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from F27P/A418E/A478T, F27R, L28S, L28S/L29T, L28S/L29T/Q113S/S135Q/M138A, L28S/L29T/Q113S/S135Q/A418E, L28S/L29T/S135Q, L28S/L29T/A418E, L29T/Q113S/P126Q/S135Q/H193Q, L29T/Q113S/S135Q, L29T/Q113S/S135Q/R455V, L29T/Q113S/M138A, L29T/T148G, L29T/A478T, K106P, K106P/M138A/L218S/M431V/S671N/Q749E, K106P/A489R/S671N, K106P/V638I, Q113S/S135Q/A418E, Q113S/A418E/R455V/A478T/K581T, Q113S/A418E/A478T/A489R/K581T, S135P/C944Y, S135Q, S135Q/T148G/S150G/A418E, S135Q/A478T/A489R/K581T, M138A/L218S/S668D/S671N, L157M, L218S/V638I/S671N, A418E, A418E/A489R, M431V/S668D/S671N, M507L/S668D, and S671N/Q749E, wherein the positions are numbered with reference to SEQ ID NO: 8. 
     The present invention also provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 12. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 4, 27, 27/28/489, 27/418/478, 28, 28/29, 28/29/113/135/138, 28/29/113/135/418, 28/29/135, 28/29/418, 29/113/126/135/193, 29/113/135, 29/113/135/455, 29/113/138, 29/148, 29/478, 106, 106/138/218/431/671/749, 106/218/281, 106/218/455, 106/218/455/507/749, 106/489/671, 106/638, 106/671/934, 113, 113/135/418, 113/418/455/478/581, 113/418/478/489/581, 135, 135/148/150/418, 135/478/489/581, 135/489, 135/944, 138/218/668/671, 138/218/749/934, 138/671/749/934, 157, 218, 218/281/431, 218/281/671, 218/431, 218/455, 218/507/749, 218/638/671, 218/749, 281/431/489/668, 345/934, 418, 418/489, 431/668/671, 489/638/934, 489/671/934, 489/749, 489/934, 507/668, 507/671/934, 671/749, 671/934, and 749/784, wherein the positions are numbered with reference to SEQ ID NO: 12. In some embodiments. the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 4H, 27P/28S/489R, 27P/418E/478T, 27R, 28S, 28S/29T, 28S/29T/113S/135Q/138A, 28S/29T/113S/135Q/418E, 28S/29T/135Q, 28S/29T/418E, 29T/113S/126Q/135Q/193Q, 29T/113S/135Q, 29T/113S/135Q/455V, 29T/113S/138A, 29T/148G, 29T/478T, 106P, 106P/138A/218S/431V/671N/749E, 106P/218S/281V, 106P/218S/455V, 106P/218S/455V/507L/749E, 106P/489R/671N, 106P/638I, 106P/671N/934R, 113S, 113S/135Q/418E, 113S/418E/455V/478T/581T, 113S/418E/478T/489R/581T, 135P/944Y, 135Q, 135Q/148G/150G/418E, 135Q/478T/489R/581T, 135Q/489R, 138A/218S/668D/671N, 138A/218S/749E/934R, 138A/671N/749E/934R, 157M, 218S, 218S/281V/431V, 218S/281V/671N, 218S/431V, 218S/455V, 218S/507L/749E, 218S/638I/671N, 218S/749E, 281V/431V/489R/668D, 345K/934R, 418E, 418E/489R, 431V/668D/671N, 489R/638I/934R, 489R/671N/934R, 489R/749E, 489R/934R, 507L/668D, 507L/671N/934R, 671N/749E, 671N/934R, and 749E/784T, wherein the positions are numbered with reference to SEQ ID NO: 12. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from P4H, F27P/L28S/A489R, F27P/A418E/A478T, F27R, L28S, L28S/L29T, L28S/L29T/Q113S/S135Q/M138A, L28S/L29T/Q113S/S135Q/A418E, L28S/L29T/S135Q, L28S/L29T/A418E, L29T/Q113S/P126Q/S135Q/H193Q, L29T/Q113S/S135Q, L29T/Q113S/S135Q/R455V, L29T/Q113S/M138A, L29T/T148G, L29T/A478T, K106P, K106P/M138A/L218S/M431V/S671N/Q749E, K106P/L218S/A281V, K106P/L218S/R455V, K106P/L218S/R455V/M507L/Q749E, K106P/A489R/S671N, K106P/V6381, K106P/S671N/L934R, Q113S, Q113S/S135Q/A418E, Q113S/A418E/R455V/A478T/K581T, Q113S/A418E/A478T/A489R/K581T, S135P/C944Y, S135Q, S135Q/T148G/S150G/A418E, S135Q/A478T/A489R/K581T, S135Q/A489R, M138A/L218S/S668D/S671N, M138A/L218S/Q749E/L934R, M138A/S671N/Q749E/L934R, L157M, L218S, L218S/A281V/M431V, L218S/A281V/S671N, L218S/M431V, L218S/R455V, L218S/M507L/Q749E, L218S/V6381/S671N, L218S/Q749E, A281V/M431V/A489R/S668D, Q345K/L934R, A418E, A418E/A489R, M431V/S668D/S671N, A489R/V638I/L934R, A489R/S671N/L934R, A489R/Q749E, A489R/L934R, M507L/S668D, M507L/S671N/L934R, S671N/Q749E, S671N/L934R, and Q749E/A784T, wherein the positions are numbered with reference to SEQ ID NO: 12. 
     The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 14. The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 16. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 22, 24, 27, 27/165, 30, 33, 34, 37/62, 37/62/79/196/696/862, 37/62/523, 37/62/523/793, 37/64/66/79/154/523/681/793/862, 37/79/154/793, 37/196, 37/528/696/793, 37/528/790, 37/528/790/793/862, 37/790/793, 39, 39/58/489/725/830/842/930/944, 39/70/109/830/842, 39/70/489/612, 39/70/725, 39/267, 39/267/489/522/612/830/842, 39/267/489/830/944, 39/489/500/612, 39/500/612, 40, 44/157, 47, 49, 50, 55, 60/500/612, 62/79/154/862, 62/79/196/681/862, 62/79/523/528/790, 62/79/790/793, 62/79/862, 62/92, 62/92/790/793, 62/106/523/528/696/793/862, 62/154/696/793/862, 62/793/862, 68, 70, 70/267/725/944, 70/267/930/944, 70/489/930, 70/725/830/860/930/944, 77, 79/154/681, 79/154/793/862, 79/862, 89, 97, 106/154, 107, 109, 109/522/612/725, 109/522/830/944, 109/612, 118, 149, 157, 158, 178, 179, 196/528/681/790/793, 207, 208, 217, 267/489/500/725/830/930, 267/522/725, 352, 385, 424, 448, 463, 489/830/944, 500, 500/612/830/860, 500/860/930, 500/930/944, 522/725, 523, 523/790/793, 528/681, 528/793, 528/862, 672, 673, 725, 734, 740, 753, 774, 778, 793, 830, 844, 862, 875, 880, 892, 902, 922, 925, 930, 932, 934, 938, and 944, wherein the positions are numbered with reference to SEQ ID NO: 14 and/or 16. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from 22R, 24E, 24R, 24W, 27A, 27G, 27G/165I, 27K, 27R, 27S, 27V, 27W, 30D, 30L, 33G, 33P, 34D, 34M, 34T, 37F/62E, 37F/62E/79S/196T/696S/862Q, 37F/62E/523N, 37F/62E/523N/793K, 37F/64Q/66G/79S/154R/523N/681Q/793K/862Q, 37F/79S/154R/793K, 37F/196T, 37F/528S/696S/793K, 37F/528S/790V, 37F/528S/790V/793K/862Q, 37F/790V/793K, 39D, 39H, 39Q, 39Q/58L/489D/725E/830K/842S/930P/944S, 39Q/70A/109P/830K/842S, 39Q/70A/489D/612D, 39Q/70A/725E, 39Q/267K, 39Q126K/489D/522V/612D/830K/Q842S, 39Q/2671Q489D/830K/944S, 39Q/489D/500A/612D, 39Q/500A/612D, 40W, 44I/157V, 47G, 47R, 49A, 49G, 50G, 50L, 50V, 55C, 55L, 60V/500A/612D, 62E/79S/154R/862Q, 62E/79S/196T/168Q/862Q, 62E/79S/523N/528S/790V, 62E/79S/790V/793K, 62.E/79S/862Q, 62E/92R, 62E/92R/790V/793K, 62E/106R/523N/528S/696S/793K/862Q, 62E/154R/696S/793K/862Q, 62E/793K/862Q, 68N, 68S, 68W, 70A/267K/725E/944S, 70A/267K/930P/944S, 70A/489D/930P, 70A/725E/830K/860F/930P/944S, 70Q, 77W, 79S/154R/681Q, 79S/154R/793K/862Q, 79S/862Q, 89R, 97D, 97G, 106R/154R, 107G, 109D, 109P/522V/612D/725E, 109P/522V/830K/944S, 109P/612D, 118F, 149R, 157Q, 158E, 158F, 178G, 178V, 1791, 196T/528S/681Q/790V/793K, 207R, 207Y, 208G, 208I, 217A, 217D, 267K/489D/500A/725E/830K/930P, 267K/522V/725E, 352K, 352V, 385G, 424K, 448L, 463A, 489D/830K/944S, 500A, 500A/612D/830K/860F, 500A/860F/93OP, 500A/930P/944S, 522V/725E, 523N, 523N/790V/793K, 528S/681Q, 528S/793K, 528S/862Q, 672E, 672K, 673N, 673R, 725F, 725V, 734K, 740G, 740Q, 753S, 774G, 774S, 778Q, 793K, 830V, 844R, 862Q, 875D, 880R, 892L, 902L, 922E, 925A, 925W, 930P, 932A, 934F, 938A, 938P, 944R, and 944S, wherein the positions are numbered with reference to SEQ ID NO: 14 and/or 16. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from I22R, L24E, L24R, L24W, F27A, F27G, F27G/M165I, F27K, F27R, F275, F27V F27W, V30D, V30L, E33G, E33P, L34D, L34M, L34T, S37F/A62E, S37F/A62E/N79S/A196T/A696S/R862Q, S37F/A62E/D523N, S37F/A62E/D523N/E793K, S37F/P64Q/R66G/N79S/K154R/D523N/E681Q/E793K/R862Q, S37F/N79S/K154R/E793K, S37F/A196T, S37F/N528S/A696S/E793K, 537F/N528S/I790V, 537F/N528S/I790V/E793K/R862Q, S37F/I790V/E793K, P39D, P39H, P39Q, P39Q/R58L/A489D/K725E/Q830K/G842S/C930P/C944S, P39Q/V70A/L109P/Q830K/G842S, P39Q/V70A/A489D/S612D, P39Q/V70A/K725E, P39Q/R267K, P39Q/R267K/A489D/E522V/S612D/Q830K/G842S, P39Q/R267K/A489D/Q830K/C944S, P39Q/A489D/D500A/S612D, P39Q/D500A/S612D, V40W, T44I/L157V, A47G, A47R, Q49A, Q49G, Q50G, Q50L, Q50V, P55C, P55L, A60V/D500A/S612D, A62E/N79S/K154R/R862Q, A62E/N79S/A196T/E681Q/R862Q, A62E/N795/D523N/N528S/I790V, A62E/N79S/790V/E793K, A62E/N79S/R862Q, A62E/Q92R, A62E/Q92R/I790V/E793K, A62E/K106R/D523N/N528S/A696S/E793K/R862Q, A62E/K154R/A696S/E793K/R862Q, A62E/E793K/R862Q, R68N, R68S, R68W, V70A/R267K/K725E/C944S, V70A/R267K/C930P/C944S, V70A/A489D/C930P, V70A/K725E/Q830K/L860F/C930P/C944S, V70Q, P77W, N79S/K154R/E681Q, N79S/K154R/E793K/R862Q, N79S/R862Q, A89R, A97D, A97G, K106R/K154R, Q107G, L109D, L109P/E522V/S612D/K725E, L109P/E522V/Q830K/C944S, L109P/S612D, W118F, P149R, L157Q, T158E, T158F, P178G, P178V, A179L, A196T/N528S/E681Q/I790V/E793K, E207R, E207Y, E208G, E208I, Q217A, Q217D, R267K/A489D/D500A/K725E/Q830K/C930P, R267K/E522V/K725E, Y352K, Y352V, R385G, H424K, R448L, E463A, A489D/Q830K/C944S, D500A, D500A/S612D/Q830K/L860F, D500A/L860F/C930P, D500A/C930P/C944S, E522V/K725E, D523N, D523N/I790V/E793K, N528S/E681Q, N528S/E793K, N528S/R862Q, L672E, L672K, P673N, P673R, K725F, K725V, H734K, E740G, E740Q, A753S, A774G, A774S, L778Q, E793K, Q830V, E844R, R862Q, N875D, E880R, Q892L, A902L, P922E, K925A, K925W, C930P, S932A, L934F, Q938A, Q938P, C944R, and C944S, wherein the positions are numbered with reference to SEQ ID NO: 14 and/or 16. 
     The present invention also provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 18, wherein the positions are numbered with reference to SEQ ID NO: 18. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 22, 24, 27, 27/165, 30, 33, 34, 37/62, 37/62/79/196/696/862, 37/62/523, 37/196, 37/528/790, 39, 39/70/109/830/842, 39/70/725, 39/267, 39/267/489/522/612/830/842, 39/267/489/830/944, 40, 70/267/725/944, 70/267/930/944, 70/489/930, 107, 109, 109/522/830/944, 217, 267/489/500/725/830/930, 267/522/725, 352, 385, 500/930/944, 673, 734, 774, 778, 875, 930, 932, and 934, wherein the positions are numbered with reference to SEQ ID NO: 18. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 22R, 24E, 24R, 24W, 27G, 27G/165I, 27K, 27R, 27W, 30D, 33G, 34D, 34M, 34T, 37F/62E, 37F/62E/79S/196T/696S/862Q, 37F/62E/523N, 37F/196T, 37F/528S/790V, 39D, 39Q, 39Q/70A/109P/830K/842S, 39Q/70A/725E, 39Q/267K, 39Q/267K/489D/522V/612D/830K/842S, 39Q/267K/489D/830K/944S, 40W, 70A/267K/725E/944S, 70A/267K/930P/9445, 70A/489D/930P, 107G, 109D, 109P/522V/830K/944S, 217D, 267K/489D/500A/725E/830K/930P, 267K/522V/725E, 352K, 352V, 385G, 500A/930P/944S, 673N, 734K, 774G, 778Q, 875D, 930P, 932A, and 934F, wherein the positions are numbered with reference to SEQ ID NO: 18. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from I22R, L24E, L24R, L24W, F27G, F27G/M165I, F27K, F27R, F27W, V30D, E33G, L34D, L34M, L34T, S37F/A62E, S37F/A62E/N79S/A196T/A696S/R862Q, S37F/A62E/D523N, S37F/A196T, S37F/N528S/I790V, P39D, P39Q, P39Q/V70A/L109P/Q830K/G842S, P39Q/V70A/K725E, P39Q/R267K, P39Q/R267K/A489D/E522V/S612D/Q830K/G842S, P39Q/R267K/A489D/Q830K/C944S, V40W, V70A/R267K/K725E/C944S, V70A/R267K/C930P/C944S, V70A/A489D/C930P, Q107G, L109D, L109P/E522V/Q830K/C944S, Q217D, R267K/A489D/D500A/K725E/Q830K/C930P, R267K/E522V/K725E, Y352K, Y352V, R385G, D500A/C930P/C944S, P673N, H734K, A774G, L778Q, N875D, C930P, S932A, and L934F, wherein the positions are numbered with reference to SEQ ID NO: 18. 
     The present invention also provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93% at least 94%, at least 95%, at least 96% at least 97% at least 98%. or at least 99% sequence identity to SEQ ID NO: 20, wherein the positions are numbered with reference to SEQ ID NO: 20. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 22/24, 22/24/27/50/107/109/489/612/725, 22/24/27/489, 22/24/27/489/612/774, 22/24/27/612/944, 22/24/50/109/267/489/774/944, 22/24/50/267/612/922/944, 22/24/107/267/489/922, 22/24/489, 22/24/612/725/944, 22/50/107/267/489/612/944, 22/50/109/267/489, 22/267/489/612, 24, 24/27/50/107/267/774/944, 24/27/89/500/842, 24/27/107/267/612/944, 24/27/267/944, 24/27/500/842, 24/27/500/842/932, 24/27/944, 24/39/49/89/97/842/932, 24/39/68/89/107/500/842, 24/39/89/97/842/932, 24/39/842/932, 24/50/489/944, 24/50/612, 24/70/107/109/489/612/725, 24/70/267/774, 24/89/500, 24/107/109/267/489/612/725/774, 24/109/612, 24/109/944, 24/267/725/944, 24/489/944, 24/725, 24/842/932, 24/944, 27/39/49/97/500/842, 27/49/68/500/842, 34/39/500/932, 39/89/97/500, 42, 48, 50/109/489/612, 50/489/774, 50/612/944, 57, 62, 68, 68/89/97/932, 71, 88, 89/97/107, 89/97/500, 89/842, 107/109, 107/500/842, 108, 109/612/774/944, 112, 123, 124, 148, 188, 193, 197, 204, 253, 264, 305, 312, 333, 381, 402, 402/781, 489, 489/944, 500/842, 500/932, 523, 527, 612, 612/725/944, 612/922, 614, 727, 742, 748, 820, 823, 832, 842/932, 858, 862, 911, 913, 914, 916, 923, 937, and 940, wherein the positions are numbered with reference to SEQ ID NO: 20. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 22R/24W, 22R/24W/27A/50V/107G/109D/489A/612S/725E, 22R/24W/27A/489A, 22R/24W/27A/489A/612S/774S, 22R/24W/27A/612S/944R, 22R/24W/50V/109D/267R/489A/774S/944R, 22R/24W/50V/267R/612S/922E/944R, 22R/24W/107G/267R/489A/922E, 22R/24W/489A, 22R/24W/612S/725E/944R, 22R/50V/107G/267R/489A/612S/944S, 22R/50V/109D/267R/489A, 22R/267R/489A/612S, 24R, 24R/27G/89R/500A/842G, 24R/27G/500A/842G, 24R/27G/500A/842G/932A, 24R/39D/68S/89R/107G/500A/842G, 24R/39H/49G/89R/97G/842G/932A, 24R/39H/89R/97D/842G/932A, 24R/39H/842G/932A, 24R/89R/500A, 24R/842G/932A, 24W, 24W/27A/50V/107G/267R/774S/944S, 24W/27A/107G/267R/612S/944S, 24W/27A/267R/944R, 24W/27A/944R, 24W/50V/489A/944S, 24W/50V/612S, 24W/70A/107G/109D/489A/612S/725E, 24W/70A/267R/774S, 24W/107G/109D/267R/489A/612S/725E/774S, 24W/109D/612S, 24W/109D/944S, 24W/267R/725E/944S, 24W/489A/944R, 24W/725E, 24W/944S, 27G/39H/49G/97G/500A/842G, 27G/49G/68S/500A/842G, 34T/39D/500A/932A, 39D/89R/97G/500A, 42G, 48Q, 48V, 48W, 50V/109D/489A/612S, 50V/489A/774S, 50V/612S/944S, 57F, 57L, 57M, 62F, 62L, 62W, 68N/89R/97G/932A, 68S, 71G, 71L, 71V, 71W, 71Y, 88L, 88R, 89R/97G/107G, 89R/97G/500A, 89R/842G, 107G/109D, 107G/500A/842G, 108R, 109D/612S/774S/944S, 112H, 123L, 123V, 124G, 124M, 124V, 148K, 148R, 188R, 188W, 193E, 193P, 197G, 204A, 253M, 264M, 305F, 312A, 333L, 381R, 381V, 381W, 402N, 402V/781Q, 489A, 489A/944R, 500A/842G, 500A/932A, 523E, 527R, 527V, 612S, 612S/725E/944S, 612S/922E, 614Q, 614R, 614W, 727W, 742V, 748V, 820A, 820V, 823F, 823V, 832A, 832R, 842G/932A, 858C, 858W, 862I, 862M, 862Q, 862Y, 911G, 911R, 913G, 913R, 913W, 914G, 914I, 914K, 914Q, 914R, 914S, 914T, 916G, 916H, 916R, 923L, 923V, 923W, 937K, and 940Q, wherein the positions are numbered with reference to SEQ ID NO: 20. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from I22R/L24W, I22R/L24W/F27A/Q50V/Q107G/L109D/D489A/D612S/K725E, I22R/L24W/F27A/D489A, I22R/L24W/F27A/D489A/D612S/A774S, I22R/L24W/F27A/D612S/C944R, I22R/L24W/Q50V/L109D/K267R/D489A/A774S/C944R, I22R/L24W/Q50V/K267R/D612S/P922E/C944R, I22R/L24W/Q107G/K267R/D489A/P922E, I22R/L24W/D489A, I22R/L24W/D612S/K725E/C944R, I22R/Q50V/Q107G/K267R/D489A/D612S/C944S, 122R/Q50V/L109D/K267R/D489A, I22R/K267R/D489A/D612S, L24R, L24R/F27G/A89R/D500A/S842G, L24R/F27G/D500A/S842G, L24R/F27G/D500A/S842G/S932A, L24R/Q39D/R68S/A89R/Q107G/D500A/S842G, L24R/Q39H/Q49G/A89R/A97G/S842G/S932A, L24R/Q39H/A89R/A97D/S842G/S932A, L24R/Q39H/S842G/S932A, L24R/A89R/D500A, L24R/S842G/S932A, L24W, L24W/F27A/Q50V/Q107G/K267R/A774S/C944S, L24W/F27A/Q107G/K267R/D612S/C944S, L24W/F27A/K267R/C944R, L24W/F27A/C944R, L24W/Q50V/D489A/C944S, L24W/Q50V/D612S, L24W/V70A/Q107G/L109D/D489A/D612S/K725E, L24W/V70A/K267R/A774S, L24W/Q107G/L109D/K267R/D489A/D612S/K725E/A774S, L24W/L109D/D612S, L24W/L109D/C944S, L24W/K267R/K725E/C944S, L24W/D489A/C944R, L24W/K725E, L24W/C944S, F27G/Q39H/Q49G/A97G/D500A/S842G, F27G/Q49G/R68S/D500A/S842G, L34T/Q39D/D500A/S932A, Q39D/A89R/A97G/D500A, E42G, H48Q, H48V, H48W, Q50V/L109D/D489A/D612S, Q50V/D489A/A774S, Q50V/D612S/C944S, P57F, P57L, P57M, A62F, A62L, A62W, R68N/A89R/A97G/S932A, R68S, P71G, P71L, P71V, P71W, P71Y, K88L, K88R, A89R/A97G/Q107G, A89R/A97G/D500A, A89R/S842G, Q107G/L109D, Q107G/D500A/S842G, G108R, L109D/D612S/A774S/C944S, A112H, P123L, P123V, S124G, S124M, S124V, T148K, T148R, E188R, E188W, H193E, H193P, P197G, E204A, A253M, S264M, L305F, V312A, I333L, E381R, E381V, E381W, S402N, S402V/P781Q, D489A, D489A/C944R, D500A/S842G, D500A/S932A, D523E, N527R, N527V, D612S, D612S/K725E/C944S, D612S/P922E, E614Q, E614R, E614W, S727W, L742V, L748V, G820A, G820V, L823F, L823V, P832A, P832R, S842G/S932A, E858C, E858W, R862I, R862M, R862Q, R862Y, N911G, N911R, V913G, V913R, V913W, P914G, P9141, P914K, P914Q, P914R, P914S, P914T, S916G, S916H, S916R, D923L, D923V, D923W, E937K, and L940Q, wherein the positions are numbered with reference to SEQ ID NO: 20. In some additional embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 22/24, 22/24/27/50/107/109/489/612/725, 22/24/27/489, 22/24/27/489/612/774, 22/24/27/612/944, 22/24/50/109/267/489/774/944, 22/24/50/267/612/922/944, 22/24/107/267/489/922, 22/24/489, 22/24/612/725/944, 22/50/107/267/489/612/944, 22/50/109/267/489, 22/267/489/612, 24, 24/27/50/107/267/774/944, 24/27/89/500/842, 24/27/107/267/612/944, 24/27/267/944, 24/27/500/842, 24/27/500/842/932, 24/27/944, 24/39/49/89/97/842/932, 24/39/68/89/107/500/842, 24/39/89/97/842/932, 24/39/842/932, 24/50/489/944, 24/50/612, 24/70/107/109/489/612/725, 24/70/267/774, 24/89/500, 24/107/109/267/489/612/725/774, 24/109/612, 24/109/944, 24/267/725/944, 24/489/944, 24/725, 24/842/932, 24/944, 27/39/49/97/500/842, 27/49/68/500/842, 34/39/500/932, 50/109/489/612, 50/612/944, 68/89/97/932, 89/97/107, 89/842, 106, 107/109, 107/500/842, 108, 109/612/774/944, 112, 148, 148/772, 188/377, 238, 240, 240/374, 243, 244, 246, 248, 249/777, 252, 253, 259, 260, 261, 262, 264, 279, 305, 309, 312, 319, 320, 329, 333, 387, 402, 421, 432, 500/842, 500/932, 556, 612, 612/725/944, 612/922, 727, 736, 737, 741, 742, 748, 815, 816, 818, 823, 832, 842/932, 911, 913, 914, 916, 923, 937, and 940, wherein the positions are numbered with reference to SEQ ID NO: 20. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 22R/24W, 22R/24W/27A/50V/107G/109D/489A/612S/725E, 22R/24W/27A/489A, 22R/24W/27A/489A/612S/774S, 22R/24W/27A/612S/944R, 22R/24W/50V/109D/267R/489A/774S/944R, 22R/24W/50V/267R/612S/922E/944R, 22R/24W/107G/267R/489A/922E, 22R/24W/489A, 22R/24W/612S/725E/944R, 22R/50V/107G/267R/489A/612S/944S, 22R/50V/109D/267R/489A, 22R/267R/489A/612S, 24R, 24R/27G/89R/500A/842G, 24R/27G/500A/842G, 24R/27G/500A/842G/932A, 24R/39D/68S/89R/107G/500A/842G, 24R/39H/49G/89R/97G/842G/932A, 24R/39H/89R/97D/842G/932A, 24R/39H/842G/932A, 24R/89R/500A, 24R/842G/932A, 24W, 24W/27A/50V/107G/267R/774S/944S, 24W/27A/107G/267R/612S/944S, 24W/27A/267R/944R, 24W/27A/944R, 24W/50V/489A/944S, 24W/50V/612S, 24W/70A/107G/109D/489A/612S/725E, 24W/70A/267R/774S, 24W/107G/109D/267R/489A/612S/725E/774S, 24W/109D/612S, 24W/109D/944S, 24W/267R/725E/944S, 24W/489A/944R, 24W/725E, 24W/944S, 27G/39H/49G/97G/500A/842G, 27G/49G/68S/500A/842G, 34T/39D/500A/932A, 50V/109D/489A/612S, 50V/612S/944S, 68N/89R/97G/932A, 89R/97G/107G, 89R/842G, 106A, 106G, 106N, 106T, 107G/109D, 107G/500A/842G, 108H, 108N, 108R, 108S, 108V, 109D/612S/774S/944S, 112H, 112P, 148E, 148G, 148H, 148K, 148R/7721, 188Q/377Q, 238Q, 240I, 240W/374T, 240Y, 243E, 243G, 243R, 243V, 244I, 244V, 246A, 246G, 248A, 248R, 248V, 249V/777N, 252V, 253G, 253P, 259G, 259N, 259S, 260W, 261E, 262P, 264C, 279E, 305F, 305G, 305R, 305V, 305Y, 309C, 309G, 312A, 319F, 320M, 329F, 333L, 333V, 387L, 402G, 402N, 421P, 432C, 500A/842G, 500A/932A, 556H, 556R, 556S, 556Y, 612S, 612S/725E/944S, 612S/922E, 727G, 727Q, 727T, 727W, 736M, 736V, 736W, 737M, 741C, 741D, 741E, 741G, 741T, 742V, 7481, 748T, 748V, 815A, 815M, 816V, 818T, 818V, 823A, 823F, 823G, 823R, 832E, 832G, 842G/932A, 911G, 913A, 913E, 913G, 913H, 913L, 913Q, 913R, 913W, 914E, 914G, 914H, 914K, 914Q, 914R, 914S, 914T, 916A, 916G, 916H, 9161, 916R, 916V, 923W, 937Q, 940G, 940Q, 940T, and 940W, wherein the positions are numbered with reference to SEQ ID NO: 20, In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from I22R/L24W, I22R/L24W/F27A/Q50V/Q107G/L109D/D489A/D612S/K725E, I22R/L24W/F27A/D489A, I22R/L24W/F27A/D489A/D612S/A774S, I22R/L24W/F27A/D612S/C944R, I22R/L24W/Q50V/L109D/K267R/D489A/A774S/C944R, I22R/L24W/Q50V/K267R/D612S/P922E/C944R, I22R/L24W/Q107G/K267R/D489A/P922E, I22R/L24W/D489A, 122R/L24W/D612S/K725E/C944R, I22R/Q50V/Q107G/K267R/D489A/D612S/C944S, I22R/Q50V/L109D/K267R/D489A, I22R/K267R/D489A/D612S, L24R, L24R/F27G/A89R/D500A/S842G, L24R/F27G/D500A/S842G, L24R/F27G/D500A/S842G/S932A, L24R/Q39D/R68S/A89R/Q107G/D500A/S842G, L24R/Q39H/Q49G/A89R/A97G/S842G/S932A, L24R/Q39H/A89R/A97D/S842G/S932A, L24R/Q39H/S842G/S932A, L24R/A89R/D500A, L24R/S842G/S932A, L24W, L24W/F27A/Q50V/Q107G/K267R/A774S/C944S, L24W/F27A/Q107G/K267R/D612S/C944S, L24W/F27A/K267R/C944R, L24W/F27A/C944R, L24W/Q50V/D489A/C944S, L24W/Q50V/D612S, L24W/V70A/Q107G/L109D/D489A/D612S/K725E, L24W/V70A/K267R/A774S, L24W/Q107G/L109D/K267R/D489A/D612S/K725E/A774S, L24W/L109D/D612S, L24W/L109D/C944S, L24W/K267R/K725E/C944S, L24W/D489A/C944R, L24W/K725E, L24W/C944S, F27G/Q39H/Q49G/A97G/D500A/S842G, F27G/Q49G/R68S/D500A/S842G, L34T/Q39D/D500A/S932A, Q50V/L109D/D489A/D612S, Q50V/D612S/C944S, R68N/A89R/A97G/S932A, A89R/A97G/Q107G, A89R/S842G, K106A, K106G, K106N, K106T, Q107G/L109D, Q107G/D500A/S842G, G108H, G108N, G108R, G108S, G108V, L109D/D612S/A774S/C944S, A112H, A112P, T148E, T148G, T148H, T148K, T148R/V772I, E188Q/R377Q, L238Q, L240I, L240W/A374T, L240Y, S243E, S243G, S243R, S243V, L244I, L244V, S246A, S246G, Y248A, Y248R, Y248V, I249V/S777N, L252V, A253G, A253P, L259G, L259N, L259S, M260W, L261E, S262P, S264C, P279E, L305F, L305G, L305R, L305V, L305Y, A309C, A309G, V312A, A319F, L320M, L329F, I333L, I333V, H387L, S402G, S402N, Q421P, M432C, D500A/S842G, D500A/S932A, F556H, F556R, F556S, F556Y, D612S, D612S/K725E/C944S, D612S/P922E, S727G, S727Q, S727T, S727W, L736M, L736V, L736W, L737M, A741C, A741D, A741E, A741G, A741T, L742V, L748I, L748T, L748V, I815A, I815M, I816V, L818T, L818V, L823A, L823F, L823G, L823R, P832E, P832G, S842G/S932A, N911G, V913A, V913E, V913G, V913H, V913L, V913Q, V913R, V913W, P914E, P914G, P914H, P914K, P914Q, P914R, P914S, P914T, S916A, S916G, S916H, S916I, S916R, S916V, D923W, E937Q, L940G, L940Q, L940T, and L940W, wherein the positions are numbered with reference to SEQ ID NO: 20. 
     The present invention further provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%. at least 98%, or at least 99% sequence identity to SEQ ID NO: 946, wherein the positions are numbered with reference to SEQ ID NO: 946. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 19/124/149/381/727, 24/39/489/862, 24/57/62/89/489/823/862, 24/57/823/862, 24/62/89/188/823/842/862, 24/89/489, 24/89/489/727/862, 24/489/500/842, 39/57/62/188/500/842, 39/57/500/862, 57, 57/62/120/527/913/916, 57/62/305/437/500/614/727/916, 57/62/305/437/500/727/913/916, 57/62/305/437/614/683/913/916/932, 57/62/305/489/907/913/916, 57/62/305/489/913/916, 57/62/305/500/913/916, 57/62/305/913, 57/62/305/916, 57/62/437/500/761/914/916, 57/62/437/527/727, 57/62/437/913/916, 57/62/913/916/932, 57/62/916, 57/188/489/823/862, 57/305, 57/305/437/916, 57/437/500/527/727/916, 57/437/500/614/727/914, 57/437/913/914, 57/489/527/914/916, 57/614/916/932, 62/89, 62/89/124/148/381/858, 62/89/124/381/858, 62/89/148/381/614/858, 62/89/148/923, 62/89/149/381, 62/89/149/381/832, 62/89/188/489/500/727/823, 62/89/381, 62/89/381/858, 62/89/381/923, 62/89/858, 62/96/614, 62/124/148/149/381/614, 62/124/149/381/832/858/937, 62/124/188/823/842/862, 62/124/381/832, 62/148/149/381/858/937, 62/148/381/614/937, 62/148/381/727, 62/148/381/858, 62/149/381/614/937, 62/149/381/858/937, 62/149/727, 62/305/437/500/727/913, 62/305/727, 62/381, 62/437/489/527/727/913/932, 62/437/489/614/727/913, 62/437/527/727, 62/437/527/916/932, 62/437/913/916, 62/489/500/932, 62/489/527/916/932, 62/489/614/916, 62/500, 62/527, 62/527/727/916, 62/614, 62/727, 62/916, 89/148/149, 89/148/149/381, 89/381, 124/148/381/727/858/937, 124/381/614, 124/500/842/862, 124/832/937, 148/832/858/937, 381, 381/614/832, 381/858/937, 437, 437/489/914/916, 437/727/914, 437/914/916, 489/500, 489/614/916, 500/727/913/916, 500/914/916, and 923, wherein the positions are numbered with reference to SEQ ID NO: 946. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 19T/124V/149R/381V/727W, 24R/39H/489A/862Q, 24R/57L/62W/89R/489A/823F/862Q, 24R/57L/823F/862Q, 24R/62W/89R/188W/823V/842G/862Q, 24R/89R/489A, 24R/89R/489A/727W/862Q, 24R/489A/500A/842G, 39H/57L/62W/188W/500A/842G, 39H/57L/500A/862Q, 57F/62L/305F/437G/500A/614Q/727W/916R, 57F/62L/305F/437G/614Q/683S/913R/916R/932A, 57F/62L/305F/500A/913R/916G, 57F/62L/305F/913R, 57F/62L/437G/500A/761F/914K/916R, 57F/62L/437G/527R/727W, 57F/62L/913R/916R/932A, 57F/62L/916G, 57F/62W/120I/527R/913R/916R, 57F/62W/305F/437G/500A/727W/913R/916R, 57F/62W/305F/489A/907K/913R/916G, 57F/62W/305F/489A/913R/916G, 57F/62W/305F/916R, 57F/62W/437G/913R/916G, 57F/305F, 57F/305F/437G/916G, 57F/437G/500A/527R/727W/916R, 57F/437G/500A/614Q/727W/914R, 57F/437G/913R/914R, 57F/489A/527R/914R/916G, 57F/614Q/916G/932A, 57L, 57L/188W/489A/823F/862Q, 62F/89R, 62F/89R/124V/148R/381W/858W, 62F/89R/148R/381V/614R/858W, 62F/89R/148R/923W, 62F/89R/149R/381W/832R, 62F/89R/381V/923W, 62F/89R/858C, 62F/96K/614R, 62F/124V/381W/832R, 62F/149R/381V/858W/937K, 62F/149R/727W, 62F/381V, 62F/614R, 62L/305F/437G/500A/727W/913R, 62L/305F/727W, 62L/437G/489A/527R/727W/913R/932A, 62L/437G/527R/727W, 62L/437G/527R/916G/932A, 62L/437G/913R/916R, 62L/489A/500A/932A, 62L/489A/614Q/916R, 62L/527R, 62L/527R/727W/916G, 62W/89R/124V/381W/858C, 62W/89R/149R/381W, 62W/89R/188W/489A/500A/727W/823F, 62W/89R/381V, 62W/89R/381W/858C, 62W/124V/148R/149R/381W/614R, 62W/124V/149R/381V/832R/858C/937K, 62W/124V/188W/823F/842G/862Q, 62W/148R/149R/381V/858C/937K, 62W/148R/381W/614R/937K, 62W/148R/381W/727W, 62W/148R/381W/858C, 62W/149R/381W/614R/937K, 62W/381V, 62W/437G/489A/614Q/727W/913R, 62W/489A/527R/916R/932A, 62W/500A, 62W/727W, 62W/916G, 89R/148R/149R, 89R/148R/149R/381W, 89R/381W, 124V/148R/381W/727W/858W/937K, 124V/381W/614R, 124V/500A/842G/862Q, 124V/832R/937K, 148R/832R/858W/937K, 381V, 381V/614R/832R, 381W/858C/937K, 437G, 437G/489A/914R/916R, 437G/727W/914K, 437G/914R/916G, 489A/500A, 489A/614Q/916G, 500A/727W/913R/916R, 500A/914R/916G, and 923W, wherein the positions are numbered with reference to SEQ ID NO: 946. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from S19T/S124V/P149R/E381V/S727W, W24R/Q39H/D489A/R862Q, W24R/P57L/A62W/A89R/D489A/L823F/R862Q, W24R/P57L/L823F/R862Q, W24R/A62W/A89R/E188W/L823V/S842G/R862Q, W24R/A89R/D489A, W24R/A89R/D489A/S727W/R862Q, W24R/D489A/D500A/S842G, Q39H/P57L/A62W/E188W/D500A/S842G, Q39H/P57L/D500A/R862Q, P57F/A62L/L305F/A437G/D500A/E614Q/S727W/S916R, P57F/A62L/L305F/A437G/E614Q/A683S/V913R/S916R/S932A, P57F/A62L/L305F/D500A/V913R/S916G, P57F/A62L/L305F/V913R, P57F/A62L/A437G/D500A/L761F/P914K/S916R, P57F/A62L/A437G/N527R/S727W, P57F/A62L/V913R/S916R/S932A, P57F/A62L/S916G, P57F/A62W/F120I/N527R/V913R/S916R, P57F/A62W/L305F/A437G/D500A/S727W/V913R/S916R, P57F/A62W/L305F/D489A/Q907K/V913R/S916G, P57F/A62W/L305F/D489A/V913R/S916G, P57F/A62W/L305F/S916R, P57F/A62W/A437G/V913R/S916G, P57F/L305F, P57F/L305F/A437G/S916G, P57F/A437G/D500A/N527R/S727W/S916R, P57F/A437G/D500A/E614Q/S727W/P914R, P57F/A437G/V913R/P914R, P57F/D489A/N527R/P914R/S916G, P57F/E614Q/S916G/S932A, P57L, P57L/E188W/D489A/L823F/R862Q, A62F/A89R, A62F/A89R/S124V/T148R/E381W/E858W, A62F/A89R/T148R/E381V/E614R/E858W, A62F/A89R/T148R/D923W, A62F/A89R/P149R/E381W/P832R, A62F/A89R/E381V/D923W, A62F/A89R/E858C, A62F/E96K/E614R, A62F/S124V/E381W/P832R, A62F/P149R/E381V/E858W/E937K, A62F/P149R/S727W, A62F/E381V, A62F/E614R, A62L/L305F/A437G/D500A/S727W/V913R, A62L/L305F/S727W, A62L/A437G/D489A/N527R/S727W/V913R/S932A, A62L/A437G/N527R/S727W, A62L/A437G/N527R/S916G/S932A, A62L/A437G/V913R/S916R, A62L/D489A/D500A/S932A, A62L/D489A/E614Q/S916R, A62L/N527R, A62L/N527R/S727W/S916G, A62W/A89R/S124V/E381W/E858C, A62W/A89R/P149R/E381W, A62W/A89R/E188W/D489A/D500A/S727W/L823F, A62W/A89R/E381V, A62W/A89R/E381W/E858C, A62W/S124V/T148R/P149R/E381W/E614R, A62W/S124V/P149R/E381V/P832R/E858C/E937K, A62W/S124V/E188W/L823F/S842G/R862Q, A62W/T148R/P149R/E381V/E858C/E937K, A62W/T148R/E381W/E614R/E937K, A62W/T148R/E381W/S727W, A62W/T148R/E381W/E858C, A62W/P149R/E381W/E614R/E937K, A62W/E381V, A62W/A437G/D489A/E614Q/S727W/V913R, A62W/D489A/N527R/S916R/S932A, A62W/D500A, A62W/S727W, A62W/S916G, A89R/T148R/P149R, A89R/T148R/P149R/E381W, A89R/E381W, S124V/T148R/E381W/S727W/E858W/E937K, S124V/E381W/E614R, S124V/D500A/S842G/R862Q, S124V/P832R/E937K, T148R/P832R/E858W/E937K, E381V, E381V/E614R/P832R, E381W/E858C/E937K, A437G, A437G/D489A/P914R/S916R, A437G/S727W/P914K, A437G/P914R/S916G, D489A/D500A, D489A/E614Q/S916G, D500A/S727W/V913R/S916R, D500A/P914R/S916G, and D923W, wherein the positions are numbered with reference to SEQ ID NO: 946. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 57/62/120/527/913/916, 57/62/305/437/500/614/727/916, 57/62/305/437/500/727/913/916, 57/62/305/437/614/683/913/916/932, 57/62/305/489/907/913/916, 57/62/305/489/913/916, 57/62/305/500/913/916, 57/62/305/913, 57/62/305/916, 57/62/437/500/761/914/916, 57/62/437/527/727, 57/62/437/913/916, 57/62/913/916/932, 57/62/916, 57/188/489/823/862, 57/305, 57/305/437/916, 57/437/500/527/727/916, 57/437/500/614/727/914, 57/437/913/914, 57/489/527/914/916, 57/614/916/932, 62/89/188/489/500/727/823, 62/124/188/823/842/862, 62/305/437/500/727/913, 62/305/727, 62/437/489/527/727/913/932, 62/437/489/614/727/913, 62/437/527/727, 62/437/527/916/932, 62/437/913/916, 62/489/500/932, 62/489/527/916/932, 62/527/727/916, 62/727, 62/916, 124/500/842/862, 437, 437/489/914/916, 437/727/914, 437/914/916, 489/614/916, 500/727/913/916, 500/914/916, and 923, wherein the positions are numbered with reference to SEQ ID NO: 946. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 57F/62L/305F/437G/500A/614Q/727W/916R, 57F/62L/305F/437G/614Q/683S/913R/916R/932A, 57F/62L/305F/500A/913R/916G, 57F/62L/305F/913R, 57F/62L/437G/500A/761F/914K/916R, 57F/62L/437G/527R/727W, 57F/62L/913R/916R/932A, 57F/62L/916G, 57F/62W/120I/527R/913R/916R, 57F/62W/305F/437G/500A/727W/913R/916R, 57F/62W/305F/489A/907K/913R/916G, 57F/62W/305F/489A/913R/916G, 57F/62W/305F/916R, 57F/62W/437G/913R/916G, 57F/305F, 57F/305F/437G/916G, 57F/437G/500A/527R/727W/916R, 57F/437G/500A/614Q/727W/914R, 57F/437G/913R/914R, 57F/489A/527R/914R/916G, 57F/614Q/916G/932A, 57L/188W/489A/823F/862Q, 62L/305F/437G/500A/727W/913R, 62L/305F/727W, 62L/437G/489A/527R/727W/913R/932A, 62L/437G/527R/727W, 62L/437G/527R/916G/932A, 62L/437G/913R/916R, 62L/489A/500A/932A, 62L/527R/727W/916G, 62W/89R/188W/489A/500A/727W/823F, 62W/124V/188W/823F/842G/862Q, 62W/437G/489A/614Q/727W/913R, 62W/489A/527R/916R/932A, 62W/727W, 62W/916G, 124V/500A/842G/862Q, 437G, 437G/489A/914R/916R, 437G/727W/914K, 437G/914R/916G, 489A/614Q/916G, 500A/727W/913R/916R, 500A/914R/916G, and 923W, wherein the positions are numbered with reference to SEQ ID NO: 946. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from P57F/A62L/L305F/A437G/D500A/E614Q/S727W/S916R, P57F/A62L/L305F/A437G/E614Q/A6835/V913R/5916R/5932A, P57F/A62L/L305F/D500A/V913R/S916G, P57F/A62L/L305F/V913R, P57F/A62L/A437G/D500A/L761F/P914K/S916R, P57F/A62L/A437G/N527R/S727W, P57F/A62L/V913R/S916R/S932A, P57F/A62L/S916G, P57F/A62W/F1201/N527R/V913R/S916R, P57F/A62W/L305F/A437G/D500A/S727W/V913R/S 916R, P57F/A62W/L305F/D489A/Q907K/V913R/S916G, P57F/A62W/L305F/D489A/V913R/S916G, P57F/A62W/L305F/S916R, P57F/A62W/A437G/V913R/S916G, P57F/L305F, P57F/L305F/A437G/S916G, P57F/A437G/D500A/N527R/S727W/S916R, P57F/A437G/D500A/E614Q/S727W/P914R, P57F/A437G/V913R/P914R, P57F/D489A/N527R/P914R/S916G, P57F/E614Q/S916G/S932A, P57L/E188W/D489A/L823F/R862Q, A62L/L305F/A437G/D500A/S727W/V913R, A62L/L305F/S727W, A62L/A437G/D489A/N527R/S727W/V913R/S932A, A62L/A437G/N527R/S727W, A62L/A437G/N527R/S916G/S932A, A62L/A437G/V913R/S916R, A62L/D489A/D500A/S932A, A62L/N527R/S727W/S916G, A62W/A89R/E188W/D489A/D500A/S727W/L823F, A62W/S124V/E188W/L823F/S842G/R862Q, A62W/A437G/D489A/E614Q/S727W/V913R, A62W/D489A/N527R/S916R/S932A, A62W/S727W, A62W/S916G, S124V/D500A/S842G/R862Q, A437G, A437G/D489A/P914R/S916R, A437G/S727W/P914K, A437G/P914R/S916G, D489A/E614Q/S916G, D500A/S727W/V913R/S916R, D500A/P914R/S916G, and D923W, wherein the positions are numbered with reference to SEQ ID NO: 946. 100161 The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 1956, wherein the positions are numbered with reference to SEQ ID NO: 1956. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 3/569, 41/53, 44, 44/347, 56, 65, 78, 78/87/176/266/536/615, 78/87/266, 78/87/266/372/386/777, 78/87/266/372/536, 78/87/266/483/924, 78/87/483/777, 78/87/536, 78/266/483/536/615, 78/266/483/795, 78/266/763, 78/372/390, 78/390, 78/536/615, 87, 87/266, 87/266/372/483, 87/266/483, 87/266/924, 87/372/777, 87/536/777, 87/615, 87/795, 105, 136, 141, 145, 154/588, 156, 157, 199, 202, 222, 225, 227, 229, 266, 266/372/536/615/763/777, 266/372/924, 266/536/615/795, 344, 348, 390/615, 412, 423, 425/678/894, 430, 446, 484, 488, 496, 499/711, 503, 530, 543, 569, 572, 573, 574, 577, 578, 579, 580, 581, 583, 585, 588, 589/663, 615, 628, 629, 631, 633, 656, 663, 669, 670, 671, 678, 679, 687, 690, 691, 692, 693, 705, 706, 708, 709, 710, 711, 726, 768, 773, 777, 779, 795, 797, 816, 826, 834, 857, 859, 868, 869, 871, 873, 877, 878, and 909, wherein the positions are numbered with reference to SEQ ID NO: 1956. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 3L/569F, 41I/53M, 44E, 44G, 44L, 44P/347I, 44R, 56A, 56L, 56R, 65L, 65V, 78E, 78E/87E/176T/266N/536T/615D, 78E/87E/266N, 78E/87E/266N/372T/386Y/777G, 78E/87E/266N/372T/536T, 78E/87E/266N/483S/924N, 78E/87E/483S/777G, 78E/87E/536T, 78E/266N/483S/536T/615D, 78E/266N/483S/795E, 78E/266N/763L, 78E/372T/390Q, 78E/390Q, 78E/536T/615D, 87E, 87E/266N, 87E/266N/372T/483S, 87E/266N/483S, 87E/266N/924N, 87E/372T/777G, 87E/536T/777G, 87E/615D, 87E/795E, 105T, 136G, 141S, 141W, 1451, 145R, 154R/588L, 156L, 157S, 199V, 202K, 202L, 202N, 202R, 202T, 222C, 222P, 225D, 227A, 229C, 266N, 266N/372T/536T/615D/763L/777G, 266N/372T/924N, 266N/536T/615D/795E, 344G, 344M, 348G, 390Q/615D, 412Y, 423V, 425R/678I/894C, 430F, 446T, 484L, 488G, 488K, 488M, 496G, 499Y/711F, 503S, 503T, 530V, 543C, 543Q, 543S, 543V, 569H, 5691, 569Q, 569S, 569T, 569V, 569Y, 572G, 572S, 573C, 573D, 573H, 573M, 573Q, 574S, 577A, 577D, 577E, 577M, 577T, 577V, 578S, 579V, 580E, 580G, 580I, 580L, 580W, 580Y, 581F, 581G, 581H, 581L, 581S, 581T, 581V, 581Y, 583C, 583G, 583K, 583L, 585F, 585L, 585M, 585Q, 585V, 588L, 588V, 589I/663F, 615G, 628I, 628M, 628V, 629A, 629C, 629G, 629I, 631I, 631L, 631M, 633V, 656M, 656V, 663A, 663F, 669R, 670E, 670F, 670I, 670Q, 670R, 670S, 670T, 670V, 670W, 671A, 671G, 671M, 671T, 678H, 678L, 678T, 678Y, 679W, 687L, 690V, 691F, 691V, 692C, 692F, 692G, 692I, 692L, 692R, 692S, 692V, 692Y, 693F, 693I, 693Y, 705M, 706F, 706M, 706V, 708C, 709S, 710K, 710L, 710M, 710N, 710S, 711C, 711F, 711G, 711H, 711L, 711R, 711W, 726E, 768S, 773V, 777G, 7771, 777R, 779E, 779H, 779R, 795E, 797L, 797M, 816L, 826G, 834H, 857T, 859T, 859Y, 868I, 868L, 869L, 869S, 871E, 871K, 871R, 873A, 873F, 873Y, 877L, 877V, 878A, 878F, 878G, 878K, 878L, 878Q, 878R, 878S, 878W, and 909F, wherein the positions are numbered with reference to SEQ ID NO: 1956. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from W3L/L569F, L41I/S53M, T44E, T44G, T44L, T44P/L347I, T44R, G56A, G56L, G56R, G65L, G65V, P78E, P78E/D87E/K176T/T266N/V536T/Q615D, P78E/D87E/T266N, P78E/D87E/T266N/S372T/A386Y/S777G, P78E/D87E/T266N/S372T/V536T, P78E/D87E/T266N/T483S/T924N, P78E/D87E/T483S/S777G, P78E/D87E/V536T, P78E/T266N/T483S/V536T/Q615D, P78E/T266N/T483S/Q795E, P78E/T266N/T763L, P78E/S372T/L390Q, P78E/L390Q, P78E/V536T/Q615D, D87E, D87E/T266N, D87E/T266N/S372T/T483S, D87E/T266N/T483S, D87E/T266N/T924N, D87E/S372T/S777G, D87E/V536T/S777G, D87E/Q615D, D87E/Q795E, A105T, S136G, T141S, T141W, T1451, T145R, K154R/F588L, I156L, L157S, P199V, S202K, S202L, S202N, S202R, S202T, V222C, V222P, N225D, T227A, A229C, T266N, T266N/S372T/V536T/Q615D/T763L/S777G, T266N/S372T/T924N, T266N/V536T/Q615D/Q795E, Q344G, Q344M, D348G, L390Q/Q615D, G412Y, L423V, Q425R/S678I/G894C, Y430F, S446T, N484L, L488G, L488K, L488M, A496G, H499Y/A711F, P503S, P503T, L530V, T543C, T543Q, T543S, T543V, L569H, L569I, L569Q, L569S, L569T, L569V, L569Y, A572G, A572S, I573C, I573D, I573H, I573M, I573Q, A574S, R577A, R577D, R577E, R577M, R577T, R577V, A578S, L579V, V580E, V580G, V580I, V580L, V580W, V580Y, K581F, K581G, K581H, K581L, K581S, K581T, K581V, K581Y, R583C, R583G, R583K, R583L, T585F, T585L, T585M, T585Q, T585V, F588L, F588V, V589I/M663F, Q615G, L628I, L628M, L628V, L629A, L629C, L629G, L629I, V631I, V631L, V631M, L633V, L656M, L656V, M663A, M663F, L669R, L670E, L670F, L670I, L670Q, L670R, L670S, L670T, L670V, L670W, S671A, S671G, S671M, S671T, S678H, S678L, S678T, S678Y, F679W, M687L, A690V, L691F, L691V, T692C, T692F, T692G, T692I, T692L, T692R, T692S, T692V, T692Y, L693F, L693I, L693Y, F705M, H706F, H706M, H706V, A708C, H709S, V710K, V710L, V710M, V710N, V710S, A711C, A711F, A711G, A711H, A711L, A711R, A711W, D726E, Q768S, E773V, S777G, S777I, S777R, P779E, P779H, P779R, Q795E, V797L, V797M, I816L, T826G, A834H, L857T, V859T, V859Y, V868I, V868L, I869L, I869S, L871E, L871K, L871R, R873A, R873F, R873Y, I877L, I877V, V878A, V878F, V878G, V878K, V878L, V878Q, V878R, V878S, V878W, and L909F, wherein the positions are numbered with reference to SEQ ID NO: 1956. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position selected from 44, 53, 56, 63, 65, 105, 125, 129, 136, 139, 141, 142, 145, 152, 156, 162, 176, 177, 185, 186, 187, 199, 199/775, 202, 265, 267, 337, 344, 348, 350, 354, 372, 373, 401, 412, 446, 469, 484, 488, 493, 496, 499, 503, 526, 543, 612, 615, 649, 677, 678, 679, 730, 752, 765, 768, 773, 777, 779, 788, 797, 822, 826, 834, 855, 856, 857, 859, 860, 924, 926, 931, and 936, wherein the positions are numbered with reference to SEQ ID NO: 1956. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position selected from 44A, 44F, 44V, 44W, 44Y, 531, 56S, 56W, 63N, 65A, 65F, 65R, 65Y, 105V, 105W, 125H, 125W, 129E, I129S, 129S, 129T, 129V, 129W, 136K, 136R, 136V, 139E, 141K, 141R, 142G, 145A, 145L, 152L, 152S, 152W, 156C, 156K, 156R, 156S, 162T, 176R, 177Q, 185L, 186H, 187I, 199A, 199G, 199I, 199R, 199T, 199V/775I, 199W, 202A, 202D, 202G, 202H, 202Q, 202Y, 265D, 265F, 265H, 267E, 267G, 267R, 337H, 344C, 348E, 348W, 350F, 350I, 354L, 354S, 372D, 373A, 373S, 401G, 401S, 412R, 412S, 412W, 446C, 446D, 446G, 446I, 446K, 469M, 469T, 469V, 484A, 484K, 484R, 488C, 488E, 488S, 493L, 496M, 496W, 499A, 499E, 499I, 499M, 499Q, 499V, 503C, 503H, 503N, 526L, 526V, 543G, 543H, 543K, 543L, 543R, 612G, 612L, 612R, 612T, 615M, 615S, 649M, 677T, 678Q, 678R, 678V, 678W, 679Y, 730K, 730L, 730R, 752F, 752G, 752L, 752N, 752S, 752W, 765W, 768I, 768K, 768V, 773P, 777M, 777W, 779I, 779M, 779S, 788A, 788H, 788I, 788L, 788N, 788Q, 788S, 788T, 788Y, 797E, 797F, 797I, 797R, 797W, 822R, 826I, 826M, 834G, 834S, 834V, 834W, 855G, 855L, 856A, 856G, 857A, 857E, 857R, 857S, 857V, 859A, 859G, 860S, 924A, 926M, 926T, 931L, 936N, 936R, and 936S, wherein the positions are numbered with reference to SEQ ID NO: 1956. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position selected from T44A, T44F, T44V, T44W, T44Y, S53I, G56S, G56W, H63N, G65A, G65F, G65R, G65Y, A105V, A105W, Y125H, Y125W, K129E, K129I, K129S, K129T, K129V, K129W, S136K, S136R, S136V, G139E, T141K, T141R, A142G, T145A, T145L, F152L, F152S, F152W, I156C, I156K, I156R, I156S, D162T, K176R, D177Q, V185L, P186H, L1871, P199A, P199G, P199I, P199R, P199T, P199V/L7751, P199W, S202A, S202D, S202G, S202H, S202Q, S202Y, W265D, W265F, W265H, K267E, K267G, K267R, P337H, Q344C, D348E, D348W, V350F, V350I, F354L, F354S, S372D, T373A, T373S, D401G, D401S, G412R, G412S, G412W, S446C, S446D, S446G, S446I, S446K, I469M, I469T, I469V, N484A, N484K, N484R, L488C, L488E, L488S, D493L, A496M, A496W, H499A, H499E, H499I, H499M, H499Q, H499V, P503C, P503H, P503N, P526L, P526V, T543G, T543H, T543K, T543L, T543R, S612G, S612L, S612R, S612T, Q615M, Q615S, L649M, Y677T, S678Q, S678R, S678V, S678W, F679Y, W730K, W730L, W730R, K752F, K752G, K752L, K752N, K752S, K752W, Y765W, Q768I, Q768K, Q768V, E773P, S777M, S777W, P779I, P779M, P779S, P788A, P788H, P788I, P788L, P788N, P788Q, P788S, P788T, P788Y, V797E, V797F, V797I, V797R, V797W, G822R, T826I, T826M, A834G, A834S, A834V, A834W, E855G, E855L, S856A, S856G, L857A, L857E, L857R, L857S, L857V, V859A, V859G, L860S, T924A, V926M, V926T, V931L, G936N, G936R, and G936S, wherein the positions are numbered with reference to SEQ ID NO: 1956. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 78/87/176/266/536/615, 78/87/266/372/386/777, 78/87/266/372/536, 78/266/763, 78/372/390, 87/266/372/483, 87/372/777, 105, 125, 129, 136, 139, 141, 142, 152, 154/588, 156, 222, 225, 227, 229, 266/372/536/615/763/777, 266/372/924, 267, 372, 401, 493, 496, 499, 569, 572, 573, 574, 577, 579, 580, 581, 583, 585, 588, 589/663, 628, 629, 631, 663, 669, 670, 671, 691, 692, 693, 706, 708, 710, 711, 765, 768, 779, 797, 826, 834, 855, 856, 857, 869, 871, 873, 878, 909, 924, and 926, wherein the positions are numbered with reference to SEQ ID NO: 1956. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 78E/87E/176T/266N/536T/615D, 78E/87E/266N/372T/386Y/777G, 78E/87E/266N/372T/536T, 78E/266N/763L, 78E/372T/390Q, 87E/266N/372T/483S, 87E/372T/777G, 105T, 105W, 125W, 129E, 129S, 136G, 136K, 136V, 139E, 141S, 142G, 152S, 152W, 154R/588L, 156C, 156L, 222C, 222P, 225D, 227A, 229C, 266N/372T/536T/615D/763L/777G, 266N/372T/924N, 267E, 372D, 401G, 493L, 496G, 499E, 499I, 499M, 499Q, 569H, 569Q, 569S, 569T, 569V, 569Y, 572G, 572S, 573C, 573D, 573H, 573M, 573Q, 574S, 577A, 577D, 577E, 577T, 579V, 580E, 580G, 580W, 581G, 581H, 581T, 583C, 583G, 585Q, 588L, 588V, 589I/663F, 628V, 629A, 629C, 629G, 629I, 631I, 631L, 631M, 663A, 663F, 669R, 670E, 670F, 670I, 670Q, 670R, 670S, 670T, 670V, 670W, 671A, 671G, 671T, 691V, 692C, 692F, 692G, 692I, 692L, 692Y, 693F, 693I, 693Y, 706F, 708C, 710K, 710L, 710M, 710N, 710S, 711C, 711G, 711H, 711W, 765W, 768I, 779E, 797E, 797F, 797I, 797L, 797M, 797W, 826G, 834G, 834H, 834S, 834W, 855G, 856G, 857A, 857E, 857S, 857T, 857V, 869L, 869S, 871E, 871K, 873A, 873F, 873Y, 878A, 878G, 878K, 878Q, 878S, 878W, 909F, 924A, 926M, and 926T, wherein the positions are numbered with reference to SEQ ID NO: 1956. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from P78E/D87E/K176T/T266N/V536T/Q615D, P78E/D87E/T266N/S372T/A386Y/S777G, P78E/D87E/T266N/S372T/V536T, P78E/T266N/T763L, P78E/S372T/L390Q, D87E/T266N/S372T/T483S, D87E/S372T/S777G, A105T, A105W, Y125W, K129E, K129S, S136G, S136K, S136V, G139E, T141S, A142G, F152S, F152W, K154R/F588L, I156C, I156L, V222C, V222P, N225D, T227A, A229C, T266N/S372T/V536T/Q615D/T763L/S777G, T266N/S372T/T924N, K267E, S372D, D401G, D493L, A496G, H499E, H499I, H499M, H499Q, L569H, L569Q, L569S, L569T, L569V, L569Y, A572G, A572S, I573C, I573D, I573H, I573M, I573Q, A574S, R577A, R577D, R577E, R577T, L579V, V580E, V580G, V580W, K581G, K581H, K581T, R583C, R583G, T585Q, F588L, F588V, V589I/M663F, L628V, L629A, L629C, L629G, L629I, V631I, V631L, V631M, M663A, M663F, L669R, L670E, L670F, L670I, L670Q, L670R, L670S, L670T, L670V, L670W, S671A, S671G, S671T, L691V, T692C, T692F, T692G, T692I, T692L, T692Y, L693F, L693I, L693Y, H706F, A708C, V710K, V710L, V710M, V710N, V710S, A711C, A711G, A711H, A711W, Y765W, Q768I, P779E, V797E, V797F, V797I, V797L, V797M, V797W, T826G, A834G, A834H, A834S, A834W, E855G, S856G, L857A, L857E, L857S, L857T, L857V, I869L, I869S, L871E, L871K, R873A, R873F, R873Y, V878A, V878G, V878K, V878Q, V878S, V878W, L909F, T924A, V926M, and V926T, wherein the positions are numbered with reference to SEQ ID NO: 1956. 
     The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95% at least 96% at least 97% at least 98% or at least 99% sequence identity to SEQ ID NO: 2496, wherein the positions are numbered with reference to SEQ ID NO: 2496. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 246, 304, 313, 569, 569/588, 569/588/589/628/629/692/711, 569/588/678/692, 569/588/711/869/871/878, 569/588/878, 569/589/628/670/678/692/711/795/871, 569/589/628/670/692/711, 569/589/628/692/711/795, 569/589/670, 569/589/670/678/692/711/795, 569/589/670/871, 569/589/678/871/878, 569/589/692/795/871/878, 569/589/711/871, 569/589/871, 569/628, 569/628/670, 569/628/670/678, 569/628/670/692/711/871, 569/628/670/711, 569/628/678/711, 569/628/692, 569/670, 569/670/678, 569/670/678/692/871, 569/670/692, 569/670/711, 569/670/711/871, 569/678/692/795, 569/678/869/878, 569/678/878, 569/692, 569/692/711, 569/692/711/869/871/878, 569/711, 569/711/795/871/878, 569/711/869/878, 569/711/871, 569/795, 569/871, 572/588/678/692/869/878, 572/588/795, 572/692/869/878, 572/692/878, 582, 584, 585, 588/589/628/678, 589, 589/670/692/795/871, 589/670/795/871, 589/871, 628/629/692/871/878, 628/670, 628/670/692/711/795, 628/711/795, 628/871, 628/878, 629/869/878, 670/678, 670/678/692/871, 670/692/871, 678/692/711/869, 678/692/795/869, 678/692/869, 678/795/871/878, 692, 692/711, 692/711/795/869, 692/711/795/869/871/878, 692/711/869/878, 692/711/871/878, 692/869, 692/869/871/878/916, 692/871, 711, 711/795/869/878, 711/869/878, 711/871, 795/878, 812, 871, and 878, wherein the positions are numbered with reference to SEQ ID NO: 2496. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 246T, 304M, 313I, 313L, 569H/589I/628M/670T/678T/692G/711H/795E/871S, 569H/628M, 569H/628M/670F/678T, 569H/628M/670T, 569H/628M/670T/692Y/711H/871K, 569H/670F/678T/692G/871S, 569H/670T/692G, 569H/678T/692G/795E, 569H/692G, 569H/692Y, 569H/711H/795E/871S/878S, 569H/711H/869S/878S, 569H/711H/871K, 569T, 569T/588L, 569T/588L/589I/628M/629I/692Y/711H, 569T/588L/678T/692Y, 569T/588L/711H/869L/871K/878S, 569T/588L/878S, 569T/589I/628M/670F/692G/711H, 569T/589I/678T/871K/878S, 569T/589I/692G/795E/871K/878S, 569T/589I/871S, 569T/628M/678T/711H, 569T/628M/692Y, 569T/670T/678T/692G/871K, 569T/670T/711H/871E, 569T/678T/869S/878S, 569T/678T/878S, 569T/692Y, 569T/692Y/711H/869L/871K/878A, 569T/711H, 569T/795E, 569T/871K, 569T/871S, 569Y/589I/628M/670T/692Y/711H, 569Y/589I/628M/692G/711H/795E, 569Y/589S/670F, 569Y/589I/670T/678T/692G/711H/795E, 569Y/589I/670T/871K, 569Y/589I/711H/871K, 569Y/628M/670T/692Y/711H/871S, 569Y/628M/670T/711H, 569Y/670F/678T, 569Y/670T, 569Y/670T/711H, 569Y/692Y/711H, 569Y/711H, 569Y/871E, 572S/588L/678T/692G/869L/878A, 572S/588L/795E, 572S/692G/869S/878S, 572S/692G/878S, 572S/692L/869S/878S, 582T, 584E, 585K, 588L/589I/628M/678T, 589I, 589I/670T/692G/795E/871K, 589I/670T/795E/871S, 589I/871E, 628M/629I/692Y/871S/878S, 628M/670F, 628M/670T/692G/711H/795E, 628M/711H/795E, 628M/871S, 628M/878S, 629I/869L/878S, 670T/678T, 670T/678T/692Y/871S, 670T/692G/871K, 678T/692G/711H/869S, 678T/692G/795E/869S, 678T/692G/869S, 678T/795E/871K/878A, 692G/711H, 692G/711H/795E/869L/871K/878A, 692G/711H/795E/869S, 692G/711H/869L/878S, 692G/711H/869S/878A, 692G/711H/871S/878A, 692G/869L/871K/878S/916R, 692G/869S, 692G/871K, 692Y, 711H, 711H/795E/869S/878S, 711H/869S/878S, 711H/871K, 795E/878S, 812E, 871K, 8715, and 8785, wherein the positions are numbered with reference to SEQ ID NO: 2496. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from S246T, L304M, V3131, V313L, L569H/V589I/L628M/L670T/S678T/T692G/A711H/Q795E/L871S, L569H/L628M, L569H/L628M/L670F/S678T, L569H/L628M/L670T, L569H/L628M/L670T/T692Y/A711H/L871K, L569H/L670F/S678T/T692G/L871S, L569H/L670T/T692G, L569H/S678T/T692G/Q795E, L569H/T692G, L569H/T692Y, L569H/A711H/Q795E/L871S/V878S, L569H/A711H/1869S/V878S, L569H/A711H/L871K, L569T, L569T/F588L, L569T/F588L/V589I/L628M/L629I/T692Y/A711H, L569T/F588L/S678T/T692Y, L569T/F588L/A711H/I869L/L871K/V878I, L569T/F588L/V878S, L569T/V589S/L628M/L670F/T692G/A711H, L569T/V589S/S678T/L871K/V878S, L569T/V589I/T692G/Q795E/L871K/V8785, L569T/V589I/L8715, L569T/L628M/S678T/A711H, L569T/L628M/T692Y, L569T/L670T/S678T/T692G/L871K, L569T/L670T/A711H/L871E, L569T/S678T/I869I/V878I, L569T/S678T/V878I, L569T/T692Y, L569T/T692Y/A711H/I869L/L871K/V878A, L569T/A711H, L569T/Q795E, L569T/L871K, L569T/L871S, L569Y/V589I/L628M/L670T/T692Y/A711H, L569Y/V589I/L628M/T692G/A711H/Q795E, L569Y/V589I/L670F, L569Y/V589I/L670T/S678T/T692G/A711H/Q795E, L569Y/V589I/L670T/L871K, L569Y/V589I/A711H/L871K, L569Y/L628M/L670T/T692Y/A711H/L871S, L569Y/L628M/L670T/A711H, L569Y/L670F/S678T, L569Y/L670T, L569Y/L670T/A711H, L569Y/T692Y/A711H, L569Y/A711H, L569Y/L871E, A572S/F588L/S678T/T692G/I869L/V878A, A572S/F588L/Q795E, A572S/T692G/I869S/V878I, A572S/T692G/V878S, A572S/T692L/I869S/V878S, A582T, G584E, T585K, F588L/V589I/L628M/S678T, V589I, V589I/L670T/T692G/Q795E/L871K, V589I/L670T/Q795E/L871S, V589I/L871E, L628M/L629I/T692Y/L871S/V878S, L628M/L670F, L628M/L670T/T692G/A711H/Q795E, L628M/A711H/Q795E, L628M/L871S, L628M/V878S, L629I/I869L/V878S, L670T/S678T, L670T/S678T/T692Y/L871S, L670T/T692G/L871K, S678T/T692G/A711H/I869S, S678T/T692G/Q795E/I869S, S678T/T692G/I869S, S678T/Q795E/L871K/V878A, T692G/A711H, T692G/A711H/Q795E/I869L/L871K/V878A, T692G/A711H/Q795E/I1869S, T692G/A711H/I869L/V878S, T692G/A711H/I869S/V878A, T692G/A711H/L871S/V878A, T692G/I869L/L871K/V878S/S916R, T692G/I869S, T692G/L871K, T692Y, A711H, A711H/Q795E/I869S/V878S, A711H/I869S/V878S, A711H/L871K, Q795E/V878S, A812E, L871K, L871S, and V878S, wherein the positions are numbered with reference to SEQ ID NO: 2496. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 60/589, 307, 313, 584, and 810, wherein the positions are numbered with reference to SEQ ID NO: 2496. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 60V/589A, 307T, 313T, 584C, and 810V, wherein the positions are numbered with reference to SEQ ID NO: 2496. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from A60V/V589A, S307T, V313T, G584C, and L810V, wherein the positions are numbered with reference to SEQ ID NO: 2496. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 60/589, 246, 304, 307, 313, 569, 569/588, 569/588/589/628/629/692/711, 569/588/678/692, 569/588/711/869/871/878, 569/588/878, 569/589/628/670/678/692/711/795/871, 569/589/628/670/692/711, 569/589/628/692/711/795, 569/589/670, 569/589/670/678/692/711/795, 569/589/670/871, 569/589/678/871/878, 569/589/692/795/871/878, 569/589/711/871, 569/589/871, 569/628, 569/628/670, 569/628/670/678, 569/628/670/692/711/871, 569/628/670/711, 569/628/678/711, 569/628/692, 569/670, 569/670/678, 569/670/678/692/871, 569/670/692, 569/670/711, 569/670/711/871, 569/678/692/795, 569/678/869/878, 569/678/878, 569/692, 569/692/711, 569/692/711/869/871/878, 569/711, 569/711/795/871/878, 569/711/869/878, 569/711/871, 569/795, 569/871, 572/588/678/692/869/878, 572/588/795, 572/692/869/878, 572/692/878, 582, 584, 585, 588/589/628/678, 589, 589/670/692/795/871, 589/670/795/871, 589/871, 628/629/692/871/878, 628/670, 628/670/692/711/795, 628/711/795, 628/871, 628/878, 629/869/878, 670/678, 670/678/692/871, 670/692/871, 678/692/711/869, 678/692/795/869, 678/692/869, 678/795/871/878, 692, 692/711, 692/711/795/869, 692/711/795/869/871/878, 692/711/869/878, 692/711/871/878, 692/869, 692/869/871/878/916, 692/871, 711, 711/795/869/878, 711/869/878, 711/871, 795/878, 810, 812, 871, and 878, wherein the positions are numbered with reference to SEQ ID NO: 2496. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 60V/589A, 246T, 304M, 307T, 313I, 313L, 313T, 569H/589I/628M/670T/678T/692G/711H/795E/871S, 569H/628M, 569H/628M/670F/678T, 569H/628M/670T, 569H/628M/670T/692Y/711H/871K, 569H/670F/678T/692G/871S, 569H/670T/692G, 569H/678T/692G/795E, 569H/692G, 569H/692Y, 569H/711H/795E/871S/878S, 569H/711H/869S/878S, 569H/711H/871K, 569T, 569T/588L, 569T/588L/589I/628M/629I/692Y/711H, 569T/588L/678T/692Y, 569T/588L/711H/869L/871K/878S, 569T/588L/878S, 569T/589I/628M/670F/692G/711H, 569T/589I/678T/871K/878S, 569T/589I/692G/795E/871K/878S, 569T/589I/871S, 569T/628M/678T/711H, 569T/628M/692Y, 569T/670T/678T/692G/871K, 569T/670T/711H/871E, 569T/678T/869S/878S, 569T/678T/878S, 569T/692Y, 569T/692Y/711H/869L/871K/878A, 569T/711H, 569T/795E, 569T/871K, 569T/871S, 569Y/589I/628M/670T/692Y/711H, 569Y/589I/628M/692G/711H/795E, 569Y/589I/670F, 569Y/589I/670T/678T/692G/711H/795E, 569Y/589I/670T/871K, 569Y/589I/711H/871K, 569Y/628M/670T/692Y/711H/871S, 569Y/628M/670T/711H, 569Y/670F/678T, 569Y/670T, 569Y/670T/711H, 569Y/692Y/711H, 569Y/711H, 569Y/871E, S725/588L/678T/692G/869L/878A, S725/588L/795E, 572S/692G/869S/878S, 572S/692G/878S, 572S/692L/869S/878S, 582T, 584C, 584E, 585K, 588L/589I/628M/678T, 589I, 589I/670T/692G/795E/871K, 589I/670T/795E/871S, S89I/871E, 628M/629I/692Y/871S/878S, 628M/670F, 628M/670T/692G/711H/795E, 628M/711H/795E, 628M/871S, 628M/878S, 629I/869L/878S, 670T/678T, 670T/678T/692Y/871S, 670T/692G/871K, 678T/692G/711H/869S, 678T/692G/795E/869S, 678T/692G/869S, 678T/795E/871K/878A, 692G/711H, 692G/711H/795E/869L/871K/878A, 692G/711H/795E/869S, 692G/711H/869L/878S, 692G/711H/869S/878A, 692G/711H/871S/878A, 692G/869L/871K/878S/916R, 692G/869S, 692G/871K, 692Y, 711H, 711H/795E/869S/878S, 711H/869S/878S, 711H/871K, 795E/878S, 810V, 812E, 871K, 8715, and 878S, wherein the positions are numbered with reference to SEQ ID NO: 2496. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from A60V/V589A, S246T, L304M, S307T, V313I, V313L, V313T, L569H/V589I/L628M/L670T/S678T/T692G/A711H/Q795E/L871S, L569H/L628M, L569H/L628M/L670F/S678T, L569H/L628M/L670T, L569H/L628M/L670T/T692Y/A711H/L871K, L569H/L670F/S678T/T692G/L871S, L569H/L670T/T692G, L569H/S678T/T692G/Q795E, L569H/T692G, L569H/T692Y, L569H/A711H/Q795E/L871S/V878S, L569H/A711H/I1869S/V878S, L569H/A711H/L871K, L569T, L569T/F588L, L569T/F588L/V589I/L628M/L629I/T692Y/A711H, L569T/F588L/S678T/T692Y, L569T/F588L/A711H/I869L/L871K/V878S, L569T/F588L/V878S, L569T/V589I/L628M/L670F/T692G/A711H, L569T/V589I/S678T/L871K/V878S, L569T/V589I/T692G/Q795E/L871K/V878S, L569T/V589I/L871S, L569T/L628M/S678T/A711H, L569T/L628M/T692Y, L569T/L670T/S678T/T692G/L871K, L569T/L670T/A711H/L871E, L569T/S678T/I869S/V878S, L569T/S678T/V878S, L569T/T692Y, L569T/T692Y/A711H/I869L/L871K/V878A, L569T/A711H, L569T/Q795E, L569T/L871K, L569T/L871S, L569Y/V589I/L628M/L670T/T692Y/A711H, L569Y/V589I/L628M/T692G/A711H/Q795E, L569Y/V589I/L670F, L569Y/V589I/L670T/S678T/T692G/A711H/Q795E, L569Y/V589I/L670T/L871K, L569Y/V589I/A711H/L871K, L569Y/L628M/L670T/T692Y/A711H/L871S, L569Y/L628M/L670T/A711H, L569Y/L670F/S678T, L569Y/L670T, L569Y/L670T/A711H, L569Y/T692Y/A711H, L569Y/A711H, L569Y/L871E, A572S/F588L/S678T/T692G/I869L/V878A, A572S/F588L/Q795E, A572S/T692G/I869S/V878S, A572S/T692G/V878S, A572S/T692L/I869I/V878S, A582T, G584C, G584E, T585K, F588L/V589I/L628M/S678T, V589I, V589I/L670T/T692G/Q795E/L871K, V589I/L670T/Q795E/L871S, V589I/L871E, L628M/L629I/T692Y/L871S/V878S, L628M/L670F, L628M/L670T/T692G/A711H/Q795E, L628M/A711H/Q795E, L628M/L871S, L628M/V878S, L629I/I869L/V878S, L670T/S678T, L670T/S678T/T692Y/L871S, L670T/T692G/L871K, S678T/T692G/A711H/I869S, S678T/T692G/Q795E/I869S, S678T/T692G/I869S, S678T/Q795E/L871K/V878A, T692G/A711H, T692G/A711H/Q795E/I869L/L871K/V878A, T692G/A711H/Q795E/I869S, T692G/A711H/I869L/V878S, T692G/A711H/I869S/V878A, T692G/A711H/L871S/V878A, T692G/I869L/L871K/V878S/S916R, T692G/I869S, T692G/L871K, T692Y, A711H, A711H/Q795E/I869S/V878S, A711H/I869S/V878S, A711H/L871K, Q795E/V878S, L810V, A812E, L871K, L871S, and V878S, wherein the positions are numbered with reference to SEQ ID NO: 2496. 
     The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 2880, wherein the positions are numbered with reference to SEQ ID NO: 2880. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 24/28/29/39/50/62/78/87/135/150/266/267/522/527/551/670/727/750/830/842/871/883/894/932, 24/28/39/50/62/78/87/135/150/266/267/522/527/551/569/727/830/842/871/883/894/913, 24/28/50/135/150/437/522/527/871/883/894/932, 24/28/62/522/569/932, 24/28/437/486/527, 24/29/39/50/62/78/87/135/150/267/437/486/522/527/551/711/727/750/830/842/871/883/894/913/932, 24/50/78/87/135/150/267/486/522/527/551/670/727/750/830/842/871/883/894/913/932, 24/50/486/527/711/727, 24/62/87/486/727, 24/62/727/830/932, 24/87/135/522/670/711/830/842/913, 24/150/522/527/727/883/894, 24/527/727/842/871/883/913/932, 24/670/727/750/842/871, 28, 28/50/78/87/135/266/267/437/486/527/551/670/727/750/830/842/871/883/894/913/932, 28/50/522/527/711/727/871, 28/62, 28/62/267/932, 28/437/527/871, 28/522/527/569/711/830/894, 28/727, 28/727/871, 29/39/50/62/65/78/87/135/150/437/551/569/670/727/750/830/842/883/894/932, 29/62/437/527, 29/78/87/150/527/727, 29/78/135/727/830, 29/87, 29/135/150/527/670/727/883, 29/150/267/727/750/871/883/932, 29/150/437/727, 29/522/670/711/871, 29/670/932, 39/50, 39/727/750/932, 50/135/150/932, 50/437/522/527, 50/711, 50/727/750/883/894, 62, 62/87/150, 62/87/150/727, 62/135/522/711/727/750/842/871/894, 62/437, 62/437/727, 78/87/486/527/670/727/750/830/842/871/913/932, 87/750, 89/109/527/678/727/842, 89/109/678/727/736/812/878, 89/109/727/932, 89/109/932, 89/527, 89/527/678/692/736/842/878/932, 89/527/678/932, 89/527/727/812/860, 89/678/692/736/932, 89/678/812/878, 89/842/878, 109/527/678/812, 109/678/692/842/860/878/932, 109/678/727/860, 109/678/736/812/878, 109/678/812, 109/678/842/878, 109/692/727/736/812, 109/692/727/812/842/860, 109/727/860/878, 109/736/932, 109/812, 109/842, 109/932, 135/670/727, 135/711/750/932, 150/527/842/871/913, 150/871/932, 150/883/932, 267/527/727, 403/527/678/692/736/812/842/860, 437/522/527/670/871, 437/750/830/932, 522, 522/527/569/727, 522/830, 527, 527/678/692/727/736/878, 527/678/692/812/932, 527/692/727/736/812, 527/692/727/736/842/860/878, 527/727/736, 527/736/932, 527/812, 670/711/871, 670/830/871, 678/692/727/812/842, 678/692/812, 678/812, 678/860/878, 678/913, 678/932, 692/727/736/842/913, 692/812, 727, 727/932, 871, and 878/932, wherein the positions are numbered with reference to SEQ ID NO: 2880. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from wherein the positions are numbered with reference to SEQ ID NO: 2880. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 24L/28L/29L/39P/50Q/62A/78P/87D/135S/150T/266T/267R/522E/527N/551V/670L/727S/750A/830 Q/842G/871L/883R/894Q/932S, 24L/28L/39P/50Q/62A/78P/87D/135S/150T/266T/267R/522E/527N/551V/569L/727S/830Q/842G/8 71L/883R/894Q/913V, 24L/28L/50Q/135S/150T/437A/522E/527N/871L/883R/894Q/932S, 24L/28L/62A/522E/569L/932S, 24L/28L/437A/486T/527N, 24L/29L/39P/50Q/62A/78P/87D/135S/150T/267R/437A/486T/522E/527N/551V/711A/727S/750A/8 30Q/842G/871L/883R/894Q/913V/932S, 24L/50Q/78P/87D/135S/150T/267R/486T/522E/527N/551V/670L/727S/750A/830Q/842G/871L/883 R/894Q/913V/932S, 24L/50Q/486T/527N/711A/727S, 24L/62A/87D/486T/727S, 24L/62A/727S/830Q/932S, 24L/87D/135S/522E/670L/711A/830Q/842G/913V, 24L/150T/522E/527N/727S/883R/894Q, 24L/527N/727S/842G/871L/883R/913V/932S, 24L/670L/727S/750A/842G/871L, 28L, 28L/50Q/78P/87D/135S/266T/267R/437A/486T/527N/551V/670L/727S/750A/830Q/842G/871L/883 R/894Q/913V/932S, 28L/50Q/522E/527N/711A/727S/871L, 28L/62A, 28L/62A/267R/932S, 28L/437A/527N/871L, 28L/522E/527N/569L/711A/830Q/894Q, 28L/727S, 28L/727S/871L, 29L/39P/50Q/62A/65R/78P/87D/135S/150T/437A/551V/569L/670L/727S/750A/830Q/842G/883R/8 94Q/932S, 29L/62A/437A/527N, 29L/78P/87D/150T/527N/727S, 29L/78P/135S/727S/830Q, 29L/87D, 29L/135S/150T/527N/670L/727S/883R, 29L/150T/267R/727S/750A/871L/883R/932S, 29L/150T/437A/727S, 29L/522E/670L/711A/871L, 29L/670L/932S, 39P/50Q, 39P/727S/750A/932S, 50Q/135S/150T/932S, 50Q/437A/522E/527N, 50Q/711A, 50Q/727S/750A/883R/894Q, 62A, 62A/87D/150T, 62A/87D/150T/727S, 62A/135S/522E/711A/727S/750A/842G/871L/894Q, 62A/437A, 62A/437A/727S, 78P/87D/486T/527N/670L/727S/750A/830Q/842G/871L/913V/932S, 87D/750A, 89R/109D/527N/678T/727S/842G, 89R/109D/678T/727S/736M/812E/878S, 89R/109D/727S/932S, 89R/109D/932S, 89R/527N, 89R/527N/678T/692G/736M/842G/878S/932S, 89R/527N/678T/932S, 89R/527N/727S/812E/860F, 89R/678T/692G/736M/932S, 89R/678T/812E/878S, 89R/842G/878S, 109D/527N/678T/812E, 109D/678T/692G/842G/860F/878S/932S, 109D/678T/727S/860F, 109D/678T/736M/812E/878S, 109D/678T/812E, 109D/678T/842G/878S, 109D/692G/727S/736M/812E, 109D/692G/727S/812E/842G/860F, 109D/727S/860F/878S, 109D/736M/932S, 109D/812E, 109D/842G, 109D/932S, 135S/670L/727S, 135S/711A/750A/932S, 150T/527N/842G/871L/913V, 150T/871L/932S, 150T/883R/932S, 267R/527N/727S, 403H/527N/678T/692G/736M/812E/842G/860F, 437A/522E/527N/670L/871L, 437A/750A/830Q/932S, 522E, 522E/527N/569L/727S, 522E/830Q, 527N, 527N/678T/692G/727S/736M/878S, 527N/678T/692G/812E/932S, 527N/692G/727S/736M/812E, 527N/692G/727S/736M/842G/860F/878S, 527N/727S/736M, 527N/736M/932S, 527N/812E, 670L/711A/871L, 670L/830Q/871L, 678T/692G/727S/812E/842G, 678T/692G/812E, 678T/812E, 678T/860F/878S, 678T/913V, 678T/932S, 692G/727S/736M/842G/913V, 692G/812E, 727S, 727S/932S, 871L, and 878S/932S, wherein the positions are numbered with reference to SEQ ID NO: 2880. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from W24L/S28L/T29L/Q39P/V50Q/L62A/E78P/E87D/Q135S/S150T/N266T/K267R/V522E/R527N/A55 1V/T670L/W727S/P750A/K830Q/S842G/E871L/H883R/G894Q/A932S, W24L/S28L/Q39P/V50Q/L62A/E78P/E87D/Q135S/S150T/N266T/K267R/V522E/R527N/A551V/T 569L/W727S/K830Q/S842G/E871L/H883R/G894Q/R913V, W24L/S28L/V50Q/Q135S/S150T/G437A/V522E/R527N/E871L/H883R/G894Q/A932S, W24L/S28L/L62A/V522E/T569L/A932S, W24L/S28L/G437A/E486T/R527N, W24L/T29L/Q39P/V50Q/L62A/E78P/E87D/Q135S/S150T/K267R/G437A/E486T/V522E/R527N/A 551V/H711A/W727S/P750A/K830Q/S842G/E871L/H883R/G894Q/R913V/A932S, W24L/V50Q/E78P/E87D/Q135S/S150T/K267R/E486T/V522E/R527N/A551V/T670L/W727S/P750 A/K830Q/S842G/E871L/H883R/G894Q/R913V/A932S, W24L/V50Q/E486T/R527N/H711A/W727S, W24L/L62A/E87D/E486T/W727S, W24L/L62A/W727S/K830Q/A932S, W24L/E87D/Q135S/V522E/T670L/H711A/K830Q/S842G/R913V, W24L/S150T/V522E/R527N/W727S/H883R/G894Q, W24L/R527N/W727S/S842G/E871L/H883R/R913V/A932S, W24L/T670L/W727S/P750A/S842G/E871L, S28L, S28L/V50Q/E78P/E87D/Q135S/N266T/K267R/G437A/E486T/R527N/A551V/T670L/W727S/P750 A/K830Q/S842G/E871L/H883R/G894Q/R913V/A932S, S28L/V50Q/V522E/R527N/H711A/W727S/E871L, S28L/L62A, S28L/L62A/K267R/A932S, S28L/G437A/R527N/E871L, S28L/V522E/R527N/T569L/H711A/K830Q/G894Q, S28L/W727S, S28L/W727S/E871L, T29L/Q39P/V50Q/L62A/G65R/E78P/E87D/Q1355/5150T/G437A/A551V/T569L/T670L/W727S/P7 50A/K830Q/S842G/H883R/G894Q/A932S, T29L/L62A/G437A/R527N, T29L/E78P/E87D/S150T/R527N/W727S, T29L/E78P/Q135S/W727S/K830Q, T29L/E87D, T29L/Q135S/S150T/R527N/T670L/W727S/H883R, T29L/S150T/K267R/W727S/P750A/E871L/H883R/A932S, T29L/S150T/G437A/W727S, T29L/V522E/T670L/H711A/E871L, T29L/T670L/A932S, Q39P/V50Q, Q39P/W727S/P750A/A932S, V50Q/Q1355/S150T/A932S, V50Q/G437A/V522E/R527N, V50Q/H711A, V50Q/W727S/P750A/H883R/G894Q, L62A, L62A/E87D/S150T, L62A/E87D/S150T/W727S, L62A/Q135S/V522E/H711A/W727S/P750A/S842G/E871L/G894Q, L62A/G437A, L62A/G437A/W727S, E78P/E87D/E486T/R527N/T670L/W727S/P750A/K830Q/S842G/E871L/R913V/A932S, E87D/P750A, A89R/L109D/R527N/S678T/W727S/S842G, A89R/L109D/S678T/W727S/L736M/A812E/V878S, A89R/L109D/W727S/A932S, A89R/L109D/A932S, A89R/R527N, A89R/R527N/S678T/T692G/L736M/S842G/V878S/A932S, A89R/R527N/S678T/A932S, A89R/R527N/W727S/A812E/L860F, A89R/S678T/T692G/L736M/A932S, A89R/S678T/A812E/V878S, A89R/S842G/V878S, L109D/R527N/S678T/A812E, L109D/S678T/T692G/S842G/L860F/V878S/A932S, L109D/S678T/W727S/L860F, L109D/S678T/L736M/A812E/V878S, L109D/S678T/A812E, L109D/S678T/S842G/V878S, L109D/T692G/W727S/L736M/A812E, L109D/T692G/W727S/A812E/S842G/L860F, L109D/W727S/L860F/V878S, L109D/L736M/A932S, L109D/A812E, L109D/S842G, L109D/A932S, Q135S/T670L/W727S, Q135S/H711A/P750A/A932S, S150T/R527N/S842G/E871L/R913V, S150T/E871L/A932S, S150T/H883R/A932S, K267R/R527N/W727S, R403H/R527N/S678T/T692G/L736M/A812E/S842G/L860F, G437A/V522E/R527N/T670L/E871L, G437A/P750A/K830Q/A932S, V522E, V522E/R527N/T569L/W727S, V522E/K830Q, R527N, R527N/S678T/T692G/W727S/L736M/V878S, R527N/S678T/T692G/A812E/A932S, R527N/T692G/W727S/L736M/A812E, R527N/T692G/W727S/L736M/S842G/L860F/V878S, R527N/W727S/L736M, R527N/L736M/A932S, R527N/A812E, T670L/H711A/E871L, T670L/K830Q/E871L, S678T/T692G/W727S/A812E/S842G, S678T/T692G/A812E, S678T/A812E, S678T/L860F/V878S, S678T/R913V, S678T/A932S, T692G/W727S/L736M/S842G/R913V, T692G/A812E, W727S, W727S/A932S, E871L, and V878S/A932S, wherein the positions are numbered with reference to SEQ ID NO: 2880. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 62/87/150, 89/109/527/678/727/842, 89/109/678/727/736/812/878, 89/109/932, 89/527/678/692/736/842/878/932, 89/527/727/812/860, 89/678/692/736/932, 89/678/812/878, 109/527/678/812, 109/678/692/842/860/878/932, 109/678/736/812/878, 109/678/812, 109/692/727/736/812, 109/692/727/812/842/860, 109/736/932, 109/812, 109/842, 109/932, 403/527/678/692/736/812/842/860, 522/830, 527/678/692/727/736/878, 527/678/692/812/932, 527/692/727/736/812, 527/692/727/736/842/860/878, 527/727/736, 527/736/932, 527/812, 678/692/727/812/842, 678/692/812, 678/812, 692/727/736/842/913, and 692/812, wherein the positions are numbered with reference to SEQ ID NO: 2880. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 62A/87D/150T, 89R/109D/527N/678T/727S/842G, 89R/109D/678T/727S/736M/812E/878S, 89R/109D/932S, 89R/527N/678T/692G/736M/842G/878S/932S, 89R/527N/727S/812E/860F, 89R/678T/692G/736M/932S, 89R/678T/812E/878S, 109D/527N/678T/812E, 109D/678T/692G/842G/860F/878S/932S, 109D/678T/736M/812E/878S, 109D/678T/812E, 109D/692G/727S/736M/812E, 109D/692G/727S/812E/842G/860F, 109D/736M/932S, 109D/812E, 109D/842G, 109D/932S, 403H/527N/678T/692G/736M/812E/842G/860F, 522E/830Q, 527N/678T/692G/727S/736M/878S, 527N/678T/692G/812E/932S, 527N/692G/727S/736M/812E, 527N/692G/727S/736M/842G/860F/878S, 527N/727S/736M, 527N/736M/932S, 527N/812E, 678T/692G/727S/812E/842G, 678T/692G/812E, 678T/812E, 692G/727S/736M/842G/913V, and 692G/812E, wherein the positions are numbered with reference to SEQ ID NO: 2880. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from L62A/E87D/S150T, A89R/L109D/R527N/S678T/W727S/S842G, A89R/L109D/S678T/W727S/L736M/A812E/V878S, A89R/L109D/A932S, A89R/R527N/S678T/T692G/L736M/S842G/V878S/A932S, A89R/R527N/W727S/A812E/L860F, A89R/S678T/T692G/L736M/A932S, A89R/S678T/A812E/V878S, L109D/R527N/S678T/A812E, L109D/S678T/T692G/S842G/L860F/V878S/A932S, L109D/S678T/L736M/A812E/V878S, L109D/S678T/A812E, L109D/T692G/W727S/L736M/A812E, L109D/T692G/W727S/A812E/S842G/L860F, L109D/L736M/A932S, L109D/A812E, L109D/S842G, L109D/A932S, R403H/R527N/S678T/T692G/L736M/A812E/S842G/L860F, V522E/K830Q, R527N/S678T/T692G/W727S/L736M/V878S, R527N/S678T/T692G/A812E/A932S, R527N/T692G/W727S/L736M/A812E, R527N/T692G/W727S/L736M/S842G/L860F/V878S, R527N/W727S/L736M, R527N/L736M/A932S, R527N/A812E, S678T/T692G/W727S/A812E/S842G, S678T/T692G/A812E, S678T/A812E, T692G/W727S/L736M/S842G/R913V, and T692G/A812E, wherein the positions are numbered with reference to SEQ ID NO: 2880. 
     The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 3104, wherein the positions are numbered with reference to SEQ ID NO: 3104. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 62, 62/89/830, 62/248/678/830/878/932, 62/678, 62/678/785, 62/678/830, 62/678/830/860, 62/678/830/860/871/878/932, 62/678/830/860/878, 62/678/830/860/878/932, 62/678/830/860/932, 62/678/830/871, 62/678/830/871/932, 62/678/830/878/932, 62/678/830/932, 62/678/860, 62/678/860/878, 62/678/860/932, 62/678/871, 62/678/871/932, 62/678/878/932, 62/678/932, 62/830, 62/830/860, 62/830/860/871/873, 62/830/860/878/932, 62/830/860/932, 62/830/871/932, 62/830/878, 62/830/932, 62/833/860/932, 62/860, 62/860/871, 62/860/871/878, 62/860/871/932, 62/860/878/932, 62/860/932, 62/871/878/932, 62/871/932, 62/878, 62/878/932, 62/932, 678, 678/830/932, 678/932, and 860/932, wherein the positions are numbered with reference to SEQ ID NO: 3104. in some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 62A, 62A/89D/830Q, 62A/248H/678T/830Q/878S/932S, 62A/678T, 62A/678T/785Q, 62A/678T/830Q, 62A/678T/830Q/860F, 62A/678T/830Q/860F/871L/878S/932S, 62A/678T/830Q/860F/878S, 62A/678T/830Q/860F/878S/932S, 62A/678T/830Q/860F/932S, 62A/678T/830Q/871L, 62A/678T/830Q/871L/932S, 62A/678T/830Q/878S/932S, 62A/678T/830Q/932S, 62A/678T/860F, 62A/678T/860F/878S, 62A/678T/860F/932S, 62A/678T/871L, 62A/678T/871L/932S, 62A/678T/878S/932S, 62A/678T/878S/932T, 62A/678T/932S, 62A/830Q, 62A/830Q/860F, 62A/830Q/860F/871L/873H, 62A/830Q/860F/878S/932S, 62A/830Q/860F/932S, 62A/830Q/871L/932S, 62A/830Q/878S, 62A/830Q/932S, 62A/833I/860F/932S, 62A/860F, 62A/860F/871L, 62A/860F/871L/878S, 62A/860F/871L/932S, 62A/860F/878S/932S, 62A/860F/932S, 62A/871L/878S/932S, 62A/871L/932S, 62A/878S, 62A/878S/932S, 62A/932S, 678T, 678T/830Q/932S, 678T/932S, and 860F/932S, wherein the positions are numbered with reference to SEQ ID NO: 3104. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from L62A, L62A/A89D/K830Q, L62A/Y248H/S678T/K830Q/V878S/A932S, L62A/S678T, L62A/S678T/P785Q, L62A/S678T/K830Q, L62A/S678T/K830Q/L860F, L62A/S678T/K830Q/L860F/E871L/V878S/A932S, L62A/S678T/K830Q/L860F/V878S, L62A/S678T/K830Q/L860F/V878S/A932S, L62A/S678T/K830Q/L860F/A932S, L62A/S678T/K830Q/E871L, L62A/S678T/K830Q/E871L/A932S, L62A/S678T/K830Q/V878S/A932S, L62A/S678T/K830Q/A932S, L62A/S678T/L860F, L62A/S678T/L860F/V878S, L62A/S678T/L860F/A932S, L62A/S678T/E871L, L62A/S678T/E871L/A932S, L62A/S678T/V878S/A932S, L62A/S678T/V878S/A932T, L62A/S678T/A932S, L62A/K830Q, L62A/K830Q/L860F, L62A/K830Q/L860F/E871L/R873H, L62A/K830Q/L860F/V878S/A932S, L62A/K830Q/L860F/A932S, L62A/K830Q/E871L/A932S, L62A/K830Q/V878S, L62A/K830Q/A932S, L62A/M8331/L860F/A932S, L62A/L860F, L62A/L860F/E871L, L62A/L860F/E871L/V878S, L62A/L860F/E871L/A932S, L62A/L860F/V878S/A932S, L62A/L860F/A932S, L62A/E871L/V878S/A932S, L62A/E871L/A932S, L62A/V878S, L62A/V878S/A932S, L62A/A932S, S678T, S678T/K830Q/A932S, S678T/A932S, and L860F/A932S, wherein the positions are numbered with reference to SEQ ID NO: 3104. 
     In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 62/89/830, 62/830, 62/830/860, 62/830/860/932, and 62/830/932, wherein the positions are numbered with reference to SEQ ID NO: 3104. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 62A/89D/830Q, 62A/830Q, 62A/830Q/860F, 62A/830Q/860F/932S, and 62A/830Q/932S, wherein the positions are numbered with reference to SEQ ID NO: 3104. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from L62A/A89D/K830Q, L62A/K830Q, L62A/K830Q/L860F, L62A/K830Q/L860F/A932S, and L62A/K830Q/A932S, wherein the positions are numbered with reference to SEQ ID NO: 3104. 
     In some embodiments, the recombinant acid alpha glucosidase comprises at least one mutation in at least one position as provided in Tables 3-1, 3-2, 4-1, 6-1, 10-1, 10-2, 12-1, 13-1, 13-2, 14-1, 14-2, 15-1, 16-1, 17-1, 17-2, 17-3, 17-4, 17-5, 17-6, 17-7, 17-8, and/or 17-9. In some additional embodiments, the recombinant acid alpha glucosidase is derived from a human acid alpha glucosidase. In yet some additional embodiments, the recombinant acid alpha glucosidase comprising the polypeptide sequence of SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. 
     In some additional embodiments, the recombinant acid alpha-glucosidase provided herein is thermostable. In some further embodiments, the recombinant acid alpha-glucosidase is resistant to proteolysis. In yet some additional embodiments, the recombinant acid alpha-glucosidase is resistant to at least one digestive tract protease. In some embodiments, the digestive tract protease is selected from chymotrypsin, trypsin, carboxypeptidases, and elastases. In some further embodiments, the recombinant acid alpha-glucosidase is acid stable. In some additional embodiments, the recombinant acid alpha-glucosidase is stable to acidic pH and neutral pH. In yet some additional embodiments, the recombinant acid alpha-glucosidase is purified. In some further embodiments, the recombinant acid alpha-glucosidase exhibits at least one improved property selected from: i) enhanced catalytic activity; ii) increased expression; iii) increased stability at neutral pH levels; iv) increased stability at acidic pH levels; iv) enhanced activity in cell lysates; and vi) decreased immunogenicity; or a combination of any of i), ii), iii), iv), v), and/or vi), as compared to a reference sequence. In some further embodiments, the recombinant acid alpha glucosidase exhibits at least one improved property selected from: i) enhanced catalytic activity; ii) increased tolerance to p1-I 7; iii) increased tolerance to pH 4; iv) increased expression; v) increased uptake into cells; vi) increased enzymatic activity in cell lysates; vii) decreased immunogenicity, or a combination of any of i), ii), iii), iv), v), vi), and/or vii), as compared to a reference sequence. In some embodiments, the reference sequence is selected from SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. In some further embodiments, the recombinant acid alpha glucosidase is more stable at pH 7 than the acid alpha glucosidase of SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. In yet some other embodiments, the recombinant acid alpha glucosidase is more stable at pH 4 than the acid alpha glucosidase of SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. In some further embodiments, the recombinant acid alpha glucosidase exhibits increased expression than the acid alpha glucosidase of SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. In still some additional embodiments, the recombinant acid alpha glucosidase is more lysosomally stable than the acid alpha glucosidase of SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. In some further embodiments, the recombinant acid alpha glucosidase is more readily taken up by cells than the acid alpha glucosidase of SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. In some additional embodiments, the recombinant acid alpha glucosidase exhibits greater enzymatic activity in cell lysates than the acid alpha glucosidase of SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. In some additional embodiments, the recombinant acid alpha glucosidase exhibits reduced or decreased immunogenicity than the acid alpha glucosidase of SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. In some embodiments, the recombinant acid alpha glucosidase is purified. 
     In some further embodiments, the recombinant acid alpha-glucosidase comprises a polypeptide sequence comprising at least about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% sequence identity to at least one of the even-numbered sequences of SEQ ID NOS: 8-3378. In some further embodiments, the recombinant acid alpha-glucosidase comprises a polypeptide sequence comprising at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to at least one of the even-numbered sequences of SEQ ID NOS: 8-3378. In some embodiments the recombinant acid alpha glucosidase comprises a polypeptide sequence at least 90% identical to at least one of the even-numbered sequences of SEQ ID NOS: 8-3378. In some further embodiments, the recombinant acid alpha-glucosidase comprises a polypeptide sequence comprises at least one of the even-numbered sequences of SEQ ID NOS: 2-3378. In some further embodiments, the recombinant acid alpha-glucosidase consists of a polypeptide sequence comprising at least one of the even-numbered sequences of SEQ ID NOS: 8-3378. 
     The present invention also provides compositions comprising at least one recombinant acid alpha-glucosidase provided herein. In some embodiments, the compositions comprise one recombinant acid alpha-glucosidase provided herein. 
     The present invention also provides recombinant polynucleotide sequences encoding at least one recombinant acid alpha-glucosidase provided herein. In some embodiment, a recombinant polynucleotide sequence encodes one recombinant acid alpha-glucosidase. In some embodiments, the recombinant polynucleotide sequence is selected from DNA, RNA, and mRNA. In some embodiments, the polynucleotide sequence is codon-optimized. In some further embodiments, the recombinant polynucleotide sequence encodes a recombinant acid alpha-glucosidase comprising a polypeptide sequence comprising at least about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% sequence identity to at least one of the even-numbered sequences of SEQ ID NOS: 8-3378. In some further embodiments, the recombinant acid alpha-glucosidase encoded by the polynucleotide sequence comprises a polypeptide sequence comprising at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to at least one of the even-numbered sequences of SEQ ID NOS: 8-3378. 
     In some further embodiments, the recombinant polynucleotide sequence is at least about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% sequence identity to at least one of the odd-numbered sequences of SEQ ID NOS: 7-3377. In some further embodiments, the recombinant polynucleotide sequence is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, identical to at least one of the odd-numbered sequences of SEQ ID NOS: 7-3377. In some additional embodiments, the recombinant polynucleotide sequence comprises a sequence comprising at least 90% sequence identity to at least one of the odd-numbered sequences of SEQ ID NOS: 7-3377. In yet some further embodiments, the recombinant polynucleotide sequence comprises an odd-numbered sequence of SEQ ID NOS: 7-3377. 
     The present invention also provides expression vectors comprising the recombinant polynucleotide sequence encoding recombinant acid alpha-glucosidase. In some embodiments, the recombinant polynucleotide sequence is operably linked to a control sequence. In some further embodiments, the control sequence is a promoter. In some additional embodiments, the promoter is a heterologous promoter. The present invention also provides the expression vector referred to herein as pDH. In some embodiments, the pDH vector comprises at least one polynucleotide sequence encoding an acid alpha glucosidase. In some additional embodiments, the pDH vector comprises at least one polynucleotide sequence encoding an acid alpha glucosidase provided herein. In some further embodiments, the pDH vector comprises at least one polynucleotide sequence selected from the odd-numbered sequences of SEQ ID NOS: 1-3377. In some additional embodiments, the pDH vector comprises at least one polynucleotide sequence encoding an acid alpha glucosidase selected from the even-numbered sequences of SEQ ID NOS: 2-3378. In some embodiments, the pDH vector comprises SEQ ID NO: 3379, while in some other embodiments, the pDH vector comprises SEQ ID NO: 3380. In some additional embodiments, SEQ ID NO:1, which is included in SEQ ID NO: 3379 is replaced with another polynucleotide sequence. In some embodiments, the SEQ ID NO: 1 in SEQ ID NO: 3379 is replaced by at least one polynucleotide sequence selected from the odd-numbered sequences of SEQ ID NOS: 1-3377. in some additional embodiments, the pDH vector comprises the plasmid provided in the map at  FIG. 9 , while in some other embodiments, the pDH vector comprises the plasmid the map at  FIG. 10 . In some embodiments, the “stuffer sequence” (i.e., the bla sequence) in the plasmid shown in  FIG. 10  is replaced by a gene of interest. In some embodiments, the “sniffer gene” ATG start codon to the last codon of the gene is numbered from base pair 724 to 1581 (for a total of 858 base pairs). As used herein, the terms “stuffer gene” and “staffer sequence” refer to a sequence within a plasmid vector that is replaced by a gene of interest. As used herein, the term “gene of interest” refers to a gene that encodes a desired polypeptide (e.g., a “polypeptide of interest”). In some additional embodiments, the stuffer sequence is replaced by a gene of interest (i.e., a gene that is desired for expression, such that a polypeptide of interest, such as a variant acid alpha glucosidase is produced). 
     The present invention also provides host cells comprising at least one expression vector provided herein. In some embodiments, the expression vector provided in the host cells is pDH. In some embodiments, the host cell is selected from eukaryotes and prokaryotes. In some further embodiments, the host cell is a mammalian cell. 
     The present invention also provides methods of producing a recombinant acid alpha glucosidase variant, comprising culturing at least one host cell provided herein, under conditions that the acid alpha glucosidase encoded by the recombinant polynucleotide is produced. In some embodiments, the methods further comprise the step of recovering the acid alpha glucosidase. In yet some further embodiments, the methods further comprise the step of purifying the acid alpha glucosidase. The present invention also provides recombinant acid alpha glucosidase variants produced according to a method provided herein. 100301 The present invention also provides compositions comprising at least one recombinant acid alpha glucosidase provided herein. The present invention also provides for use of the compositions provided herein. In some embodiments, the present invention provides pharmaceutical compositions for the treatment of Pompe disease, comprising at least one composition provided herein. In some additional embodiments, the pharmaceutical composition further comprises at least one pharmaceutically acceptable carrier and/or excipient. In some further embodiments, the pharmaceutical composition is suitable for parenteral injection or infusion to a human. In yet some additional embodiments, the present invention provides pharmaceutical compositions comprising at least one recombinant polynucleotide provided herein. In yet some further embodiments, the present invention provides pharmaceutical compositions comprising at least one recombinant polypeptide provided herein. In yet some additional embodiments, the present invention provides compositions comprising at least one recombinant polynucleotide and at least one recombinant polypeptide provided herein. 
     The present invention also provides methods for treating and/or preventing the symptoms of Pompe disease in a subject, comprising providing a subject having Pompe disease and at least one pharmaceutical composition provided herein, and administering the pharmaceutical composition to the subject. In some embodiments, the symptoms of Pompe disease are ameliorated. In some additional embodiments, the subject is an infant or child. In yet some further embodiments, the subject is an adult or young adult. 
    
    
     
       DESCRIPTION OF THE DRAWINGS 
         FIG. 1  provides a graph showing the kinetic assay results for three GAA variants, as described in Example 9. 
         FIG. 2  provides a graph showing the glycogen hydrolysis to glucose activity of four GAA variants, as described in Example 9. 
         FIG. 3  provides a graph showing the 4-MuGlu hydrolysis levels of four GAA variants, as described in Example 9. 
         FIG. 4  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 5 hours incubation at 37° C. with cultured Pompe patient fibroblasts, followed by 24 hr incubation. 
         FIG. 5  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 24 hours incubation at 37° C. with cultured Pompe patient fibroblasts. 
         FIG. 6  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 5 hours incubation at 37° C. with cultured C2C12 GAA−/− myoblasts, followed by 24 hr incubation. 
         FIG. 7  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 24 hours incubation at 37° C. with cultured C2C12 GAA−/− myoblasts. 
         FIG. 8  provides a graph showing the cellular uptake of different purified GAA variants, expressed as relative activity, after 1-7 days incubation at 37° C. with cultured Pompe patient fibroblasts. 
         FIG. 9  provides a plasmid map of the pDH vector containing WT GAA. 
         FIG. 10  provides a plasmid map showing the pDH vector comprising the stuffer sequence bla (i.e., beta-lactamase). 
         FIG. 11  provides a graph showing the stability at neutral pH and 37° C., expressed as normalized residual RFU activity, of eight GAA variants. 
         FIG. 12  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 24 hours incubation at 37° C. with cultured Pompe patient fibroblasts. 
         FIG. 13  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 72 hours incubation at 37° C. with cultured Pompe patient fibroblasts. 
         FIG. 14  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 24 hours incubation at 37° C. with cultured C2C12 GAA−/− myoblasts. 
         FIG. 15  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 72 hours incubation at 37° C. with cultured C2C12 GAA−/− myoblasts. 
         FIG. 16  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 4 hours incubation at 37° C. with cultured Pompe patient fibroblasts, followed by cell washing and an additional 20 hr incubation. 
         FIG. 17  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 24 hours incubation at 37° C. with cultured Pompe patient fibroblasts. 
         FIG. 18  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 72 hours incubation at 37° C. with cultured Pompe patient fibroblasts. 
         FIG. 19  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 4 hours incubation at 37° C. with cultured C2C12 GAA−/− myoblasts, followed by cell washing and an additional 20 hr incubation. 
         FIG. 20  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 24 hours incubation at 37° C. with cultured C2C12 GAA−/− myoblasts. 
         FIG. 21  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 72 hours incubation at 37° C. with cultured C2C12 GAA−/− myoblasts. 
         FIG. 22  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 96 hours incubation at 37° C. with cultured Pompe patient fibroblasts. 
         FIG. 23  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 96 hours incubation at 37° C. with cultured C2C12 GAA−/− myoblasts. 
         FIG. 24  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 48 hours incubation at 37° C. with cultured Pompe patient fibroblasts. 
         FIG. 25  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 48 hours incubation at 37° C. with cultured C2C12 GAA−/− myoblasts. 
         FIG. 26  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 1 hour incubation at 37° C. with cultured Pompe patient fibroblasts, followed by cell washing and an additional 71 hr incubation. 
         FIG. 27  provides a graph showing the cellular uptake of different purified GAA variants, expressed as RFU activity, after 1 hour incubation at 37° C. with cultured C2C12 GAA−/− myoblasts, followed by cell washing and an additional 71 hr incubation. 
     
    
    
     DESCRIPTION OF THE INVENTION 
     The present invention provides engineered acid alpha-glucosidase (GAA) polypeptides and compositions thereof. In some embodiments, the engineered GAA polypeptides have been optimized to provide enhanced catalytic activity and enhanced acid stability, while reducing sensitivity to proteolysis. The invention also provides methods for utilization of the compositions comprising the engineered GAA polypeptides for therapeutic and other purposes. 
     Abbreviations and Definitions: 
     Unless defined otherwise, all technical and scientific terms used herein generally have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Generally, the nomenclature used herein and the laboratory procedures of cell culture, molecular genetics, microbiology, organic chemistry, analytical chemistry and nucleic acid chemistry described below are those well-known and commonly employed in the art. Such techniques are well-known and described in numerous texts and reference works well known to those of skill in the art. Standard techniques, or modifications thereof, are used for chemical syntheses and chemical analyses. All patents, patent applications, articles and publications mentioned herein, both supra and infra, are hereby expressly incorporated herein by reference. 
     Although any suitable methods and materials similar or equivalent to those described herein find use in the practice of the present invention, some methods and materials are described herein. It is to be understood that this invention is not limited to the particular methodology, protocols, and reagents described, as these may vary, depending upon the context they are used by those of skill in the art. Accordingly, the terms defined immediately below are more fully described by reference to the application as a whole. All patents, patent applications, articles and publications mentioned herein, both supra and infra, are hereby expressly incorporated herein by reference. 
     Also, as used herein, the singular “a”, “an,” and “the” include the plural references, unless the context clearly indicates otherwise. 
     Numeric ranges are inclusive of the numbers defining the range. Thus, every numerical range disclosed herein is intended to encompass every narrower numerical range that falls within such broader numerical range, as if such narrower numerical ranges were all expressly written herein. It is also intended that every maximum (or minimum) numerical limitation disclosed herein includes every lower (or higher) numerical limitation, as if such lower (or higher) numerical limitations were expressly written herein. 
     The term “about” means an acceptable error for a particular value. In some instances “about” means within 0.05%, 0.5%, 1.0%, or 2.0%, of a given value range. In some instances, “about” means within 1, 2, 3, or 4 standard deviations of a given value. In some instances, “about” encompasses values that are within 2.5%, 3%, 3.5%, 4%, 4.5%, 5%, 5.5%, 6%, 6.5%, 7%, 7.5%, 8%, 8.5%, 9%, 9.5%, or 10% of a given value. 
     Furthermore, the headings provided herein are not limitations of the various aspects or embodiments of the invention which can be had by reference to the application as a whole. Accordingly, the terms defined immediately below are more fully defined by reference to the application as a whole. Nonetheless, in order to facilitate understanding of the invention, a number of terms are defined below. 
     Unless otherwise indicated, nucleic acids are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively. 
     As used herein, the term “comprising” and its cognates are used in their inclusive sense (i.e., equivalent to the term “including” and its corresponding cognates). 
     “EC” number refers to the Enzyme Nomenclature of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). The IUBMB biochemical classification is a numerical classification system for enzymes based on the chemical reactions they catalyze. 
     “ATCC” refers to the American Type CultureCollection whose biorepository collection includes genes and strains. 
     “NCBI” refers to National Center for Biological Information and the sequence databases provided therein. 
     As used herein, the terms “acid alpha-glucosidase,” “acid α-glucosidase,” “acid alpha-glucosidase polypeptide” “lysosomal alpha-glucosidase,” and “GAA” refer to enzymes within a family (EC 3.2.1.20) of enzymes that break down glycogen present in lysosomes. The enzyme is also sometimes referred to as “alpha-1,4-glucosidase,” α-1,4-glucosidase,” “acid maltase,” “glucoinvertase,” “glucosidosucrase,” “lysosomal alpha-glucosidase,” “lysosomal a-glucosidase,” “maltase,” or “maltase-glucoamylase.” One reaction catalyzed by the enzyme is the hydrolysis of terminal, non-reducing (1 to 4) linked alpha-D-glucose residues with release of alpha-D-glucose. 
     As used herein, “Pompe disease” refers to a glycogen storage disease type II, which is an autosomal recessive genetic disorder that results in a metabolic disorder characterized by lysosomal accumulation of glycogen in skeletal muscle and other tissues. It is characterized based on age of onset, organ involvement, severity, and rate of progression. The more severe form is infantile-onset Pompe disease (IOPD), which occurs in infants. The other form, referred to as “late-onset Pompe disease” (LOPD), occurs in individuals with an onset of disease before 12 months of age, but without the cardiomyopathy associated with IOPD, and all individuals with an onset of disease after 12 months of age. Synonyms for Pompe disease include “acid alpha-glucosidase deficiency,” acid maltase deficiency,” “GAA deficiency,” “glycogen storage disease type II,” “GSD II,” “GSD2,” and “glycogenosis type II.” 
     “Protein,” “polypeptide,” and “peptide” are used interchangeably herein to denote a polymer of at least two amino acids covalently linked by an amide bond, regardless of length or post-translational modification (e.g., glycosylation or phosphorylation). 
     “Amino acids” are referred to herein by either their commonly known three-letter symbols or by the one-letter symbols recommended by IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single letter codes. 
     The terms “engineered,” “recombinant,” “non-naturally occurring,” and “variant,” when used with reference to a cell, a polynucleotide or a polypeptide refers to a material or a material corresponding to the natural or native form of the material that has been modified in a manner that would not otherwise exist in nature or is identical thereto but produced or derived from synthetic materials and/or by manipulation using recombinant techniques. 
     As used herein, “wild-type” and “naturally-occurring” refer to the form found in nature. For example, a wild-type polypeptide or polynucleotide sequence is a sequence present in an organism that can he isolated from a source in nature and which has not been intentionally modified by human manipulation. 
     “Coding sequence” refers to that part of a nucleic acid (e.g., a gene) that encodes an amino acid sequence of a protein. 
     The term “percent (%) sequence identity” is used herein to refer to comparisons among polynucleotides and polypeptides, and are determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence for optimal alignment of the two sequences. The percentage may be calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Alternatively, the percentage may be calculated by determining the number of positions at which either the identical nucleic acid base or amino acid residue occurs in both sequences or a nucleic acid base or amino acid residue is aligned with a gap to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Those of skill in the art appreciate that there are many established algorithms available to align two sequences. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith and Waterman (Smith and Waterman, Adv. Appl. Math., 2:482 [1981]), by the homology alignment algorithm of Needleman and Wunsch (Needleman and Wunsch, J. Mol. Biol., 48:443 [1970), by the search for similarity method of Pearson and Lipman (Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85:2444 [1988]), by computerized implementations of these algorithms (e.g., GAP, BESTFIT, FASTA, and TFASTA in the GCG Wisconsin Software Package), or by visual inspection, as known in the art. Examples of algorithms that are suitable for determining percent sequence identity and sequence similarity include, but are not limited to the BLAST and BLAST 2.0 algorithms, which are described by Altschul et al. (See, Altschul et al., J. Mol. Biol., 215: 403-410 [1990]; and Altschul et al., 1977, Nucleic Acids Res., 3389-3402 [1977], respectively). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information website. This algorithm involves first identifying high scoring sequence pairs (HSPS) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as, the neighborhood word score threshold (See, Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always &gt;0) and N (penalty score for mismatching residues; always &lt;0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (See, Henikoff and Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 [1989]). Exemplary determination of sequence alignment and % sequence identity can employ the BESTFIT or GAP programs in the GCG Wisconsin Software package (Accelrys, Madison WI), using default parameters provided. 
     As used herein, the term “reference sequence” refers to a defined sequence used as a basis for a sequence comparison. A reference sequence may be a subset of a larger sequence, for example, a segment of a full-length gene or polypeptide sequence. Generally, a reference sequence is at least 20 nucleotide or amino acid residues in length, at least 25 residues in length, at least 50 residues in length, at least 100 residues in length or the full length of the nucleic acid or polypeptide. Since two polynucleotides or polypeptides may each (1) comprise a sequence (i.e., a portion of the complete sequence) that is similar between the two sequences, and (2) may further comprise a sequence that is divergent between the two sequences, sequence comparisons between two (or more) polynucleotides or polypeptide are typically performed by comparing sequences of the two polynucleotides or polypeptides over a “comparison window” to identify and compare local regions of sequence similarity. In some embodiments, a “reference sequence” can be based on a primary amino acid sequence, where the reference sequence is a sequence that can have one or more changes in the primary sequence. “Comparison window” refers to a conceptual segment of at least about 20 contiguous nucleotide positions or amino acids residues wherein a sequence may be compared to a reference sequence of at least 20 contiguous nucleotides or amino acids and wherein the portion of the sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The comparison window can be longer than 20 contiguous residues, and includes, optionally 30, 40, 50, 100, or longer windows. 
     “Corresponding to”, “reference to” or “relative to” when used in the context of the numbering of a given amino acid or polynucleotide sequence refers to the numbering of the residues of a specified reference sequence when the given amino acid or polynucleotide sequence is compared to the reference sequence. In other words, the residue number or residue position of a given polymer is designated with respect to the reference sequence rather than by the actual numerical position of the residue within the given amino acid or polynucleotide sequence. For example, a given amino acid sequence, such as that of an engineered GAA, can he aligned to a reference sequence by introducing gaps to optimize residue matches between the two sequences. In these cases, although the gaps are present, the numbering of the residue in the given amino acid or polynucleotide sequence is made with respect to the reference sequence to which it has been aligned. 
     “Amino acid difference” or “residue difference” refers to a difference in the amino acid residue at a position of a polypeptide sequence relative to the amino acid residue at a corresponding position in a reference sequence. The positions of amino acid differences generally are referred to herein as “Xn,” where n refers to the corresponding position in the reference sequence upon which the residue difference is based. For example, a “residue difference at position X27 as compared to SEQ ID NO: 2” refers to a difference of the amino acid residue at the polypeptide position corresponding to position 27 of SEQ ID NC): 2. Thus, if the reference polypeptide of SEQ ID NO: 2 has a phenylalanine at position 2, then a “residue difference at position X27 as compared to SEQ ID NO: 2” an amino acid substitution of any residue other than phenylalanine at the position of the polypeptide corresponding to position 27 of SEQ ID NO: 2. In most instances herein, the specific amino acid residue difference at a position is indicated as “XnY” where “Xn” specified the corresponding position as described above, and “Y” is the single letter identifier of the amino acid found in the engineered polypeptide (i.e., the different residue than in the reference polypeptide). In some instances (e.g., as shown in in Tables 3-1, 3-2, 4-1, 6-1, 10-1, 10-2, 12-1, 13-1, 13-2, 14-1, 14-2, 15-1, 16-1, 17-1, 17-2, 17-3, 17-4, 17-5, 17-6, 17-7, 17-8, and/or 17-9), the present disclosure also provides specific amino acid differences denoted by the conventional notation “AnB”, where A is the single letter identifier of the residue in the reference sequence, “n” is the number of the residue position in the reference sequence, and B is the single letter identifier of the residue substitution in the sequence of the engineered polypeptide. In some instances, a polypeptide of the present disclosure can include one or more amino acid residue differences relative to a reference sequence, which is indicated by a list of the specified positions where residue differences are present relative to the reference sequence. In some embodiments, where more than one amino acid can be used in a specific residue position of a polypeptide, the various amino acid residues that can be used are separated by a “/” (e.g., X27P/X27R or X27P/R). In some embodiments, the enzyme variants comprise more than one substitution. These substitutions are separated by a slash for ease in reading (e.g., F27P/C944W). In some cases, the “X” does not precede the position number in the present application. The present application includes engineered polypeptide sequences comprising one or more amino acid differences that include either/or both conservative and non-conservative amino acid substitutions. 
     “Conservative amino acid substitution” refers to a substitution of a residue with a different residue having a similar side chain, and thus typically involves substitution of the amino acid in the polypeptide with amino acids within the same or similar defined class of amino acids. By way of example and not limitation, an amino acid with an aliphatic side chain may be substituted with another aliphatic amino acid (e.g., alanine, valine, leucine, and isoleucine); an amino acid with hydroxyl side chain is substituted with another amino acid with a hydroxyl side chain (e.g., serine and threonine); an amino acids having aromatic side chains is substituted with another amino acid having an aromatic side chain (e.g., phenylalanine, tyrosine, tryptophan, and histidine); an amino acid with a basic side chain is substituted with another amino acid with a basis side chain (e.g., lysine and arginine); an amino acid with an acidic side chain is substituted with another amino acid with an acidic side chain (e.g., aspartic acid or glutamic acid); and/or a hydrophobic or hydrophilic amino acid is replaced with another hydrophobic or hydrophilic amino acid, respectively. 
     “Non-conservative substitution” refers to substitution of an amino acid in the polypeptide with an amino acid with significantly differing side chain properties. Non-conservative substitutions may use amino acids between, rather than within, the defined groups and affects (a) the structure of the peptide backbone in the area of the substitution (e.g., proline for glycine) (b) the charge or hydrophobicity, or (c) the hulk of the side chain. By way of example and not limitation, an exemplary non-conservative substitution can be an acidic amino acid substituted with a basic or aliphatic amino acid; an aromatic amino acid substituted with a small amino acid; and a hydrophilic amino acid substituted with a hydrophobic amino acid. 
     “Deletion” refers to modification to the polypeptide by removal of one or more amino acids from the reference polypeptide. Deletions can comprise removal of 1 or more amino acids, 2 or more amino acids, 5 or more amino acids, 10 or more amino acids, 15 or more amino acids, or 20 or more amino acids, up to 10% of the total number of amino acids, or up to 20% of the total number of amino acids making up the reference enzyme while retaining enzymatic activity and/or retaining the improved properties of an engineered enzyme. Deletions can be directed to the internal portions and/or terminal portions of the polypeptide. In various embodiments, the deletion can comprise a continuous segment or can be discontinuous. 
     “insertion” refers to modification to the polypeptide by addition of one or more amino acids from the reference polypeptide. Insertions can be in the internal portions of the polypeptide, or to the carboxy or amino terminus. Insertions as used herein include fusion proteins as is known in the art. The insertion can be a contiguous segment of amino acids or separated by one or more of the amino acids in the naturally occurring polypeptide. 
     A “functional fragment” or a “biologically active fragment” used interchangeably herein refers to a polypeptide that has an amino-terminal and/or carboxy-terminal deletion(s) and/or internal deletions, but where the remaining amino acid sequence is identical to the corresponding positions in the sequence to which it is being compared (e.g., a full-length engineered GAA of the present invention) and that retains substantially all of the activity of the full-length polypeptide. 
     “Isolated polypeptide” refers to a polypeptide which is substantially separated from other contaminants that naturally accompany it (e.g., protein, lipids, and polynucleotides). The term embraces polypeptides which have been removed or purified from their naturally-occurring environment or expression system (e.g., host cell or in vitro synthesis). The recombinant GAA polypeptides may be present within a cell, present in the cellular medium, or prepared in various forms, such as lysates or isolated preparations. As such, in some embodiments, the recombinant GAA polypeptides can be an isolated polypeptide. 
     “Substantially pure polypeptide” refers to a composition in which the polypeptide species is the predominant species present (i.e., on a molar or weight basis it is more abundant than any other individual macromolecular species in the composition), and is generally a substantially purified composition when the object species comprises at least about 50 percent of the macromolecular species present by mole or % weight. Generally, a substantially pure GAA composition comprises about 60% or more, about 70% or more, about 80% or more, about 90% or more, about 95% or more, and about 98% or more of all macromolecular species by mole or % weight present in the composition. In some embodiments, the object species is purified to essential homogeneity (i.e., contaminant species cannot be detected in the composition by conventional detection methods) wherein the composition consists essentially of a single macromolecular species. Solvent species, small molecules (&lt;500 Daltons), and elemental ion species are not considered macromolecular species. In some embodiments, the isolated recombinant GAA polypeptides are substantially pure polypeptide compositions. 
     “Improved enzyme property” refers to an engineered GAA polypeptide that exhibits an improvement in any enzyme property as compared to a reference GAA polypeptide and/or as a wild-type GAA polypeptide or another engineered GAA polypeptide. Improved properties include but are not limited to such properties as increased protein expression, increased thermoactivity, increased thermostability, increased pH activity, increased stability, increased enzymatic activity, increased substrate specificity or affinity, increased specific activity, increased resistance to substrate or end-product inhibition, increased chemical stability, improved chemoselectivity, improved solvent stability, increased tolerance to acidic, neutral, or basic pH, increased tolerance to proteolytic activity (i.e., reduced sensitivity to proteolysis), reduced aggregation, increased solubility, reduced immunogenicity, improved post-translational modification (e.g., glycosylation), altered temperature profile, increased lysosomal stability, etc. 
     “Increased enzymatic activity” or “enhanced catalytic activity” refers to an improved property of the engineered GAA polypeptides, which can be represented by an increase in specific activity (e.g., product produced/time/weight protein) or an increase in percent conversion of the substrate to the product (e.g., percent conversion of starting amount of substrate to product in a specified time period using a specified amount of GAA) as compared to the reference GAA enzyme. Exemplary methods to determine enzyme activity are provided in the Examples. Any property relating to enzyme activity may be affected, including the classical enzyme properties of K m , V max  or k cat , changes of which can lead to increased enzymatic activity. Improvements in enzyme activity can be from about 1.1 fold the enzymatic activity of the corresponding wild-type enzyme, to as much as 2-fold, 5-fold, 10-fold, 20-fold, 25-fold, 50-fold, 75-fold, 100-fold, 150-fold, 200-fold or more enzymatic activity than the naturally occurring GAA or another engineered GAA from which the GAA polypeptides were derived. 
     In some embodiments, the engineered GAA polypeptides have a of at least 0.1/sec, at least 0.5/sec, at least 1.0/sec, at least 5.0; sec, at least 10.0/sec and in some preferred embodiments greater than 10.01sec. In some embodiments, the K m  is in the range of about 1 μM to about 5 mM; in the range of about 5 μM to about 10 mM; in the range of about 30 μM to about 30 mM; or in the range of about 50 μM to about 50 mM. In some specific embodiments, the engineered GAA enzyme exhibits improved enzymatic activity after exposure to certain conditions in the range of 1.5 to 10 fold, 1.5 to 25 fold, 1.5 to 50 fold, 1.5 to 100 fold or greater than that of a reference GAA enzyme (e.g., a wild-type GAA or any other reference GAA, such as SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104). 
     GAA activity can be measured by any suitable method known in the art (e.g., standard assays, such as monitoring changes in spectrophotometric properties of reactants or products). In some embodiments, the amount of products produced can be measured by High-Performance Liquid Chromatography (HPLC) separation combined with UV absorbance or fluorescent detection. In some embodiments, the amount of product produced can be measured by monitoring fluorescence (Ex. 355 nm, Em. 460 nm) after hydrolysis of a 4-methylumbelliferyl-alpha-D-glucopyranoside (4-MUG1u) molecule. Comparisons of enzyme activities are made using a defined preparation of enzyme, a defined assay under a set condition, and one or more defined substrates, as further described in detail herein. Generally, when lysates are compared, the numbers of cells and the amount of protein assayed are determined as well as use of identical expression systems and identical host cells to minimize variations in amount of enzyme produced by the host cells and present in the lysates. 
     The term “improved tolerance to acidic pH” means that a recombinant GAA according to the invention will have increased stability (higher retained activity at about p1-I 4.8, after exposure to an acidic pH for a specified period of time (e.g., 1 hour, up to 24 hours)) as compared to a reference GAA or another enzyme. 
     The term “improved tolerance to neutral pH” means that a recombinant GAA according to the invention will have increased stability (higher retained activity at about pH 7, after exposure to a neutral pH for a specified period of time (e.g., 1 hour, up to 24 hours)) as compared to a reference GAA or another enzyme. 
     The term “improved cellular uptake” means that a recombinant GAA provided herein exhibits increased endocytosis into cells, as compared to a reference GAA (including wild-type GAA) or another enzyme. In some embodiments, the cells are cultured Pompe patient cells (higher retained intracellular activity after incubation with cultured cells over a specified period of time, as compared to a reference GAA or another enzyme). In some additional embodiments, the recombinant GAA provided herein exhibits greater retained intracellular activity with cultured cells over a specific period of time as compared to a reference GAA (including wild-type GAA) or another enzyme. In some additional embodiments, the time period is about 4 hours, while in some other embodiments, the time period is less than 4 hours (e.g., 1, 2, or 3 hours), and in some alternative embodiments, the time period is more than 4 hours (e.g., 5, 6, 7, 8, or more hours). 
     The terms “reduced immunogenicity” and “decreased immunogenicity” mean that a recombinant GAA provided herein induces a reduced immune response as compared to a wild-type or another reference GAA. 
     “Physiological pH” as used herein means the pH range generally found in a subject&#39;s (e.g., human) blood. 
     The term “basic pH” (e.g., used with reference to improved stability to basic pH conditions or increased tolerance to basic pH) means a pH range of about 7 to 11. 
     The term “acidic pH” (e.g., used with reference to improved stability to acidic pH conditions or increased tolerance to acidic pH) means a pH range of about 1.5 to 4.5. 
     “Conversion” refers to the enzymatic conversion (or biotransformation) of a substrate(s) to the corresponding product(s). “Percent conversion” refers to the percent of the substrate that is converted to the product within a period of time under specified conditions. Thus, the “enzymatic activity” or “activity” of a GAA polypeptide can be expressed as “percent conversion” of the substrate to the product in a specific period of time. 
     “Hybridization stringency” relates to hybridization conditions, such as washing conditions, in the hybridization of nucleic acids. Generally, hybridization reactions are performed under conditions of lower stringency, followed by washes of varying but higher stringency. The term “moderately stringent hybridization” refers to conditions that permit target-DNA to bind a complementary nucleic acid that has about 60% identity, preferably about 75% identity, about 85% identity to the target DNA, with greater than about 90% identity to target-polynucleotide. Exemplary moderately stringent conditions are conditions equivalent to hybridization in 50% formamide, 5× Denhart&#39;s solution, 5×SSPE, 0.2% SDS at 42° C., followed by washing in 0.2×SSPE, 0.2% SDS, at 42° C. “High stringency hybridization” refers generally to conditions that are about 10° C. or less from the thermal melting temperature T m  as determined under the solution condition for a defined polynucleotide sequence. In some embodiments, a high stringency condition refers to conditions that permit hybridization of only those nucleic acid sequences that form stable hybrids in 0.018M NaCl at 65° C. (i.e., if a hybrid is not stable in 0.018M NaCl at 65° C., it will not be stable under high stringency conditions, as contemplated herein). High stringency conditions can be provided, for example, by hybridization in conditions equivalent to 50% formamide, 5×Denhart&#39;s solution, 5xSSPE, 0.2% SDS at 42° C., followed by washing in 0.1×SSPE, and 0.1% SDS at 65° C. Another high stringency condition is hybridizing in conditions equivalent to hybridizing in 5× SSC containing 0.1% (w:v) SDS at 65° C. and washing in 0.1× SSC containing 0.1% SDS at 65° C. Other high stringency hybridization conditions, as well as moderately stringent conditions, are described in the references cited above. 
     “Codon optimized” refers to changes in the codons of the polynucleotide encoding a protein to those preferentially used in a particular organism such that the encoded protein is more efficiently expressed in the organism of interest. Although the genetic code is degenerate in that most amino acids are represented by several codons, called “synonyms” or “synonymous” codons, it is well known that codon usage by particular organisms is nonrandom and biased towards particular codon triplets. This codon usage bias may be higher in reference to a given gene, genes of common function or ancestral origin, highly expressed proteins versus low copy number proteins, and the aggregate protein coding regions of an organism&#39;s genome. In some embodiments, the polynucleotides encoding the GAA enzymes may be codon optimized for optimal production from the host organism selected for expression. 
     “Control sequence” refers herein to include all components, which are necessary or advantageous for the expression of a polynucleotide and/or polypeptide of the present application. Each control sequence may be native or foreign to the nucleic acid sequence encoding the polypeptide. Such control sequences include, but are not limited to, a leader, polyadenylation sequence, propeptide sequence, promoter sequence, signal peptide sequence, initiation sequence and transcription terminator. At a minimum, the control sequences include a promoter, and transcriptional and translational stop signals. The control sequences may be provided with linkers for the purpose of introducing specific restriction sites facilitating ligation of the control sequences with the coding region of the nucleic acid sequence encoding a polypeptide. 
     “Operably linked” is defined herein as a configuration in which a control sequence is appropriately placed (i.e., in a functional relationship) at a position relative to a polynucleotide of interest such that the control sequence directs or regulates the expression of the polynucleotide and/or polypeptide of interest. 
     “Promoter sequence” refers to a nucleic acid sequence that is recognized by a host cell for expression of a polynucleotide of interest, such as a coding sequence. The promoter sequence contains transcriptional control sequences, which mediate the expression of a polynucleotide of interest. The promoter may be any nucleic acid sequence which shows transcriptional activity in the host cell of choice including mutant, truncated, and hybrid promoters, and may be obtained from genes encoding extracellular or intracellular polypeptides either homologous or heterologous to the host cell. 
     “Suitable reaction conditions” refers to those conditions in the enzymatic conversion reaction solution (e.g., ranges of enzyme loading, substrate loading, temperature, pH, buffers, co-solvents, etc.) under which a GAA polypeptide of the present application is capable of converting a substrate to the desired product compound, Exemplary “suitable reaction conditions” are provided in the present application and illustrated by the Examples. “Loading”, such as in “compound loading” or “enzyme loading” refers to the concentration or amount of a component in a reaction mixture at the start of the reaction. “Substrate” in the context of an enzymatic conversion reaction process refers to the compound or molecule acted on by the GAA polypeptide. “Product” in the context of an enzymatic conversion process refers to the compound or molecule resulting from the action of the GAA polypeptide on a substrate. 
     As used herein the term “culturing” refers to the growing of a population of microbial cells under any suitable conditions (e.g., using a liquid, gel or solid medium). 
     Recombinant polypeptides can be produced using any suitable methods known the art. Genes encoding the wild-type polypeptide of interest can be cloned in vectors, such as plasmids, and expressed in desired hosts, such as E. coli, S. cerevisiae, etc. Variants of recombinant polypeptides can be generated by various methods known in the art. Indeed, there is a wide variety of different mutagenesis techniques well known to those skilled in the art. In addition, mutagenesis kits are also available from many commercial molecular biology suppliers. Methods are available to make specific substitutions at defined amino acids (site-directed), specific or random mutations in a localized region of the gene (regio-specific), or random mutagenesis over the entire gene (e.g., saturation mutagenesis). Numerous suitable methods are known to those in the art to generate enzyme variants, including but not limited to site-directed mutagenesis of single-stranded DNA or double-stranded DNA using PCR, cassette mutagenesis, gene synthesis, error-prone PCR, shuffling, and chemical saturation mutagenesis, or any other suitable method known in the art. Non-limiting examples of methods used for DNA and protein engineering are provided in the following patents: US Pat. Nos. 6,117,679; 6,420,175; 6,376,246; 6,586,182; 7,747,391; 7,747,393; 7,783,428; and 8,383,346. After the variants are produced, they can be screened for any desired property (e.g., high or increased activity, or low or reduced activity, increased thermal activity, increased thermal stability, and/or acidic pH stability, etc.). In some embodiments, “recombinant GAA polypeptides” (also referred to herein as “engineered GAA polypeptides,” “variant GAA enzymes,” and “GAA variants”) find use. 
     As used herein, a “vector” is a DNA construct for introducing a DNA sequence into a cell. In some embodiments, the vector is an expression vector that is operably linked to a suitable control sequence capable of effecting the expression in a suitable host of the polypeptide encoded in the DNA sequence. In some embodiments, an “expression vector” has a promoter sequence operably linked to the DNA sequence (e.g., transgene) to drive expression in a host cell, and in some embodiments, also comprises a transcription terminator sequence. In some preferred embodiments, the pDH vector provided herein finds use. 
     As used herein, the term “gene therapy vector” refers to vehicles or carriers suitable for delivery of polynucleotide sequences to cells. In some embodiments, the vectors encapsulate genes (e.g., therapeutic genes) or polynucleotide sequences for delivery to cells or tissues, including but not limited to adenovirus (AV), adeno-associated virus (AAV), lentivirus (LV), and non-viral vectors, such as liposomes. It is not intended that the present invention be limited to any specific gene therapy vector, as any vehicle suitable for a given setting finds use. The gene therapy vector may be designed to deliver genes to a specific species or host, or may find more general applicability. 
     As used herein, the term “expression” includes any step involved in the production of the polypeptide including, but not limited to, transcription, post-transcriptional modification, translation, and post-translational modification. In some embodiments, the term also encompasses secretion of the polypeptide from a cell. 
     As used herein, the term “produces” refers to the production of proteins and/or other compounds by cells. It is intended that the term encompass any step involved in the production of polypeptides including, but not limited to, transcription, post-transcriptional modification, translation, and post-translational modification. In some embodiments, the term also encompasses secretion of the polypeptide from a cell. 
     As used herein, an amino acid or nucleotide sequence (e.g., a promoter sequence, signal peptide, terminator sequence, etc.) is “heterologous” to another sequence with which it is operably linked if the two sequences are not associated in nature. 
     As used herein, the terms “host cell” and “host strain” refer to suitable hosts for expression vectors comprising DNA provided herein (e.g., the polynucleotides encoding the GAA variants). In some embodiments, the host cells are prokaryotic or eukaryotic cells that have been transformed or transfected with vectors constructed using recombinant DNA techniques as known in the art. 
     The term “analogue” means a polypeptide having more than 70% sequence identity but less than 100% sequence identity (e.g., more than 75%, 78%, 80%, 83%, 85%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity) with a reference polypeptide. In some embodiments, the term analogue refers to polypeptides that contain one or more non-naturally occurring amino acid residues including, but not limited, to homoarginine, ornithine and norvaline, as well as naturally occurring amino acids. In some embodiments, analogues also include one or more D-amino acid residues and non-peptide linkages between two or more amino acid residues. 
     The term “therapeutic” refers to a compound administered to a subject who shows signs or symptoms of pathology having beneficial or desirable medical effects. 
     The term “pharmaceutical composition” refers to a composition suitable for pharmaceutical use in a mammalian subject (e.g., human) comprising a pharmaceutically effective amount of an engineered GAA polypeptide encompassed by the invention and an acceptable carrier. 
     The term “gene therapy” refers to the delivery of a gene, polydeoxyribonucleotide, or polynucleotide sequence(s) with a gene therapy vector to cells or tissues for the modification of those cells or tissues for the treatment of prevention of a disease. Gene therapy may include replacing a mutated gene that causes disease with a healthy copy of the gene, or inactivating, or “knocking out,” a mutated gene that is functioning improperly. In some embodiments, gene therapy is used in the treatment of disease in patients. 
     The term “mRNA therapy” refers to the delivery of an mRNA polyribonucleotide sequence to cells or tissues for the modification of those cells or tissues for the treatment or prevention of a disease. In some embodiments, the mRNA polynucleotide sequences for delivery to cells or tissue, are formulated, for instance, but not limited to, in liposomes. In some embodiments, mRNA therapy is used in the treatment of disease in patients. 
     The term “cell therapy” refers to the delivery of living cells that have been modified exogenously to patients to provide a missing gene for the treatment or prevention of a disease. The modified cells are then reintroduced into the body. 
     The term “effective amount” means an amount sufficient to produce the desired result. One of general skill in the art may determine what the effective amount by using routine experimentation. 
     The terms “isolated” and “purified” are used to refer to a molecule (e.g., an isolated nucleic acid, polypeptide, etc.) or other component that is removed from at least one other component with which it is naturally associated. The term “purified” does not require absolute purity, rather it is intended as a relative definition. 
     The term “subject” encompasses mammals such as humans, non-human primates, livestock, companion animals, and laboratory animals (e.g., rodents and lagomorphs). It is intended that the term encompass females as well as males. 
     As used herein, the term “patient” means any subject that is being assessed for, treated for, or is experiencing disease. 
     The term “infant” refers to a child in the period of the first month after birth to approximately one (1) year of age. As used herein, the term “newborn” refers to child in the period from birth to the 28 th  day of life. The term “premature infant” refers to an infant born after the twentieth completed week of gestation, yet before full term, generally weighing ˜500 to ˜2499 grams at birth. A “very low birth weight infant” is an infant weighing less than 1500 g at birth. 
     As used herein, the term “child” refers to a person who has not attained the legal age for consent to treatment or research procedures. In some embodiments, the term refers to a person between the time of birth and adolescence. 
     As used herein, the term “adult” refers to a person who has attained legal age for the relevant jurisdiction (e.g., 18 years of age in the United States). In some embodiments, the term refers to any fully grown, mature organism. In some embodiments, the term “young adult” refers to a person less than 18 years of age, but who has reached sexual maturity. 
     As used herein, “composition” and “formulation” encompass products comprising at least one engineered GAA of the present invention, intended for any suitable use (e.g., pharmaceutical compositions, dietary/nutritional supplements, feed, etc.). 
     The terms “administration” and “administering” a composition mean providing a composition of the present invention to a subject (e.g., to a person suffering from the effects of Pompe disease). 
     The term “carrier” when used in reference to a pharmaceutical composition means any of the standard pharmaceutical carrier, buffers, and excipients, such as stabilizers, preservatives, and adjuvants. 
     The term “pharmaceutically acceptable” means a material that can be administered to a subject without causing any undesirable biological effects or interacting in a deleterious manner with any of the components in which it is contained and that possesses the desired biological activity. 
     As used herein, the term “excipient” refers to any pharmaceutically acceptable additive, carrier, diluent, adjuvant, or other ingredient, other than the active pharmaceutical ingredient (API; e.g., the engineered GAA polypeptides of the present invention). Excipients are typically included for formulation and/or administration purposes. 
     The term “therapeutically effective amount” when used in reference to symptoms of disease/condition refers to the amount and/or concentration of a compound (e.g., engineered GAA polypeptides) that ameliorates, attenuates, or eliminates one or more symptom of a disease/condition or prevents or delays the onset of symptom(s). 
     The term “therapeutically effective amount” when used in reference to a disease/condition refers to the amount and/or concentration of a composition (e.g., engineered GAA polypeptides) that ameliorates, attenuates, or eliminates the disease/condition. In some embodiments, the term is use in reference to the amount of a composition that elicits the biological (e.g., medical) response by a tissue, system, or animal subject that is sought by the researcher, physician, veterinarian, or other clinician. 
     It is intended that the terms “treating,” “treat” and “treatment” encompass preventative (e.g., prophylactic), as well as palliative treatment. 
     Engineered GAA Polypeptides: 
     In some embodiments, engineered GAA polypeptides are produced by cultivating a microorganism comprising at least one polynucleotide sequence encoding at least one engineered GAA polypeptide under conditions which are conducive for producing the engineered GAA polypeptide(s). In some embodiments, the engineered GAA polypeptide is recovered from the resulting culture medium and/or cells. 
     The present invention provides exemplary engineered GAA polypeptides having GAA activity. The Examples provide Tables showing sequence structural information correlating specific amino acid sequence features with the functional activity of the engineered GAA polypeptides. This structure-function correlation information is provided in the form of specific amino acid residues differences relative to a reference engineered polypeptide, as indicated in the Examples. The Examples further provide experimentally determined activity data for the exemplary engineered GAA polypeptides. 
     Polynucleotides Encoding Engineered Polypeptides, Expression Vectors and Host Cells: 
     The present invention provides polynucleotides encoding the engineered GAA polypeptides described herein. In some embodiments, the polynucleotides are operatively linked to one or more heterologous regulatory sequences that control gene expression to create a recombinant polynucleotide capable of expressing the polypeptide. Expression constructs containing a heterologous polynucleotide encoding the engineered GAA polypeptides can be introduced into appropriate host cells to express the corresponding GAA polypeptide. 
     As will be apparent to the skilled artisan, availability of a protein sequence and the knowledge of the codons corresponding to the various amino acids provide a description of all the polynucleotides capable of encoding the subject polypeptides. The degeneracy of the genetic code, where the same amino acids are encoded by alternative or synonymous codons, allows an extremely large number of nucleic acids to he made, all of which encode the engineered GAA polypeptide. Thus, having knowledge of a particular amino acid sequence, those skilled in the art could make any number of different nucleic acids by simply modifying the sequence of one or more codons in a way which does not change the amino acid sequence of the protein. In this regard, the present invention specifically contemplates each and every possible variation of polynucleotides that could be made encoding the polypeptides described herein by selecting combinations based on the possible codon choices, and all such variations are to be considered specifically disclosed for any polypeptide described herein, including the variants provided in Tables 3-1, 3-2, 4-1, 6-1, 10-1, 10-2, 12-1, 13-1, 13-2, 14-1, 14-2, 15-1, 16-1, 17-1, 17-2, 17-3, 17-4, 17-5, 17-6, 17-7, 17-8, and/or 17-9, as well as SEQ ID NOS: 2, 8, and/or 14. 
     In various embodiments, the codons are preferably selected to fit the host cell in which the protein is being produced. For example, preferred codons used in bacteria are used for expression in bacteria. Consequently, codon optimized polynucleotides encoding the engineered GAA polypeptides contain preferred codons at about 40%, 50%, 60%, 70%, 80%, or greater than 90% of codon positions of the full-length coding region. 
     In some embodiments, as described above, the polynucleotide encodes an engineered polypeptide having GAA activity with the properties disclosed herein, wherein the polypeptide comprises an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identity to a reference sequence selected from SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104, or the amino acid sequence of any variant as disclosed in Tables 3-1, 3-2, 4-1, 6-1, 10-1, 10-2, 12-1, 13-1, 13-2, 14-1, 14-2, 15-1, 16-1, 17-1, 17-2, 17-3, 17-4, 17-5, 17-6, 17-7, 17-8, and/or 17-9, and one or more residue differences as compared to the reference polypeptide of SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104, or the amino acid sequence of any variant as disclosed in Table 3-1, 3-2, 4-1, 6-1, 10-1, 10-2, 12-1, 13-1, 13-2, 14-1, 14-2, 15-1, 16-1, 17-1, 17-2, 17-3, 17-4. 17-5, 17-6, 17-7, 17-8, and/or 17-9 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acid residue positions). In some embodiments, the reference sequence is selected from SEQ ID NOS: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. 
     The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to SEQ ID NO: 2. The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 2. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 27, 27/944, 28, 29/478, 30, 88, 107, 109, 109/842, 110, 113, 135, 137, 138, 148, 150, 247, 274, 276, 278, 375, 403, 414, 418, 418/499, 421, 426, 437, 444, 455, 463, 471, 471/478, 476, 489, 527, 547, 581, 610, 642, 668, 670, 692, 725/732, 750, 753, 786, 820, 862, 871, 895, 897, 930, 934, and 944, wherein the positions are numbered with reference to SEQ ID NO: 2. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from 27P, 27P/944W, 27R, 28P, 28R, 28S, 29T/478T, 30G, 30K, 30T, 88G, 88S, 107G, 107P, 109G/842E, 109P, 110G, 110L, 113S, 135A, 135Q, 137P, 138A, 148G, 148Y, 150G, 247R, 274G, 276F, 276Y, 278A, 278G, 375E, 403W, 414P, 418E/499R, 418R, 421S, 426R, 437S, 444T, 455V, 463A, 471Q/478S, 471S, 476A, 476H, 489R, 527R, 547G, 581G, 581T, 610A, 610G, 610S, 642M, 642Q, 642S, 668H, 670N, 692Q, 725N/732I, 750P, 753T, 786P, 786Y, 820E, 862G, 871E, 895R, 897V, 930R, 934R, 944G, and 9448 , wherein the positions are numbered with reference to SEQ ID NC): 2. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from F27P, F27P/C944W, F27R, 128P, 128R, L285, L29T/A478T, V30G, V30K, V30T, K88G, K88S, Q107G, Q107P, L109G/G842E, L109P, Q110G, Q110L, Q113S, S135A, S135Q, E137P, M138A, T148G, T148Y, T150G, Q247R, D274G, A276F, A276Y, T278A, T278G, I375E, R403W, R414P, A418E/H499R, A418R, Q421S, G426R, A437S, A444T, R455V, E463A, K471Q/A478S, K471S, S476A, S476H, A489R, N527R, A547G, K581G, K581T, W610A, W610G, W610, L642M, L642Q, L642S, S668H, L670N, T692Q, K725N/V732I, A750P, A753T, R786P, R786Y, G820E, R862G, L871E, K895R, T897V, C930R, L934R, C944G, and C944R, wherein the positions are numbered with reference to SEQ ID NO: 2. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 29/218/240/668/700/744/869, 291218/240/700/869, 29/240/596/668/700/744/869, 29/240/596/668/869, 36/106/150/218/527/750/883/894, 106/112/1501218/4141527/793/883, 106/150/169/218/414/486/527/750/894, 106/150/169/218/414/486/527/894, 106/150/169/218/414/486/749/793/883/894, 106/150/169/218/414/486/750/793/883/894, 106/150/169/218/414/486/793/883, 106/150/169/218/414/486/894, 106/150/169/218/414/749/750/793/883, 106/150/169/218/414/749/793, 106/150/169/218/414/749/793/883, 106/150/169/218/486/527/749/793/894, 106/150/169/218/486/749/883, 106/150/169/218/486/883, 106/150/169/218/749/800, 106/150/169/414/486/749/750/883, 106/150/169/527/749/793/883, 106/150/169/749/793/883/894, 106/150/218/331/414/486/527/733/749/793, 106/150/218/414/486/642/750/793/883, 106/150/218/414/486/750/793/894, 106/150/218/414/527/749/750/883, 106/150/218/414/527/749/793/883/894, 106/150/218/414/749/750/793/883/894, 106/150/218/414/749/793/883, 106/150/218/486/527/749/894, 106/150/218/486/793/883, 106/150/218/527/749/750/793, 106/150/218/527/793/894, 106/150/218/749/750/793, 106/150/218/793, 106/150/218/793/894, 106/150/245/793/883/894, 106/150/414/749/750/793/894, 106/150/414/749/793/894, 106/150/486/527/750/793, 106/150/486/749/793/883/894, 106/150/749/793/883, 106/169/185/218/414/749/750/793, 106/191/280/402/414/444/727, 106/191/414/444/522/928/944, 106/191/414/489/928/944, 106/280/402/414/444/489/727/944, 150/169/218/414/527/793, 150/218/414/486/749/750, 150/218/414/486/750/793, 150/218/41/486/750/793/883, 150/218/414/749/750/793/894, 150/218/414/749/793, 150/218/527/749/793, 150/218/749/750/793, 150/218/749/793, 150/414/486/527/750/894, 150/414/486/749/750/793, 150/486/750/883/894, 169/486/750/793/883, 180/275/402/518/547/610/638/669/671, 180/402/431/507/547/610/669/671/793, 180/402/507/547/610/671, 191/280/402/414/444/465/842/928, 191/280/402/414/444/489/500/944, 191/280/414/444/489/500/522/842/928/944, 191/280/414/444/489/522/727/944, 191/280/414/489/842/928/944, 191/280/414/944, 191/414/522/842/944, 196/402/431/547/610/638, 218/668/700/869, 224/402/507/518/547/638/668, 269/275/431/518/547/638/668/669, 275/281/402/431/507/518/610/668, 275/281/402/431/518/547/610/669/671, 275/281/402/507/518/547/638/669/671, 275/281/402/518/547/610/638/671, 275/281/402/518/547/610/668/669/887, 275/281/402/547/610/638/669/671, 275/281/431/518/547/638/669/671, 275/281/507/547/669/671, 275/281/610/638/668/669, 275/281/671, 275/377/402/507/518/669/671/715, 275/402/431/507/547/671, 275/402/431/518/610/638/669/671/922, 275/402/507/547/610/638/668/669, 275/402/507/547/610/638/669/671, 275/402/507/547/610/671, 275/402/547/610/638/669/671, 275/402/547/638/669/671, 275/402/638/669/671, 275/431/507/518/547/668/669/671, 275/431/507/518/610/669/671, 275/431/507/5471610/638/671, 275/431/518/547/638/668, 275/431/518/610/638/669/671, 275/431/638, 275/507/518/547/610/638/668/669, 275/507/518/547/638/669/671, 275/507/547/610/638/669/671, 275/507/547/668/669/671, 275/518/671, 280/402/536/928, 281/402/507/518/547/610/638/669/671, 281/402/507/547/638/669/671, 281/402/518/547/610/638/668/669, 281/02/518/547/668, 281/431/507/518/547/610/638/668, 402/431/518/547/610/668, 402/431/518/547/671, 402/431/518/610, 402/431/547/638/671, 431/507/518/541/547/638/669/671, 431/507/518/669/671, 507/547/610, 507/547/638/669/671, 547/610/638/671, and 547/638/668, wherein the positions are numbered with reference to SEQ ID NO: 2. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from 29Q/218S/240I/668D/700F/744V/869L, 29Q/240I/596P/668D/869L, 29Q/240I/596S/668D/700F/744V/869T, 29V/218S/240I/700F/869T, 36R/106P/150S/218S/527D/750P/883H/894R, 106P/112S/150S/218S/414G/527D/793K/883H, 106P/150S/169S/218S/414G/486E/527D/750P/894R, 106P/150S/169S/218S/414G/486E/527D/894R, 106P/150S/169S/218S/414G/486E/749E/793K/883H/894R, 106P/150S/169S/218S/414G/486/E750P/793K883H/894R, 106P/150S/169S/218S/414G/486E/793K/883H, 106P/150S/169S/218S/414G/486E/894R, 106P/150S/169S/218S/414G/749E/750P/793K/883H, 106P/150S/169S/218S/414G/749E/793K, 106P/150S/169S/218S/414G/749E/793K/883H, 106P/150S/169S/218S/486E/527D/749E/793K/894R, 106P/150S/169S/218S/486E/749E/883H, 106P/150S/169S/218S/486E/883H, 106P/150S/169S/218S/749E/800A, 106P/150S/169S/414G/486E/749E/750P/883H, 106P/150S/169S/527D/749E/793K/883H, 106P/150S/169S/749E/793K/883H/894R, 106P/150S/218S/331 A/414G/486E/527D/733E/749E/793K, 106P/150S/218S/414G/486E/642F/750P/793K/883H, 106P/150S/218S/414G/486E/750P/793K/894R, 106P/150S/218S/414G/527D/749E/750P/883H, 106P/150S/218S/414G/527D/749E/793K/883H/894G, 106P/150S/218S/414G/749E/750P/793K/883H/894R, 106P/150S/218S/414G/749E/793K/883H, 106P/150S/218S/486E/527D/749E/894R, 106P/150S/218S/486E/793K/883H, 106P/150S/218S/527D/749E/750P/793K, 106P/150S/218S/527D/793K/894G, 106P/150S/218S/749E/750P/793K, 106P/150S/218S/793K, 106P/150S/218S/793K/894R, 106P/150S/245S/793K/883H/894R, 106P/150S/414G/749E/750P/793K/894R, 106P/150S/414G/749E/793K/894R, 106P/150S/486E/527D/750P/793K, 106P/150S/486E/749E/793K/883H/894G, 106P/150S/749E/793K/883H, 106P/169S/185G/218S/414G/749E/750P/793K, 106P/191R/280D/402A/414G/444P/727P, 106P/191R/414G/444P/522V/928T/944S, 106P/191R/414G/489D/928T/944S, 106P/280D/402A/414G/444P/489D/727P/944S, 150S/169S/218S/414G/527D/793K, 150S/218S/414G/486A/750P/793K, 150S/218S/414G/486E/749E/750P, 150S/218S/414G/486E/750P/793K/883H, 150S/218S/414G/749E/750P/793K/894R, 150S/218S/414G/749E/793K, 150S/218S/527D/749E/793K, 150S/218S/749E/750P/793K, 150S/218S/749E/793K, 150S/414G/486E/527D/750P/894R, 150S/414G/486E/749E/750P/793K, 150S/486E/750P/883H/894G, 169S/486E/750P/793K/883H, 180H/275M/402A/518V/547G/610R/638I/669H/671N, 180H/402A/431V/507L/547G/610R/669H/671N/793G, 180H/402A/507L/547G/610R/671N, 191R/280D/402A/414G/444P/465E/842S/928T, 191R/280D/402A/414G/444P/489D/500A/944S, 191R/280D/414G/444P/489D/500A/522V/842S/928T/944S, 191R/280D/414G/444P/489D/522V/727P/944S, 191R/280D/414G/489D/842S/928T/944S, 191R/280D/414G/944S, 191R/414G/522V/842S/944S, 196V/402A/431V/547G/610R/638I, 218S/668D/700F/869T, 224F/402 A/507L/518V/547G/638I/668D, 269N/275M/431V/518V/547G/638I/668D/669H, 275M/281V/402A/431V/507L518V/610R/668D, 275M/281V/402A/507L/518 V/547G/638I/669H/671N, 275M/281V/402A/518V/547G/610R/638I/671N, 275M/281V/402A/518V/547G/610R/668D/669H/887D, 275M/281V/402A/547G/610R/638I/669H/671N, 275M/281V/507L/547G/669H/671N, 275M/281V/610R/638I/668D/669H, 275M/402A/431V/507L/547G/671N, 275M/402A/507L/547G610R/671N, 275M/402A/547G/638I/669H/671N, 275M/431V/518V/547G/638I/668D, 275M/431V/518V/610R/638I/669H/671N, 275M/431V/638I, 275M/507L/547G/668D/669H/671N, 275V/281V/402A/431V/518V/547G/610R/669H/671N, 275 V/281V/431V/518V/547G/638I/669H/671N, 275V/281V/671N, 275V/377K/402A/507L/518V/669H/671N/715G, 275V/402A/431V/518V/610R/638I/669H/671N/922L, 275 V/402A/507L/547G/610R/638I/668D/669H, 275 V/402A/507L/547G/610R/638I/669H/671N, 275V/402A/547G/610R/638I/669H/671N, 275V/402A/638I/669H/671N, 275V/431V/507L/518V/547G/668D/669H/671 N, 275V/431V/507L/518V/610R/669H/671N, 275V/431V/507L/547G/610R/638I/671N, 275V/507L/518V/547G/610R/638I/668D/669H, 275 V/507L/518V/547G/638I/669H/671N, 275 V/507L/547G/610R/638I/669H/671N, 275V/518V/671N, 280D/402A/536I/928T, 281V/402A/507L/518V/547G/610R/638I/669H/671N, 281V/402A/507L/547G/638I/669H/671N, 281V/402A/518V/547G/610R/638I/668D/669H, 281V/402A/518V/547G/668D, 281V/431V/507L/518V/547G/610R/638I/668D, 402A/431V/518V/547G/610R/668D, 402A/431V/518V/547G/671N, 402A/431V/518V/610R, 402A/431V/547G/638I/671N, 431V/507L/518V/541E/547G/638I/669H/671N, 431V/507L/518V/669H/671N, 507L/547G/610R, 507L/547G/638I/669H/671N, 547G/610R/638I/671N, and 547G/638I/668D, wherein the positions are numbered with reference to SEQ ID NO: 2. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from L29Q/L218S/L240I/S668D/H700F/I744V/I869L, L29Q/L240I/A596P/S668D/I869L, L29Q/L240I/A596S/S668D/H700F/I744V/I869T, L29V/L218S/L240I/H700F/I869T, G36R/K106P/T150S/L218S/N527D/A750P/R883H/Q894R, K106P/A112S/T150S/L218S/R414G/N527D/E793K/R883H, K106P/T150S/N169S/L218S/R414G/T486E/N527D/A750P/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/N527D/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/Q749E/E793K1R883H/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/A750P/E793K/R883H/Q894R, K106P/T150S/N169S/L218S/R414G/T486E/E793K/R883H, K106P/T150S/N169S/L218S/R414G/T486E/Q894R, K106P/T150S/N169S/L218S/R414G/Q749E/A750P/E793K/R883H, K106P/T150S/N169S/L218S/R414G/Q749E/E793K, K106P/T150S/N169S/L218S/R414G/Q749E/E793K/R883H, K106P/T150S/N169S/L218S/T486E/N527D/Q749E/E793K/Q894R, K106P/T150S/N169S/L218S/T486E/Q749E/R883H, K106P/T150S/N169S/L218S/T486E/R883H, K106P/T150S/N169S/L218S/Q749E/P800A, K106P/T150S/N169S/R414G/T486E/Q749E/A750P/R883H, K106P/T150S/N169S/N527D/Q749E/E793K/R883H, K106P/T150S/N169S/Q749E/E793K/R883H/Q894R, K106P/T150S/L218S/V331A/R414G/T486E/N527D/D733E/Q749E/E793K, K106P/T150S/L218S/R414G/T486E/L642F/A750P/E793K/R883H, K106P/T150S/L218S/R414G/T486E/A750P/E793K/Q894R, K106P/T150S/L218S/R414G/N527D/Q749E/A750P/R883H, K106P/T150S/L218S/R414G/N527D/Q749E/E793K/R883H/Q894G, K106P/T150S/L218S/R414G/Q749E/A750P/E793K/R883H/Q894R, K106P/T150S/L218S/R414G/Q749E/E793K/R883H, K106P/T150S/L218S/T486E/N527D/Q749E/Q894R, K106P/T150S/L218S/T486E/E793K/R883H, K106P/T150S/L218S/N527D/Q749E/A750P/E793K, K106P/T150S/L218S/N527D/E793K/Q894G, K106P/T150S/L218S/Q749E/A750P/E793K, K106P/T150S/L218S/E793K, K106P/T150S/L218S/E793K/Q894R, K106P/T150S/P245S/E793K/R883H/Q894R, K106P/T150S/R414G/Q749E/A750P/E793K/Q894R, K106P/T150S/R414G/Q749E/E793K/Q894R, K106P/T150S/T486E/N527D/A750P/E793K, K106P/T150S/T486E/Q749E/E793K/R883H/Q894G, K106P/T150S/Q749E/E793K/R883H, K106P/N169S/V185G/L218S/R414G/Q749E/A750P/E793K, K106P/H191R/G280D/S402A/R414G/A444P/S727P, K106P/H191R/R414G/A444P/E522V/D928T/C944S, K106P/H191R/R414G/A489D/D928T/C944S, K106P/G280D/S402A/R414G/A444P/A489D/S727P/C944S, T150S/N169S/L218S/R414G/N527D/E793K, T150S/L218S/R414G/T486A/A750P/E793K, T150S/L218S/R414G/T486E/Q749E/A750P, T150S/L218S/R414G/T486E/A750P/E793K/R883H, T150S/L218S/R414G/Q749E/A750P/E793K/Q894R, T150S/L218S/R414G/Q749E/E793K, T150S/L218S/N527D/Q749E/E793K, T150S/L218S/Q749E/A750P/E793K, T150S/L218S/Q749E/E793K, T150S/R414G/T486E/N527D/A750P/Q894R, T150S/R414G/T486E/Q749E/A750P/E793K, T150S/T486E/A750P/R883H/Q894G, N169S/T486E/A750P/E793K/R883H, N180H/L275M/S402A/I518V/A547G/W610R/V638I/L669H/S671N, N180H/S402A/M431V/M507L/A547G/W610R/L669H/S671N/E793G, N180H/S402A/M507L/A547G/W610R/S671N, H191R/G280D/S402A/R414G/A444P/G465E/G842S/D928T, H191R/G280D/S402A/R414G/A444P/A489D/D500A/C944S, H191R/G280D/R414G/A444P/A489D/D500A/E522V/G842S/D928T/C944S, H191R/G280D/R414G/A444P/A489D/E522V/S727P/C944S, H191R/G280D/R414G/A489D/G842S/D928T/C,944S, H191R/G280D/R414G/C944S, H191R/R414G/E522V/G842S/C944S, A196V/S402A/M431V/A547G/W610R/V638I, L218S/S668D/H700F/I869T, L224F/S402A/M507/I518V/A547G/V638I/S668D, T269N/L275M/M431V/1518V/A547G/V638I/S668D/L669H, L275M/A281V/S402A/M431V/M507L/I518V/W610R/S668D, L275M/A281 V/S402A/M507L/I518V/A547G/V638I/L669H/S671N, L275M/A281V/S402A/I518V/A547G/W610R/V638I/S671N, L275M/A281V/S402A/I518V/A547G/W610R/S668D/L669H/E887D, L275M/A281V/S402A/A547G/W610R/V638I/L669H/S671N, L275M/A281V/M507L/A547G/L669H/S671N, L275M/A281V/W610R/V638I/S668D/L669H, L275M/S402A/M431V/M507L/A547G/S671N, L275M/S402A/M507L/A547G/W610R/S671N, L275M/S402A/A547G/V638I/L669H/S671N, L275M/M431V/I518V/A547G/V638/S668D, L275M/M431V/I518V/W610R/V638I/L669H/S671N, L275M/M431V/V638I, L275M/M507L/A547G/S668D/L669H/S671N, L275 V/A281 V/S402 A/M431V/I518V/A547G/W610R/L669H/S671N, L275V/A281V/M431V/I518V/A547G/V638I/L669H/S671N, L275V/A281V/S671N, L275V/R377K/S402A/M507L/I518V/L669H/S671N/V715G, L275V/S402A/M431V/I518V/W610R/V638I/L669H/S671N/P922L, L275V/S402A/M507L/A547G/W610R/V638I/S668D/L669H, L275V/S402 A/M507L/A547G/W610R/V638I/L669H/S671N, L275V/S402A/A547G/W610R/V638I/L669H/S671N, L275V/S402A/V638I/L669H/S671N, L275 V/M431V/M507L/I518V/A547G/S668D/L669H/S671N, L275V/M431V/M507L/I518V/W610R/L669H/S671N, L275V/M431V/M507L/A547G/W610R/V638I/S671N, L275V/M507L/I518V/A547G/W610R/V638I/S668D/L669H, L275V/M507L/I518V/A547G/V638I/L669H/S671N, L275V/M507L/A547G/W610R/V638I/L669H/S671N, L275V/I518V/S671N, G280D/S402A/V536I/D928T, A281V/S402A/M507L/I518V/A547G/W610R/V638I/L669H/S671N, A281V/S402A/M507L/A547G/V638I/L669I/S671N, A281V/S402A/I518V/A547G/W610R/V638I/S668D/L669H, A281V/S402A/I518V/A547G/S668D, A281V/M431V/M507L/I518V/A547G/W610R/V638I/S668D, S402A/M431V/I518V/A547G/W610R/S668D, S402A/M431V/I518V/A547G/S671N, S402A/M431V/I518V/W610R, S402A/M431V/A547G/V638I/S671N, M431V/M507L/I518V/G541E/A547G/V638I/L669H/S671N, M431V/M507L/I518V/L669H/S671N, M507L/A547G/W610R, M507L/A547G/V638I/L669H/S671N, A547G/W610R/V638I/S671N, and A547G/V638I/S668D, wherein the positions are numbered with reference to SEQ ID NO: 2. 
     The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to SEQ ID NO: 8. The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 8. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 4, 27, 27/28/489, 27/418/478, 28, 28/29, 28/29/113/135/138, 28/29/113/135/418, 28/29/135, 28/29/418, 29/113/126/135/193, 29/113/135, 29/113/135/455, 29/113/138, 29/148, 29/478, 106, 106/138/218/431/671/749, 106/218/281, 106/218/455, 106/218/455/507/749, 106/489/671, 106/638, 106/671/934, 113, 113/135/418, 113/418/455/478/581, 113/418/478/489/581, 135, 135/148/150/418, 135/478/489/581, 135/489, 135/944, 138/218/668/671, 138/218/749/934, 138/671/749/934, 157, 218, 218/281, 218/281/431, 218/281/671, 218/431, 218/431/489/507/749/934, 218/455, 218/507/749, 218/507/934, 218/638/671, 218/749, 281/431/489/668, 345/934, 418, 418/489, 431/668/671, 489/638/934, 489/671/934, 489/749, 489/934, 507/668, 507/671/934, 671/749, 671/934, and 749/784, wherein the positions are numbered with reference to SEQ ID NO: 8. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from 4H, 27P/28S/489R, 27P/418E/478T, 27R, 28S, 28S/29T, 28S/29T/113S/135Q/138A, 28S/29T/113S/135Q/418E, 28S/29T/135Q, 28S/29T/418E, 29T/113S/126Q/135Q/193Q, 29T/113S/135Q, 29T/113S/135Q/455V, 29T/113S/138A, 29T/148G, 29T/478T, 106P, 106P/138A/218S/431V/671N/749E, 106P/218S/281V, 106P/218S/455V, 106P/218S/455V/507L/749E, 106P/489R/671N, 106P/638I, 106P/671N/934R, 113S, 113S/135Q/418E, 113S/418E/455V/478T/581T, 113S/418E/478T/489R/581T, 135P/944Y, 135Q, 135Q/148G/150G/418E, 135Q/478T/489R/581T, 135Q/489R, 138A/218S/668D/671N, 138A/218S/749E/934R, 138A/671N/749E/934R, 157M, 218S, 218S/281V, 218S/281V/431V, 218S/281V/671N, 218S/431V, 218S/431V/489R/507L/749E/934R, 218S/455V, 218S/507L/749E, 218S/507L/934R, 218S/638I/671N, 218S/749E, 281V/431V/489R/668D, 345K/934R, 418E, 418E/489R, 431V/668D/671N, 489R/638I/934R, 489R/671N/934R, 489R/749E, 489R/934R, 507L/668D, 507L/671N/934R, 671N/749E, 671N/934R, and 749E/784T, wherein the positions are numbered with reference to SEQ ID NO: 8. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from P4H, F27P/L28S/A489R, F27P/A418E/A478T, F27R, L285, L28S/L29T, L28S/L29T/Q113S/S135Q/M138A, L28S/L29T/Q113S/S135Q/A418E, L28S/L29T/S135Q, L28S/L29T/A418E, L29T/Q113S/P126Q/S135Q/H193Q, L29T/Q113S/S135Q, L29T/Q113S/S135Q/R455V, L29T/Q113S/M138A, L29T/T148G, L29T/A478T, K106P, K106P/M138A/L218S/M431V/S671N/Q749E, K106P/L218S/A281V, K106P/L218S/R455V, K106P/L218S/R455V/M507L/Q749E, K106P/A489R/S671N, K106P/V638I, K106P/S671N/L934R, Q113S, Q113S/135Q/A418E, Q113S/A418E/R455V/A478T/K581T, Q113S/A418E/A478T/A489R/K581T, S135P/C944Y, S135Q, S135Q/T148G/S150G/A418E, S 135Q/A478T/A489R/K581T, S135Q/A489R, M138A/L218S/S668D/S671N, M138A/L218S/Q749E/L934R, M138A/S671N/Q749E/L934R, L157M, L218S, L218S/A281V, L218S/A281V/M431V, L218S/A281V/S671N, L218S/M431V, L218S/M431V/A489R/M507L/Q749E/L934R, L218S/R455V, L218S/M507L/Q749E, L218S/M507L/L934R, L218S/V638I/S671N, L218S/Q749E, A281V/M431V/A489R/S668D, Q345K/L934R, A418E, A418E/A489R, M431V/S668D/S671N, A489R/V638I/L934R, A489R/S671N/L934R, A489R/Q749E, A489R/L934R, M507L/S668D, M507L/S671N/L934R, S671N/Q749E, 5671N/L934R, and Q749E/A784 , wherein the positions are numbered with reference to SEQ ID NO: 8. 
     The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to SEQ ID NO: 14. The present invention provides recombinant acid alpha-glucosidases and/or biologically active recombinant acid alpha-glucosidase fragments comprising an amino acid sequence comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 14. In some embodiments, the acid alpha-glucosidase comprises at least one substitution at position or set of positions selected from 22, 24, 27, 27/165, 30, 33, 34, 37/62, 37/62/79/196/696/862, 37/62/523, 37/62/523/793, 37/64/66/79/154/523/681/793/862, 37/79/154/793, 37/196, 37/528/696/793, 37/528/790, 37/528/790/793/862, 37/790/793, 39, 39/58/489/725/830/842/930/944, 39/70/109/830/842, 39/70/489/612, 39/70/725, 39/267, 39/267/489/522/612/830/842, 39/267/489/830/944, 39/489/500/612, 39/500/612, 40, 44/157, 47, 49, 50, 55, 60/500/612, 62/79/154/862, 62/79/196/681/862, 62/79/523/528/790, 62/79/790/793, 62/79/862, 62/92, 62/92/790/793, 62/106/523/528/696/793/862, 62/154/696/793/862, 62/793/862, 68, 70, 70/267/725/944, 70/267/930/944, 70/489/930, 70/725/830/860/930/944, 77, 79/154/681, 79/154/793/862, 79/862, 89, 97, 106/154, 107, 109, 109/522/612/725, 109/522/830/944, 109/612, 118, 149, 157, 158, 178, 179, 196/528/681/790/793, 207, 208, 217, 267/489/500/725/830/930, 267/522/725, 352, 385, 424, 448, 463, 489/830/944, 500, 500/612/830/860, 500/860/930, 500/930/944, 522/725, 523, 523/790/793, 528/681, 528/793, 528/862, 672, 673, 725, 734, 740, 753, 774, 778, 793, 830, 844, 862, 875, 880, 892, 902, 922, 925, 930, 932, 934, 938, and 944, wherein the positions are numbered with reference to SEQ ID NO: 14. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from 22R, 24E, 24R, 24W, 27A, 27G, 27G/165I, 27K, 27R, 27S, 27V, 27W, 30D, 30L, 33G, 33P, 34D, 34M, 34T, 37F/62E, 37F/62E/79S/196T/696S/862Q, 37F/62E/523N, 37F/62.E/523N/793K, 37F/64Q/66G/795/154R/523N/681Q/793K/862Q, 37F/79S/154R/793K, 37F/196T, 37F/528S/696S/793K, 37F/528S/790V, 37F/528S/790V/793K/862Q, 37F/790V/793K, 39D, 39H, 39Q, 39Q/58L/489D/725E/830K/842S/930P/944S, 39Q/70A/109P/830K/842S, 39Q/70A/489D/612D, 39Q/70A/725E, 39Q/267K, 39K/267K/489D/522V/612D/830K/842S, 39Q/267K/489D/830K/944S, 39Q/489D/500A/612D, 39Q/500A/612D, 40W, 44I/157V, 47G, 47R, 49A, 49G, 50G, 50L, 50OV, 55C, 55L, 60V/500A/612D, 62E/79S/154R/862Q, 62E/79S/196T/681Q/862Q, 62E/79S/523N/528S/790V, 62E/79S/790V/793K, 62E/79S/862Q, 62E/92R, 62E/92R/790V/793K, 62E/106R/523N/528S/696S/793K/862Q, 62E/154R/696S/793K/862Q, 62E/793K/862Q, 68N, 68S, 68W, 70A/267K/725E/944S, 70A/267K/930P/944S, 70A/489D/930P, 70A/725E/830K/860F/930P/944S, 70Q, 77W, 79S/154R/681Q, 79S/154R/793K/862Q, 79S/862Q, 89R, 97D, 97G, 106R/154R, 107G, 109D, 109P/522V/612D/725E, 109P/522V/830K/944S, 109P/612D, 118F, 149R, 157Q, 158E, 158F, 178G, 178V, 179I, 196T/528S/681Q/790V/793K, 207R, 207Y, 208G, 208I, 217A, 217D, 267K/489D/500A/725E/830K/930P, 267K/522V/725E, 352K, 352V, 385G, 424K, 448L, 463A, 489D/830K/944S, 500A, 500A/612D/830K/860F, 500A/860F/930P, 500A/930P/944S, 522V/725E, 523N, 523N/790V/793K, 528S/681Q, 528S/793K, 528S/862Q, 672E, 672K, 673N, 673R, 725F, 725V, 734K, 740G, 740Q, 753S, 774G, 774S, 778Q, 793K, 830V, 844R, 862Q, 875D, 880R, 892L, 902L, 922E, 925A, 925W, 930P, 932A, 934F, 938A, 938P, 944R, and 944S, wherein the positions are numbered with reference to SEQ ID NO: 14. In some embodiments, the acid alpha-glucosidase comprises at least one substitution or substitution sets at one or more positions selected from I22R, L24E, L24R, L24W, F27A, F27G, F27G/M165I, F27K, F27R, F27S, F27V, F27W, V30D, V30L, E33G, E33P, L34D, L34M, L34T, S37F/A62E, S37F/A62E/N79S/A196T/A696S/R862Q, S37F/A62E/D523N, S37F/A62E/D523N/E793K, S37F/P64Q/R66G/N79S/K154R/D523N/E681Q/E793K/R862Q, S37F/N79S/K154R/E793K, S37F/A196T, S37F/N528S/A696S/E793K, S37F/N528S/I790V, S37F/N528S/I790V/E793K/R862Q, S37F/I790V/E793K, P39D, P39H, P39Q, P39Q/R58L/A489D/K725E/Q830K/G842S/C930P/C944S, P39Q/V70A/L109P/Q830K/G842S, P39Q/V70A/A489D/S612D, P39Q/V70A/K725E, P39Q/R267K, P39Q/R267K/A489D/E522V/S612D/Q830K/G842S, P39Q/R267K/A489D/Q830K/C944S, P39Q/A489D/D500A/S612D, P39Q/D500A/S612D, V40W, T44I/L157V, A47G, A47R, Q49A, Q49G, Q50G, Q50L, Q50V, P55C, P55L, A60V/D500A/S612D, A62E/N79S/K154R/R862Q, A62E/N79S/A196T/E681Q/R862Q, A62E/N79S/D523N/N528S/I790V, A62E/N79S/I790V/E793K, A62E/N79S/R862Q, A62E/Q92R, A62E/Q92R/I790V/E793K, A62E/K106R/D523N/N528S/A696S/E793K/R862Q, A62E/K154R/A696S/E793K/R862Q, A62E/E793K/R862Q, R68N, R68S, R68W, V70A/R267K/K725E/C944S, V70A/R267K/C930P/C944S, V70A/A489D/C930P, V70A/K725E/Q830K/L860F/C930P/C944S, V70Q, P77W, N79S/K154R/E681Q, N79S/K154R/E793K/R862Q, N79S/R862Q, A89R, A97D, A97G, K106R/K154R, Q107G, L109D, L109P/E522V/S612D/K725E, L109P/E522V/Q830K/C944S, L109P/S612D, W118F, P149R, L157Q, T158E, T158F, P178G, P178V, A179L, A196T/N528S/E681Q/I790V/E793K, E207R, E207Y, E208G, E208I, Q217A, Q217D, R267K/A489D/D500A/K725E/Q830K/C930P, R267K/E522V/K725E, Y352K, Y352V, R385G, H424K, R448L, E463A, A489D/Q830K/C944S, D500A, D500A/S612D/Q830K/L860F, D500A/L860F/C930P, D500A/C930P/C944S, E522V/K725E, D523N, D523N/I790V/E793K, N528S/E681Q, N528S/E793K, N528S/R862Q, L672E, L672K, P673N, P673R, K725F, K725V, H734K, E740G, E740Q, A753S, A774G, A774S, L778Q, E793K, Q830V, E844R, R862Q, N875D, E880R, Q892L, A902L, P922E, K925A, K925W, C930P, S932A, L934F, Q938A, Q938P, C944R, and C944S, wherein the positions are numbered with reference to SEQ ID NO: 14. 
     In some embodiments, the recombinant acid alpha glucosidase comprises at least one mutation in at least one position as provided in Tables 3-1, 3-2, 4-1, 6-1, 10-1, 10-2, 12-1, 13-1, 13-2, 14-1, 14-2, 15-1, 16-1, 17-1, 17-2, 17-3, 17-4, 17-5, 17-6, 17-7, 17-8, and/or 17-9. In some additional embodiments, the recombinant acid alpha glucosidase is derived from a human acid alpha glucosidase. In yet some additional embodiments, the recombinant acid alpha glucosidase comprising the polypeptide sequence of SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104. 
     In some embodiments, the polynucleotide encoding the engineered GAA polypeptides comprises a polynucleotide sequence selected from a polynucleotide sequence encoding SEQ ID NO: 1, 5, 7, 11, 13, 15, 17, 19, 945, 1955, 2495, 2879, and/or 3103. In some embodiments, the polynucleotide encoding an engineered GAA polypeptide has at least about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% nucleotide residue identity to SEQ ID NO: 1, 5, 7, 11, 13, 15, 17, 19, 945, 1955, 2495, 2879, and/or 3103. In some embodiments, the polynucleotide encoding an engineered GAA polypeptide has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% nucleotide residue identity to SEQ ID NO: 1, 5, 7, 11, 13, 15, 17, 19, 945, 1955, 2495, 2879, and/or 3103. In some embodiments, the polynucleotide encoding an engineered GAA polypeptide comprises SEQ ID NO: 1, 5, 7, 11, 13, 15, 17, 19, 945, 1955, 2495, 2879, and/or 3103. In some embodiments, the polynucleotide encoding an engineered GAA polypeptide consists of SEQ ID NO: 1, 5, 7, 11, 13, 15, 17, 19, 945, 1955, 2495, 2879, and/or 3103. In some embodiments, the polynucleotides are capable of hybridizing under highly stringent conditions to a reference polynucleotide sequence selected from SEQ ID NO: 1, 5, 7, 11, 13, 15, 17, 19, 945, 1955, 2495, 2879, and/or 3103, or a complement thereof, or a polynucleotide sequence encoding any of the variant GAA polypeptides provided herein. 
     In some embodiments, an isolated polynucleotide encoding any of the engineered GAA polypeptides provided herein is manipulated in a variety of ways to provide for expression of the polypeptide. In some embodiments, the polynucleotides encoding the polypeptides are provided as expression vectors where one or more control sequences is present to regulate the expression of the polynucleotides and/or polypeptides. Manipulation of the isolated polynucleotide prior to its insertion into a vector may be desirable or necessary depending on the expression vector. The techniques for modifying polynucleotides and nucleic acid sequences utilizing recombinant DNA methods are well known in the art. 
     In some embodiments, the control sequences include among other sequences, promoters, Kozak sequence, leader sequences, polyadenylation sequences, propeptide sequences, signal peptide sequences, DNA based regulatory elements for gene therapy retention and transcription terminators. As known in the art, suitable promoters can be selected based on the host cells used. For bacterial host cells, suitable promoters for directing transcription of the nucleic acid constructs of the present application, include, but are not limited to the promoters obtained from the  E. coli  lac operon,  Streptomyces coelicolor  agarase gene (dagA),  Bacillus subtilis  levansucrase gene (sacB),  Bacillus licheniformis  alpha-amylase gene (amyL),  Bacillus stearothermophilus  maltogenic amylase gene (amyM),  Bacillus amyloliquefaciens  alpha-amylase gene (amyQ),  Bacillus licheniformis  penicillinase gene (pent),  Bacillus subtilis  xyIA and xyIB genes, and prokaryotic beta-lactamase gene (See e.g., Villa-Kamaroff et al., Proc. Natl Acad. Sci. USA 75: 3727-3731 [1978]), as well as the tac promoter (See e.g., DeBoer et al., Proc. Natl. Acad. Sci. USA 80: 21-25 [1983]). Exemplary promoters for filamentous fungal host cells, include promoters obtained from the genes for  Aspergillus oryzae  TAKA amylase,  Rhizomucor miehei  aspartic proteinase,  Aspergillus niger  neutral alpha-amylase,  Aspergillus niger  acid stable alpha-amylase,  Aspergillus niger  or  Aspergillus awamori  glucoamylase (glaA),  Rhizomucor miehei  lipase,  Aspergillus oryzae  alkaline protease,  Aspergillus oryzae  triose phosphate isomerase, Aspergillus nidulans acetamidase, and  Fusarium oxysporum  trypsin-like protease (See e.g., WO 96/00787), as well as the NA2-tpi promoter (a hybrid of the promoters from the genes for  Aspergillus niger  neutral alpha-amylase and  Aspergillus  oryzae triose phosphate isomerase), and mutant, truncated, and hybrid promoters thereof. Exemplary yeast cell promoters can be from the genes can be from the genes for  Saccharomyces cerevisiae  enolase (ENO-1),  Saccharomyces cerevisiae  galactokinase (GAL1),  Saccharomyces cerevisiae  alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH21GAP), and  Saccharomyces cerevisiae  3-phosphoglycerate kinase. Other useful promoters for yeast host cells are known in the art (See e.g., Romanos et al., Yeast 8:423-488 [1992]). Exemplary promoters for use in mammalian cells include, but are not limited to those from cytomegalovirus (CMV), chicken β-actin promoter fused with the CMV enhancer, Simian vacillating virus 40 (SV40), from  Homo sapiens  phosphoglycerate kinase, beta actin, elongation factor-la or glyceraldehyde-3-phosphate dehydrogenase, or from  Gallus gallus  β-actin. 
     In some embodiments, the control sequence is a suitable transcription terminator sequence, a sequence recognized by a host cell to terminate transcription. The terminator sequence is operably linked to the 3′ terminus of the nucleic acid sequence encoding the polypeptide. Any terminator which is functional in the host cell of choice finds use in the present invention. For example, exemplary transcription terminators for filamentous fungal host cells can he obtained from the genes for  Aspergillus oryzae  TAKA amylase,  Aspergillus niger  glucoamylase,  Aspergillus nidulans  anthranilate synthase,  Aspergillus niger  alpha-glucosidase, and  Fusarium oxysporum  trypsin-like protease. Exemplary terminators for yeast host cells can he obtained from the genes for  Saccharomyces cerevisiae  enolase,  Saccharomyces cerevisiae  cytochrome C (CYC1), and  Saccharomyces cerevisiae  glyceraldehyde-3-phosphate dehydrogenase. Other useful terminators for yeast host cells are known in the art (See e.g., Romanos et al., supra). Exemplary terminators for mammalian cells include, but are not limited to those from cytomegalovirus (CMV), Simian vacillating virus 40 (SV40), from  Homo sapiens  growth hormone hGH, from bovine growth hormone BGH, and from human or rabbit beta globulin. 
     In some embodiments, the control sequence is a suitable leader sequence, 5′-cap modification, 5′ UTR, etc. In some embodiments, these regulatory sequence elements mediate binding to molecules involved in mRNA trafficking and translation, inhibit 5′-exonucleolytic degradation and confer resistance to de-capping. The leader sequence is operably linked to the 5′ terminus of the nucleic acid sequence encoding the polypeptide. Any leader sequence that is functional in the host cell of choice may be used. Exemplary leaders for filamentous fungal host cells are obtained from the genes for  Aspergillus oryzae  TAKA amylase and  Aspergillus nidulans  triose phosphate isomerase. Suitable leaders for yeast host cells include, but are not limited to those obtained from the genes for  Saccharomyces cerevisiae  enolase (ENO-1),  Saccharomyces cerevisiae  3-phosphoglycerate kinase,  Saccharomyces cerevisiae  alpha-factor, and Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP). Suitable leaders for mammalian host cells include but are not limited to the 5′-UTR element present in orthopoxvirus mRNA. 
     In some embodiments, the control sequence comprises a 3′ untranslated nucleic acid region and polyadenylation tail nucleic acid sequence, sequences operably linked to the 3′ terminus of the protein coding nucleic acid sequence and which mediate binding to proteins involved in mRNA trafficking and translation and mRNA half-life. Any polyadenylation sequence and 3′ UTR which is functional in the host cell of choice may be used in the present invention. Exemplary polyadenylation sequences for filamentous fungal host cells include, but are not limited to those from the genes for  Aspergillus oryzae  TAKA amylase,  Aspergillus niger  glucoamylase,  Aspergillus nidulans  anthranilate synthase,  Fusarium oxysporum  trypsin-like protease, and  Aspergillus niger  alpha-glucosidase. Useful polyadenylation sequences for yeast host cells are also known in the art (See e.g., Guo and Sherman, Mol. Cell. Biol., 15:5983-5990 [1995]). Useful polyadenylation and 3′ UTR sequences for mammalian host cells include, but are not limited to the 3′-UTRs of α- and β-globin mRNAs that harbor several sequence elements that increase the stability and translation of mRNA. 
     In some embodiments, the control sequence is a signal peptide coding region that codes for an amino acid sequence linked to the amino terminus of a polypeptide and directs the encoded polypeptide into the cell&#39;s secretory pathway. The 5′ end of the coding sequence of the nucleic acid sequence may inherently contain a signal peptide coding region naturally linked in translation reading frame with the segment of the coding region that encodes the secreted polypeptide. Alternatively, the 5′ end of the coding sequence may contain a signal peptide coding region that is foreign to the coding sequence. Any signal peptide coding region that directs the expressed polypeptide into the secretory pathway of a host cell of choice finds use for expression of the engineered GAA polypeptides provided herein. Effective signal peptide coding regions for bacterial host cells include, but are not limited to the signal peptide coding regions obtained from the genes for  Bacillus  NCIB 11837 maltogenic amylase,  Bacillus stearothermophilus  alpha-amylase,  Bacillus licheniformis  subtilisin,  Bacillus licheniformis  beta-lactamase,  Bacillus stearothermophilus  neutral proteases (nprT, nprS, nprM), and  Bacillus subtilis  prsA. Further signal peptides are known in the art (See e.g., Simonen and Palva, Microbiol. Rev., 57:109-137 [1993]). Effective signal peptide coding regions for filamentous fungal host cells include, but are not limited to the signal peptide coding regions obtained from the genes for  Aspergillus oryzae  TAKA amylase,  Aspergillus niger  neutral amylase,  Aspergillus niger  glucoamylase,  Rhizomucor miehei  aspartic proteinase,  Humicola insolens  cellulase, and  Humicola lanuginosa  lipase. Useful signal peptides for yeast host cells include, but are not limited to those from the genes for  Saccharomyces cerevisiae  alpha-factor and  Saccharomyces cerevisiae  invertase. Un some embodiments, the  S. cerevisiae  a-mating factor prepro peptide (Mfalpha) finds use (e.g., SEQ ID NOS: 3383 and 3384). Useful signal peptides for mammalian host cells include, but are not limited to those from the genes for immunoglobulin gamma (IgG). Additional signal peptides useful for mammalian hosts include mouse signal peptides. In some embodiments, a synthetic mouse IG signal peptide finds use (e.g., SEQ ID NOS: 3381 and 3382). 
     In some embodiments, the control sequence is a propeptide coding region that codes for an amino acid sequence positioned at the amino term of a polypeptide. The resultant polypeptide is referred to as a “proenzyme,” “propolypeptide,” or “zymogen,” in some cases). A propolypeptide can be converted to a mature active polypeptide by catalytic or autocatalytic cleavage of the propeptide from the propolypeptide. The propeptide coding region includes, but is not limited to the genes for  Bacillus subtilis  alkaline protease (aprE),  Bacillus subtilis  neutral protease (nprT),  Saccharomyces cerevisiae  alpha-factor,  Rhizomucor miehei  aspartic proteinase, and  Myceliophthora thermophila  lactase (See e.g., WO 95/33836). Where both signal peptide and propeptide regions are present at the amino terminus of a polypeptide, the propeptide region is positioned next to the amino terminus of a polypeptide and the signal peptide region is positioned next to the amino terminus of the propeptide region. 
     In some embodiments, regulatory sequences are also utilized. These sequences facilitate the regulation of the expression of the polypeptide relative to the growth of the host cell. Examples of regulatory systems are those which cause the expression of the gene to be turned on or off in response to a chemical or physical stimulus, including the presence of a regulatory compound. In prokaryotic host cells, suitable regulatory sequences include, but are not limited to the lac, tac, and trp operator systems. In yeast host cells, suitable regulatory systems include, but are not limited to the ADH2 system or GAL1 system. In filamentous fungi, suitable regulatory sequences include, but are not limited to the TAKA alpha-amylase promoter,  Aspergillus niger  glucoamylase promoter, and  Aspergillus oryzae  glucoamylase promoter. 
     In another aspect, the present invention also provides a recombinant expression vector comprising a polynucleotide encoding an engineered GAA polypeptide, and one or more expression regulating regions such as a promoter and a terminator, a replication origin, etc., depending on the type of hosts into which they are to be introduced. in some embodiments, the various nucleic acid and control sequences described above are joined together to produce a recombinant expression vector which includes one or more convenient restriction sites to allow for insertion or substitution of the nucleic acid sequence encoding the variant GAA polypeptide at such sites. Alternatively, the polynucleotide sequence(s) of the present invention are expressed by inserting the polynucleotide sequence or a nucleic acid construct comprising the polynucleotide sequence into an appropriate vector for expression. In creating the expression vector, the coding sequence is located in the vector so that the coding sequence is operably linked with the appropriate control sequences for expression. 
     The recombinant expression vector may be any suitable vector (e.g., a plasmid or virus including but not limited to adenovirus (AV), adeno-associated virus (AAV), lentivirus (LV), and non-viral vectors, such as liposomes), that can be conveniently subjected to recombinant DNA procedures and can result in the expression of the variant GAA polynucleotide sequence. The choice of the vector will typically depend on the compatibility of the vector with the host cell into which the vector is to be introduced. The vectors may he linear or closed circular plasmids. Indeed, it is not intended that the present invention be limited to any specific vector. 
     In some embodiments, the expression vector is an autonomously replicating vector (i.e., a vector that exists as an extra-chromosomal entity, the replication of which is independent of chromosomal replication, such as a plasmid, an extra-chromosomal element, a minichromosome, or an artificial chromosome). The vector may contain any means for assuring self-replication. In some alternative embodiments, the vector may be one which, when introduced into the host cell, is integrated into the genome and replicated together with the chromosome(s) into which it has been integrated. Furthermore, a single vector or plasmid or two or more vectors or plasmids which together contain the total DNA to be introduced into the genome of the host cell, or a transposon may be used. 
     In some embodiments, the expression vector is pDH. A plasmid map of this vector containing SEQ ID NO:1 is provided in  FIG. 9 . The sequence of this plasmid is provided as SEQ ID NO: 3379. A plasmid map of this vector containing a beta-lactamase staffer sequence is provided in  FIG. 10 . The sequence of this plasmid is provided as SEQ ID NO: 3380. It is contemplated that the pDH vector will find use in expression of various genes, including but not limited to the polynucleotide sequences encoding the acid alpha-glucosidases provided herein. Indeed, it is contemplated that the stater sequence (or SEQ ID NO: 1 present in SEQ ID NO: 3379) will he substituted with any suitable gene of interest. 
     In some embodiments, the expression vector preferably contains one or more selectable markers, which permit easy selection of transformed cells. A “selectable marker” is a gene the product of which provides for biocide or viral resistance, resistance to heavy metals, prototrophy to auxotrophs, and the like. Examples of bacterial selectable markers include, but are not limited to the dal genes from  Bacillus subtilis  or  Bacillus licheniformis , or markers, which confer antibiotic resistance such as ampicillin, kanamycin, chloramphenicol or tetracycline resistance. Suitable markers for yeast host cells include, but are not limited to ADE2, HIS3, LEU2, LYS2, MET3, TRP1, and URA3. Selectable markers for use in a filamentous fungal host cell include, but are not limited to, amdS (acetamidase), argB (ornithine carbamoyltransferases), bar (phosphinothricin acetyltransferase), hph (hygromycin phosphotransferase), niaD (nitrate reductase), pyrG (orotidine-5′-phosphate decarboxylase), sC (sulfate adenyltransferase), and trpC (anthranilate synthase), as well as equivalents thereof. In another aspect, the present invention provides a host cell comprising a polynucleotide encoding at least one engineered GAA polypeptide of the present application, the polynucleotide being operatively linked to one or more control sequences for expression of the engineered GAA enzyme(s) in the host cell. Host cells for use in expressing the polypeptides encoded by the expression vectors of the present invention are well known in the art and include but are not limited to, bacterial cells, such as  E. coli, Vibrio fluvialis, Streptomyces  and  Salmonella typhimurium  cells, fungal cells, such as yeast cells (e.g.,  Saccharomyces cerevisiae  and  Pichia pastoris  [ATCC Accession No. 201178]) ; insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells (e.g., CHO, CHO-K1, COS, and BHK), and human cells (e.g., HEK293T, human fibroblast, THP-1, Jurkat and Bowes melanoma cell lines); and plant cells. 
     Accordingly, in another aspect, the present invention provides methods for producing the engineered GAA polypeptides, where the methods comprise culturing a host cell capable of expressing a polynucleotide encoding the engineered GAA polypeptide under conditions suitable for expression of the polypeptide. In some embodiments, the methods further comprise the steps of isolating and/or purifying the GAA polypeptides, as described herein. 
     Appropriate culture media and growth conditions for the above-described host cells are well known in the art. Polynucleotides for expression of the GAA polypeptides may be introduced into cells by various methods known in the art. Techniques include, among others, electroporation, biolistic particle bombardment, liposome mediated transfection, calcium chloride transfection, and protoplast fusion. 
     The engineered GAA with the properties disclosed herein can be obtained by subjecting the polynucleotide encoding the naturally occurring or engineered GAA polypeptide to mutagenesis and/or directed evolution methods known in the art, and as described herein. An exemplary directed evolution technique is mutagenesis and/or DNA shuffling (See e.g., Stemmer, Proc. Natl. Acad. Sci. USA 91:10747-10751 [1994]; WO 95/22625; WO 97/0078; WO 97/35966; WO 98/27230; WO 00/42651; WO 01/75767 and U.S. Pat. 6,537,746). Other directed evolution procedures that can be used include, among others, staggered extension process (StEP), in vitro recombination (See e.g., Zhao et al., Nat. Biotechnol., 16:258-261 [1998]), mutagenic PCR (See e.g., Caldwell et al., PCR Methods Appl., 3:S136-S140 [1994]), and cassette mutagenesis (See e.g., Black et al., Proc. Natl. Acad. Sci. USA 93:3525-3529 [1996]). 
     For example, mutagenesis and directed evolution methods can be readily applied to polynucleotides to generate variant libraries that can be expressed, screened, and assayed. Mutagenesis and directed evolution methods are well known in the art (See e.g. U.S. Pat. Nos. 5,605,793, 5,811,238, 5,830,721, 5,834,252, 5,837,458, 5,928,905, 6,096,548, 6,117,679, 6,132,970, 6,165,793, 6,180,406, 6,251,674, 6,265,201, 6,277,638, 6,287,861, 6,287,862, 6,291,242, 6,297,053, 6,303,344, 6,309,883, 6,319,713, 6,319,714, 6,323,030, 6,326,204, 6,335,160, 6,335,198, 6,344,356, 6,352,859, 6,355,484, 6,358,740, 6,358,742, 6,365,377, 6,365,408, 6,368,861, 6,372,497, 6,337,186, 6,376,246, 6,379,964, 6,387,702, 6,391,552, 6,391,640, 6,395,547, 6,406,855, 6,406,910, 6,413,745, 6,413,774, 6,420,175, 6,423,542, 6,426,224, 6,436,675, 6,444,468, 6,455,253, 6,479,652, 6,482,647, 6,483,011, 6,484,105, 6,489,146, 6,500,617, 6,500,639, 6,506,602, 6,506,603, 6,518,065, 6,519,065, 6,521,453, 6,528,311, 6,537,746, 6,573,098, 6,576,467, 6,579,678, 6,586,182, 6,602,986, 6,605,430, 6,613,514, 6,653,072, 6,686,515, 6,703,240, 6,716,631, 6,825,001, 6,902,922, 6,917,882, 6,946,296, 6,961,664, 6,995,017, 7,024,312, 7,058,515, 7,105,297, 7,148,054, 7,220,566, 7,288,375, 7,384,387, 7,421,347, 7,430,477, 7,462,469, 7,534,564, 7,620,500, 7,620,502, 7,629,170, 7,702,464, 7,747,391, 7,747,393, 7,751,986, 7,776,598, 7,783,428, 7,795.030, 7,853,410, 7,868,138, 7,783,428, 7,873,477, 7,873,499, 7,904,249, 7,957,912, 7,981,614, 8,014,961, 8,029,988, 8,048,674, 8,058,001, 8,076,138, 8,108,150, 8,170,806, 8,224,580, 8,377,681, 8,383,346, 8,457,903, 8,504,498, 8,589,085, 8,762,066, 8,768,871, 9,593,326, 9,684,771, 9,665,694; and WO 95/22625; WO 97/0078; WO 97/35966; WO 98/27230; WO 00/42651; WO 01/75767; WO 2009/152336, WO 2013/138339, WO 2015/048572, and WO 2015/048573; and all related US and non-US counterparts of these listed patents and applications; Ling et al., Anal. Biochem., 254:157-78 [1997]; Dale et al., Meth. Mol. Biol., 57:369-74 [1996]; Smith, Ann. Rev. Genet., 19:423-462 [1985]; Botstein et al., Science, 229:1193-1201 [1985]; Carter, Biochem. J., 237:1-7 [1986]; Kramer et al., Cell, 38:879-887 [1984]; Wells et al., Gene, 34:315-323 [1985]; Minshull et al., Curr. Op. Chem. Biol., 3:284-290 [1999]; Christians et al., Nat. Biotechnol., 17:259-264 [1999]; Crameri et al., Nature, 391:288-291 [1998]; Crameri, et al., Nat. Biotechnol., 15:436-438 [1997]; Zhang et al., Proc. Nat. Acad. Sci. U.S.A., 94:4504-4509 [1997]; Crameri et al., Nat. Biotechnol, 14:315-319 [1996]; Stemmer, Nature, 370:389-391 [1994]; and Stemmer, Proc. Nat. Acad. Sci. USA, 91:10747-10751 [1994]; all of which are incorporated herein by reference). 
     In some embodiments, the enzyme clones obtained following mutagenesis treatment are screened by subjecting the enzymes to a defined temperature (or other assay conditions) and measuring the amount of enzyme activity remaining after heat treatments or other assay conditions. Clones containing a polynucleotide encoding a GAA polypeptide are then isolated from the gene, sequenced to identify the nucleotide sequence changes (if any), and used to express the enzyme in a host cell. Measuring enzyme activity from the expression libraries can be performed using any suitable method known in the art (e.g., standard biochemistry techniques, such as HPLC analysis). 
     For engineered polypeptides of known sequence, the polynucleotides encoding the enzyme can be prepared by standard solid-phase methods, according to known synthetic methods. In some embodiments, fragments of up to about 100 bases can be individually synthesized, then joined (e.g., by enzymatic or chemical litigation methods, or polymerase mediated methods) to form any desired continuous sequence. For example, polynucleotides and oligonucleotides disclosed herein can be prepared by chemical synthesis using the classical phosphoramidite method (See e.g., Beaucage et al., Tetra. Lett., 22:1859-69 [1981]; and Matthes et ad., EMBO J., 3:801-05 [1984]), as it is typically practiced in automated synthetic methods. According to the phosphoramidite method, oligonucleotides are synthesized (e.g., in an automatic DNA synthesizer), purified, annealed, ligated and cloned in appropriate vectors. 
     Accordingly, in some embodiments, a method for preparing the engineered GAA polypeptide can comprise: (a) synthesizing a polynucleotide encoding a polypeptide comprising an amino acid sequence selected from the amino acid sequence of any variant provided in Table 3-1, 3-2, 4-1, 6-1, 10-1, 10-2, 12-1, 13-1, 13-2, 14-1, 14-2, 15-1, 16-1, 17-1, 17-2, 17-3, 17-4, 17-5, 17-6, 17-7, 17-8, and/or 17-9, as well as SEQ ID NOS: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104, and (b) expressing the GAA polypeptide encoded by the polynucleotide. In some embodiments of the method, the amino acid sequence encoded by the polynucleotide can optionally have one or several (e.g., up to 3, 4, 5, or up to 10) amino acid residue deletions, insertions and/or substitutions. In some embodiments, the amino acid sequence has optionally 1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 1-15, 1-20, 1-21, 1-22, 1-23, 1-24, 1-25, 1-30, 1-35, 1-40, 1-45, or 1-50 amino acid residue deletions, insertions and/or substitutions. In some embodiments, the amino acid sequence has optionally 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 30, 35, 40, 45, or 50 amino acid residue deletions, insertions and/or substitutions. In some embodiments, the amino acid sequence has optionally 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 20, 21, 22, 23, 24, or 25 amino acid residue deletions, insertions and/or substitutions. In some embodiments, the substitutions can be conservative or non-conservative substitutions. 
     The expressed engineered GAA polypeptide can be measured for any desired improved property (e.g., activity, selectivity, stability, acid tolerance, protease sensitivity, etc.), using any suitable assay known in the art, including but not limited to the assays and conditions described herein. 
     In some embodiments, any, some, or all of the engineered GAA polypeptides expressed in a host cell are recovered from the cells and/or the culture medium using any one or more of the well-known techniques for protein purification, including, among others, lysozyme treatment, sonication, filtration, salting-out, ultra-centrifugation, and chromatography. 
     Chromatographic techniques for isolation of the GAA polypeptides include, among others, reverse phase chromatography high performance liquid chromatography, ion exchange chromatography, hydrophobic interaction chromatography, gel electrophoresis, and affinity chromatography. Conditions for purifying a particular enzyme depends, in part, on factors such as net charge, hydrophobicity, hydrophilicity, molecular weight, molecular shape, etc., and will be apparent to those having skill in the art. In some embodiments, affinity techniques may be used to isolate the improved variant GAA enzymes. In some embodiments utilizing affinity chromatography purification, any antibody which specifically binds the variant GAA polypeptide finds use. For the production of antibodies, various host animals, including but not limited to rabbits, mice, rats, etc., are immunized by injection with a GAA polypeptide (e.g., a GAA variant), or a fragment thereof. In some embodiments, the GAA polypeptide or fragment is attached to a suitable carrier, such as BSA, by means of a side chain functional group or linkers attached to a side chain functional group. 
     In some embodiments, the engineered GAA polypeptide is produced in a host cell by a method comprising culturing a host cell (e.g.,  S. cerevisiae, Daucus carota, Nicotiana tabacum, H. sapiens  [e.g., HEK293T], or  Cricetulus griseus  [e.g., CHO]) comprising a polynucleotide sequence encoding an engineered GAA polypeptide as described herein under conditions conducive to the production of the engineered GAA polypeptide and recovering the engineered GAA polypeptide from the cells and/or culture medium. 
     In some embodiments, the engineered GAA polypeptide is produced in a host cell by a method comprising culturing a host cell comprising a polynucleotide sequence encoding an engineered GAA polypeptide as described herein under conditions conducive to the production of the engineered GAA polypeptide and recovering the engineered GAA polypeptide from the cells and/or culture medium. 
     In some preferred embodiments, the invention encompasses a method of producing an engineered GAA polypeptide comprising culturing a recombinant bacterial cell comprising a polynucleotide sequence encoding an engineered GAA polypeptide having at least 85% ,90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to reference sequences SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104, and one or more amino acid residue differences as compared to SEQ ID NO: 2, 6, 8, 12, 14, 16, 18, 20, 946, 1956, 2496, 2880, and/or 3104, and/or combinations thereof when aligned, under suitable culture conditions to allow the production of the engineered GAA polypeptide and optionally recovering the engineered GAA polypeptide from the culture and/or cultured bacterial cells. 
     In some embodiments, once the engineered GAA polypeptides are recovered from the recombinant host cells or cell culture and they are further purified by any suitable method(s) known in the art. In some additional embodiments, the purified GAA polypeptides are combined with other ingredients and compounds to provide compositions and formulations comprising the engineered GAA polypeptide as appropriate for different applications and uses (e.g., pharmaceutical compositions). 
     Compositions: 
     The present invention provides engineered GAA polypeptides suitable for use in pharmaceutical and other compositions, such as dietary/nutritional supplements, as well as for other purposes. 
     Pharmaceutical Compositions: 
     Depending on the mode of administration, the compositions comprising a therapeutically effective amount of an engineered GAA according to the present invention are in the form of a solid, semi-solid, gel, or liquid. In some embodiments, the compositions include other pharmaceutically acceptable components such as diluents, buffers, excipients, salts, emulsifiers, preservatives, stabilizers, fillers, and other ingredients. Details on techniques for formulation and administration are well known in the art and described in the literature. 
     In some embodiments, the engineered GAA polypeptides are formulated for use in oral pharmaceutical compositions. Any suitable format for use in delivering the engineered GAA polypeptides find use in the present invention, including but not limited to pills, tablets, gel tabs, capsules, lozenges, dragees, powders, soft gels, sol-gels, gels, emulsions, implants, patches, sprays, ointments, liniments, creams, pastes, jellies, paints, aerosols, chewing gums, demulcents, sticks, suspensions (including but not limited to oil-based suspensions, oil-in water emulsions, etc.), slurries, syrups, controlled release formulations, suppositories, etc. In some embodiments, the engineered GAA polypeptides are provided in a format suitable for injection (i.e., in an injectable formulation). In some embodiments, the engineered GAA polypeptides are provided in biocompatible matrices such as sol-gels, including silica-based (e.g., oxysilane) sol-gels. In some embodiments, the engineered GAA polypeptides are encapsulated. In some alternative embodiments, the engineered GAA polypeptides are encapsulated in nanostructures (e.g., nanotubes, nanotubules, nanocapsules, or microcapsules, microspheres, liposomes, etc.). Indeed, it is not intended that the present invention be limited to any particular delivery formulation and/or means of delivery. It is intended that the engineered GAA polypeptides be administered by any suitable means known in the art, including but not limited to parenteral, oral, topical, transdermal, intranasal, intraocular, intrathecal, via implants, etc. 
     In some embodiments, the engineered GAA polypeptides are chemically modified by glycosylation, pegylation (i.e., modified with polyethylene glycol [PEG] or activated PEG, etc.) or other compounds (See e.g., Ikeda, Amino Acids 29:283-287 [2005]; U.S. Pat. Nos. 7,531,341, 7,534,595, 7,560,263, and 7,53,653; US Pat. Appln. Publ. Nos. 2013/0039898, 2012/0177722, etc.). Indeed, it is not intended that the present invention be limited to any particular delivery method and/or mechanism. 
     In some additional embodiments, the engineered GAA polypeptides are provided for delivery to cells or tissues via gene therapy, including viral delivery vectors, including but not limited to adenovirus (AV), adeno-associated virus (AAV), lentivirus (LV), or non-viral vectors (e.g., liposomes). In some embodiments, the engineered GAA polypeptides are provided for delivery to cells or tissues via mRNA therapy following formulation of polyribonucleotide sequences in a encapsulated delivery, such as liposomes. In some additional embodiments, the engineered GAA polypeptides are provided for delivery to cells or tissues via cell therapy, where the polynucleotide sequence encoding the engineered GAA polypeptides is introduced into exogenous cell and that cell (or cells) are introduced into a recipient (e.g., a patient exhibiting or at risk for developing Pompe disease). 
     In some additional embodiments, the engineered GAA polypeptides are provided in formulations comprising matrix-stabilized enzyme crystals. In some embodiments, the formulation comprises a cross-linked crystalline engineered GAA enzyme and a polymer with a reactive moiety that adheres to the enzyme crystals. The present invention also provides engineered GAA polypeptides in polymers. 
     In some embodiments, compositions comprising the engineered GAA polypeptides of the present invention include one or more commonly used carrier compounds, including but not limited to sugars (e.g., lactose, sucrose, mannitol, and/or sorbitol), starches (e.g., corn, wheat, rice, potato, or other plant starch), cellulose (e.g., methyl cellulose, hydroxypropylmethyl cellulose, sodium carboxy-methylcellulose), gums (e.g., arabic, tragacanth, guar, etc.), and/or proteins (e.g,. gelatin, collagen, etc.). Additional components in oral formulations may include coloring and or sweetening agents (e.g., glucose, sucrose, and mannitol) and lubricating agents (e.g., magnesium stearate), as well as enteric coatings (e.g., methacrylate polymers, hydroxyl propyl methyl cellulose phthalate, and/or any other suitable enteric coating known in the art). In some embodiments, disintegrating or solubilizing agents are included (e.g., cross-linked polyvinyl pyrrolidone, agar, alginic acid or salts thereof, such as sodium alginate). In some embodiments, the engineered GAA polypeptide are be combined with various additional components, including but not limited to preservatives, suspending agents, thickening agents, wetting agents, alcohols, fatty acids, and/or emulsifiers, particularly in liquid formulations. In some embodiments, the engineered GAA polypeptides are administered to subjects in combination with other compounds, molecules, and/or materials used in the treatment of Pompe disease, including but not limited to pharmacological chaperones, as well as any other suitable compounds. In some additional embodiments, the pharmaceutical composition is suitable for parenteral injection into a human. In some embodiments, the pharmaceutical composition comprises a pill, tablet, capsule, or gelcap that further comprises an enteric coating. 
     In some embodiments, the present invention provides engineered GAA polypeptides suitable for use in decreasing the concentration of glycogen in tissues. The dosages of engineered GAA polypeptide(s) administered to an animal depend upon the condition or disease, the general condition of the animal, and other factors known to those in the art. In some embodiments, the compositions are intended for single or multiple administrations to an animal. In some embodiments, it is contemplated that the concentration of engineered GAA polypeptide(s) in the composition(s) administered to an animal (e.g., a human with Pompe disease) is sufficient to effectively treat, ameliorate and/or prevent the symptoms of disease (e.g., Pompe disease and/or Pompe disease-related conditions, diseases and/or symptoms), In some embodiments, the engineered GAA polypeptides are administered in combination with other pharmaceutical and/or dietary compositions. 
     The foregoing and other aspects of the invention may be better understood in connection with the following non-limiting examples. The examples are provided for illustrative purposes only and are not intended to limit the scope of the present invention in any way. 
     Experimental 
     The following Examples, including experiments and results achieved, are provided for illustrative purposes only and are not to be construed as limiting the present invention. 
     In the experimental disclosure below, the following abbreviations apply; ppm (parts per million); M (molar); mM (millimolar), uM and pM (micromolar); nM (nanomolar); mol (moles); gm and g (gram); mg (milligrams); ug and pg (micrograms); L and l (liter); ml and mL (milliliter); cm (centimeters); mm (millimeters); um and μm (micrometers); sec. (seconds); min(s) (minute(s)); h(s) and hr(s) (hour(s)); U (units); MW (molecular weight); rpm (rotations per minute); ° C. (degrees Centigrade); CDS (coding sequence); DNA (deoxyribonucleic acid); RNA (ribonucleic acid); E. coli W3110 (commonly used laboratory  E. coli  strain, available from the Coli Genetic Stock Center [CGSC], New Haven, Conn.); DPBS (Dulbecco&#39;s phosphate buffered saline); LB (Luria-Burtani); TB (terrific broth); 4-MUGIu (4-methylumbelliferyl α-D-glucopyranoside; SD-Ura (single drop out medium without uracil); HPLC (high pressure liquid chromatography); SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis); MU-Glu (4-methylumbelliferyl α-D-glucopyranoside); IPTG (isopropyl β-D-1-thiogalactopyranoside); PMBS (polymyxin B sulfate); FIOPC (fold improvements over positive control); PBMC (peripheral blood mononuclear cells); LB (Luria broth); MeOH (methanol); Axygen (Axygen, Inc., Union City, Calif.); Athens Research (Athens Research Technology, Athens, Ga.); ProSpec (ProSpec Tany Technogene, East Brunswick, N.J.); Sigma-Aldrich (Sigma-Aldrich, St. Louis, Mo.); Ram Scientific (Ram Scientific, Inc., Yonkers, N.Y.); Pall Corp. (Pall, Corp., Pt. Washington, N.Y.); Millipore (Millipore, Corp., Billerica Mass.); Difco (Difco Laboratories, BD Diagnostic Systems, Detroit, Mich.); Molecular Devices (Molecular Devices, LLC, Sunnyvale, Calif.); Kuhner (Adolf Kuhner, AG, Basel, Switzerland); Microfluidics (Microfluidics Corp., Westwood, Mass.); Thermotron (Thermotron, Inc., Holland, Mi.); Cambridge Isotope Laboratories, (Cambridge Isotope Laboratories, Inc., Tewksbury, Mass.); Applied Biosystems (Applied Biosystems, part of Life Technologies, Corp., Grand Island, N.Y.); Greiner Bio-One (Greiner Bio-One North America, Monroe, N.C.); Agilent (Agilent Technologies, Inc., Santa Clara, Calif.); Thermo Scientific (part of Thermo Fisher Scientific, Waltham, Mass.); Corning (Corning, Inc., Palo Alto, Calif.); Megazyme (Megazyme International, Wicklow, Ireland); Enzo (Enzo Life Sciences, Inc., Farmingdale, N.Y.); GE Healthcare (GE Healthcare Bio-Sciences, Piscataway, N.J.); Pierce (Pierce Biotechnology (now part of Thermo Fisher Scientific), Rockford, Ill.); Phenomenex (Phenomenex, Inc., Torrance, Calif.); Optimal (Optimal Biotech Group, Belmont, Calif.); and Bio-Rad (Bio-Rad Laboratories, Hercules, Calif.). 
     EXAMPLE 1 
     GAA Gene Acquisition and Construction of Expression Vectors 
     In this Example, GAA gene acquisition and expression vector construction are described. A synthetic gene coding for a WT human GAA (Uniprot ID P10253) with the native signal peptide removed was designed for optimized gene expression in  Saccharomyces cerevisiae  and fused to the yeast MFa signal peptide sequence (SEQ ID NO: 3383) to generate the gene sequence represented by SEQ ID NO:2, which was cloned into the yeast expression vector pYT-72, as previously described (See e.g. US Pat. Appln. Publn. No. 2017/0360900 A1). Recombination cloning and gene expression were performed in  S. cerevisiae  strain INVSc1. Directed evolution techniques were used to generate libraries of gene variants from this plasmid construct (See e.g., U.S. Pat. No. 8,383,346 and WO2010/144103). 
     For secreted expression and transient transfection in mammalian cells, a chimeric GAA expression construct encoding the synthetic mouse IG signal peptide (residues 1-19 of Uniprot accession number: A0N1R5; SEQ ID NO: 3381) fused to a synthetic gene coding for the different GAA variants was generated as follows. In some embodiments, the synthetic GAA gene variants are based on a GAA sequence that is codon-optimized for yeast (SEQ ID NO: 3), while in some alternative embodiments, the synthetic GAA variants are based on a GAA sequence that is codon-optimized for mammalian (SEQ ID NO: 5) expression. Oligonucleotides containing restriction enzyme flanks to enable cloning into either the BamHI/XhoI site or HindIII/XhoI site were used to amplify a fragment coding for the synthetic mouse IG signal peptide (SEQ ID NOS: 3381 and 3382) and the coding sequence for the mature form of GAA. For mammalian expression, the PCR product was ligated into the linearized vector pcDNA3.1(+) either at the BamHI/XhoI site or HindIII/XhoI site (Invitrogen). Directed evolution was used to generate specific gene variants derived from SEQ ID NOS: 18 to 828, within the pcDNA3.1(+) plasmid construct (See e.g., U.S. Pat. No. 8,383,346 and WO2010/144103, each of which is incorporated by reference in its entirety). 
     The pDH vector was generated to optimize for vector copy number, desired selection drug, and base pair length, to enable compatibility with library variant generation. For mammalian expression, the PCR product was ligated into the linearized vector pDH either at the BamHI/XhoI site or HindIII/NhoI site. Directed evolution was used to generate specific gene variants (SEQ ID NOS: 829 to 3378) derived from SEQ ID NO: 20, within the pDH plasmid construct. A plasmid map for pDH containing WT GAA is shown in  FIG. 9  and the plasmid sequence is provided as SEQ ID NO: 3379. In addition, a plasmid map for pDH containing a beta-lactamase (bla) stuffer sequence is provided in  FIG. 10  and the sequence is provided as SEQ ID NO: 3380. 
     In some experiments, expression of GAA variants was performed using a linear PCR amplification product of the expression cassettes described above (i.e., a chimeric expression construct composed of the synthetic mouse IG signal peptide (residues 1-19 of Uniprot accession number: A0N1R5; SEQ ID NO: 3381) fused to a synthetic gene coding for the different GAA variants) in pcDNA3.1(+) or pDH. PCR amplification was performed with optimizations generally known by those skilled in the art with primer pair (SEQ ID NOS: 3387 and 3388) for pcDNA3.1(+) and primer pair (SEQ ID NOS: 3385 and 3386; or SEQ ID NOS: 3387 and 3388) for pDH. In some cases, phosphorothioate primers were used. 
     EXAMPLE 2 
     High-Throughput Growth of  Saccharomyces cerevisiae  and GAA Assays 
     In this Example, experiments involving high-throughput growth of cells producing GAA variants, and assays to determine GAA activity are described. 
     High-Throughput (HTP) Growth of  S. cerevisiae    
     Yeast (INVSc1) cells transformed with vectors expressing GAA and GAA variants using the lithium acetate method as known in the art, were selected on SD-Ura agar plates. After 72 h incubation at 30° C., colonies were placed into the wells of AXYGEN® 1.1 ml 96-well deep well plates (Axygen) filled with 200 μl/well SD-Ura broth (2 g/L SD-Ura, 6.8 g/L yeast nitrogen base without amino acids [Sigma Aldrich]), 3.06 g/L sodium dihydrogen phosphate, 0.804 g/L disodium hydrogen phosphate, pH 6.0, supplemented with 6% glucose. The cells were grown for 20-24 hours in a Kuhner shaker (250 rpm, 30° C., and 85% relative humidity). Overnight culture samples (20 μL) were transferred into COSTAR® 96-well deep plates (Corning), filled with 380 μL of SD-ura broth supplemented with 2% glucose. The plates were incubated for 66-84 h in a Kuhner shaker (250 rpm, 30° C., and 85% relative humidity). The cells were then pelleted (4000 rpm×20 mM), and the supernatants (conditioned media) stored at 4° C. until analyzed. 
     HTP-Analysis of Supernatants 
     GAA variant activity was determined by measuring the hydrolysis of 4-methylumbelliferyl α-D-glucopyranoside (4-MUGlu). For the unchallenged assay, 50 μL: of SD-URA conditioned media. produced as described above was mixed with 50 μL of 1 mM 4-MUGIu in McIlvaine Buffer (McIlvaine, J. Biol. Chem., 49:183-186 [1921]), pH 4.5, in a 96-well, black, opaque bottom plate. The reactions were mixed briefly and incubated at 37° C. for 4-24 hours, prior to quenching with 100 μL of 0.5 M sodium carbonate pH 10.5. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader (Molecular Devices), by monitoring fluorescence (Ex. 355 nm, Em. 460 nm). 
     HTP-Analysis of Supernatants Challenged with Neutral Buffer 
     GAA variants were challenged with neutral to near neutral (pH 6.5-7.5) buffer to simulate the pH that the variants encounter in the blood following their administration to a patient. First, 50 μL of GAA variants in SD-URA conditioned media and 50 pL of McIlvaine buffer (pH 6.5-7.4) were added to the wells of a 96-well round bottom plate. The plates were sealed and incubated at 37° C. for 1 h. Then, 50 μL of each challenged sample were mixed with 50 μL of 1 mM 4-MUGlu in McIlvaine buffer pH 4.4. The reactions were mixed briefly and incubated at 37° C. for 4-24 hrs, prior to quenching with 100 μL of 0.5 M sodium carbonate, pH 10.5. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader (Molecular Devices) by monitoring fluorescence (Ex. 355 nm, Em. 460 nm). 
     HTP-Analysis of Supernatants Pretreated with Acid 
     GAA variants were challenged with acidic (pH 3) buffer to simulate the pH that the variants encounter in the lysosome following their administration to a patient. First, 50 μL of GAA variants in SD-URA conditioned media and 50 μL of McIlvaine buffer (pH 3) were added to the wells of a 96-well round bottom plate. The plates were sealed and incubated at 37° C. for 1 h. Then, 50 μL of each challenged sample were mixed with 50 μL of 1 mM 4-MUGIu in McIlvaine buffer pH 4.4. The reactions were mixed briefly and incubated at 37° C. for 4-24 hrs, prior to quenching with 100 μL of 0.5 M sodium carbonate pH 10.5. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader (Molecular Devices) monitoring fluorescence (Ex. 355 nm, Em. 460 nm). 
     HTP-Analysis of Supernatants with Glycogen Substrate 
     The hydrolytic activity of the GAA variants was determined by measuring the hydrolysis of glycogen to glucose. For the unchallenged assay, 504 of SD-URA conditioned media produced as described above was mixed with 50 μL of 5 mM glycogen in pH 4.5 McIlvaine buffer (7.71 mL of 0.2 M Na 2 HPO 4  and 12.29 of 0.1 M citric acid) in a 96-well, black, opaque bottom plate. The reactions were mixed briefly and incubated at 37° C. for 24 hours. After incubation, 20 uL of the glycogen hydrolysis reaction mixtures were mixed with 80 uL of AMPLEX® Red Glucose Assay Kit (Sigma) to determine the glucose content of each reaction. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader (Molecular Devices) by monitoring fluorescence (Ex. 544 nm, Em. 585 nm) 
     EXAMPLE 3 
     GAA and GAA Variants 
     GAA and GAA variant activity was determined by assaying the enzyme activity after a series of independent challenges. The results for all of the variants and the substitutions in each of the polypeptide sequences are reported in reference to SEQ ID NO: 2. These variants were tested for GAA 4-MUGlu activity (Unchallenged Activity FIOPC), after pH 6.5 incubation (pH 6.5 Stability Activity FIOPC), and for glycogen hydrolysis (Glycogen Activity FIOPC), as described in Example 2. Tables 3-1 and 3-2 provide the results of these assays. 
     
       
         
           
               
             
               
                 TABLE 3-1 
               
             
            
               
                   
               
               
                 Activity of GAA Variants Under Various Conditions 1   
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 SEQ 
                 Amino Acid 
                 Un- 
                 pH 6.5 
                   
               
               
                   
                 ID 
                 Differences 
                 challenged 
                 Stability 
                 Glycogen 
               
               
                   
                 NO: 
                 (Relative to 
                 Activity 
                 Activity 
                 Activity 
               
               
                   
                 (nt/aa) 
                 SEQ ID NO: 2) 
                 FIOPC 
                 FIOPC 
                 FIOPC 
               
               
                   
                   
               
               
                   
                 21/22 
                 A276F 
                 ++ 
                 +++ 
                 + 
               
               
                   
                 23/24 
                 A276Y 
                 +++ 
                 +++ 
                 + 
               
               
                   
                 25/26 
                 A418E/H499R 
                   
                   
                 ++ 
               
               
                   
                 27/28 
                 A418R 
                   
                 ++ 
                 + 
               
               
                   
                 29/30 
                 A437S 
                 + 
                 + 
                   
               
               
                   
                 31/32 
                 A444T 
                   
                 ++ 
                 + 
               
               
                   
                 33/34 
                 A489R 
                 ++ 
                 ++ 
                 +++ 
               
               
                   
                 35/36 
                 A547G 
                 + 
                 ++ 
                   
               
               
                   
                 37/38 
                 A750P 
                 + 
                 + 
                 + 
               
               
                   
                 39/40 
                 A753T 
                 + 
                 + 
                 + 
               
               
                   
                 41/42 
                 C930R 
                 + 
                 + 
                 + 
               
               
                   
                 43/44 
                 C944G 
                 + 
                 + 
                 + 
               
               
                   
                 45/46 
                 C944R 
                 + 
                 + 
                 + 
               
               
                   
                 47/48 
                 D274G 
                   
                 ++ 
                   
               
               
                   
                 49/50 
                 E137P 
                 + 
                 ++ 
                 + 
               
               
                   
                 51/52 
                 E463A 
                   
                 ++ 
                 + 
               
               
                   
                 53/54 
                 F27P 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 55/56 
                 F27P/C944W 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 57/58 
                 F27R 
                   
                 +++ 
                 ++ 
               
               
                   
                 59/60 
                 G426R 
                   
                 ++ 
                 + 
               
               
                   
                 61/62 
                 G820E 
                   
                 ++ 
                 + 
               
               
                   
                 63/64 
                 I375E 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 65/66 
                 K471Q/A478S 
                 + 
                 + 
                 + 
               
               
                   
                 67/68 
                 K471S 
                 + 
                 + 
                   
               
               
                   
                 69/70 
                 K581G 
                 + 
                   
                 + 
               
               
                   
                 71/72 
                 K581T 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 73/74 
                 K725N/V732I 
                 + 
                 ++ 
                   
               
               
                   
                 75/76 
                 K88G 
                 ++ 
                 ++ 
                   
               
               
                   
                 77/78 
                 K88S 
                   
                 ++ 
                   
               
               
                   
                 79/80 
                 K895R 
                   
                 ++ 
                 ++ 
               
               
                   
                 81/82 
                 L109G/G842E 
                 ++ 
                 +++ 
                 + 
               
               
                   
                 83/84 
                 L109P 
                 + 
                 + 
                 + 
               
               
                   
                 85/86 
                 L28P 
                 ++ 
                 + 
                 + 
               
               
                   
                 87/88 
                 L28R 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 89/90 
                 L28S 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 91/92 
                 L29T/A478T 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 93/94 
                 L642M 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 95/96 
                 L642Q 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 97/98 
                 L642S 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 99/100 
                 L670N 
                   
                 ++ 
                   
               
               
                   
                 101/102 
                 L871E 
                   
                 ++ 
                 + 
               
               
                   
                 103/104 
                 L934R 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 105/106 
                 M138A 
                 + 
                 + 
                 + 
               
               
                   
                 107/108 
                 N527R 
                   
                 ++ 
                 + 
               
               
                   
                 109/110 
                 Q107G 
                   
                 ++ 
                 + 
               
               
                   
                 111/112 
                 Q107P 
                   
                   
                 + 
               
               
                   
                 113/114 
                 Q110G 
                   
                 +++ 
                 + 
               
               
                   
                 115/116 
                 Q110L 
                   
                 ++ 
                 + 
               
               
                   
                 117/118 
                 Q113S 
                 + 
                 + 
                 ++ 
               
               
                   
                 119/120 
                 Q247R 
                   
                 + 
                 + 
               
               
                   
                 121/122 
                 Q421S 
                   
                   
                 + 
               
               
                   
                 123/124 
                 R403W 
                 + 
                 + 
                 + 
               
               
                   
                 125/126 
                 R414P 
                 + 
                 + 
                 ++ 
               
               
                   
                 127128 
                 R455V 
                   
                   
                 ++ 
               
               
                   
                 129/130 
                 R786P 
                   
                 ++ 
                 + 
               
               
                   
                 131/132 
                 R786Y 
                   
                 ++ 
                   
               
               
                   
                 133/134 
                 R862G 
                   
                 ++ 
                 + 
               
               
                   
                 135/136 
                 S135A 
                   
                 ++ 
                 + 
               
               
                   
                 137/138 
                 S135Q 
                 + 
                 +++ 
                 ++ 
               
               
                   
                 139/140 
                 S476A 
                   
                 ++ 
                 + 
               
               
                   
                 141/142 
                 S476H 
                   
                 ++ 
                   
               
               
                   
                 143/144 
                 S668H 
                 ++ 
                 ++++ 
                   
               
               
                   
                 145/146 
                 T148G 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 147/148 
                 T148Y 
                 + 
                 + 
                   
               
               
                   
                 149/150 
                 T150G 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 151/152 
                 T278A 
                 + 
                 + 
                   
               
               
                   
                 153/154 
                 T278G 
                   
                 ++ 
                 + 
               
               
                   
                 155/156 
                 T692Q 
                 + 
                 + 
                 + 
               
               
                   
                 157/158 
                 T897V 
                   
                 ++ 
                   
               
               
                   
                 159/160 
                 V30G 
                   
                   
                 ++ 
               
               
                   
                 161/162 
                 V30K 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 163/164 
                 V30T 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 165/166 
                 W610A 
                 ++ 
                 + 
                   
               
               
                   
                 167/168 
                 W610G 
                 ++ 
                 ++ 
                   
               
               
                   
                 169/170 
                 W610S 
                 + 
                 ++ 
                 + 
               
               
                   
                   
               
               
                   
                   1 All activities were determined relative to the reference polypeptide of SEQ ID NO: 2. Levels of increased activity are defined as follows: 
               
               
                   
                 ““+”” = 0.9 to 1.1; 
               
               
                   
                 “++” &gt; 1.1; 
               
               
                   
                 “++++” &gt; 2; and 
               
               
                   
                 “++++” &gt; 3.5. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3-2 
               
             
            
               
                   
               
               
                 Activity of GAA Variants Relative to SEQ ID NO: 2 1   
               
            
           
           
               
               
               
               
               
            
               
                 SEQ  
                   
                 Un- 
                 pH 6.5 
                   
               
               
                 ID 
                   
                 challenged 
                 Stability 
                 Glycogen 
               
               
                 NO: 
                 Amino Acid Differences 
                 Activity 
                 Activity 
                 Activity 
               
               
                 (nt/aa) 
                 (Relative to SEQ ID NO: 2) 
                 FIOPC 
                 FIOPC 
                 FIOPC 
               
               
                   
               
               
                 171/172 
                 G280D/S402A/V536I/D928T 
                   
                   
                 ++ 
               
               
                 173/174 
                 H191R/G280D/S402A/R414G/ 
                 + 
                 + 
                 ++ 
               
               
                   
                 A444P/G465E/G842S/D928T 
                   
                   
                   
               
               
                 175/176 
                 L275V/A281V/S671N 
                 ++ 
                 + 
                 ++ 
               
               
                 177/178 
                 K106P/H191R/R414G/A444P/ 
                 ++ 
                 + 
                 + 
               
               
                   
                 E522V/D928T/C944S 
                   
                   
                   
               
               
                 179/180 
                 H191R/G280D/R414G/A444P/ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 A489D/D500A/E522V/G842S/ 
                   
                   
                   
               
               
                   
                 D928T/C944S 
                   
                   
                   
               
               
                 181/182 
                 K106P/H191R/R414G/A489D/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 D928T/C944S 
                   
                   
                   
               
               
                 183/184 
                 L275M/A281V/S402A/M431V/ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 M507L/I518V/W610R/S668D 
                   
                   
                   
               
               
                 185/186 
                 L275M/M507L/A547G/S668D/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 L669H/S671N 
                   
                   
                   
               
               
                 187/188 
                 L275M/M431V/V638I 
                 ++ 
                 ++ 
                 ++ 
               
               
                 189/190 
                 A281V/S402A/I518V/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 A547G/S668D 
                   
                   
                   
               
               
                 191/192 
                 L275V/I518V/S671N 
                 ++ 
                 ++ 
                 + 
               
               
                 193/194 
                 L275V/M431V/M507L/1518V/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 A547G/S668D/L669H/S671N 
                   
                   
                   
               
               
                 195/196 
                 S402A/M431V/I518V/W610R 
                 ++ 
                 ++ 
                 + 
               
               
                 197/198 
                 K106P/H191R/G280D/S402A/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 R414G/A444P/S727P 
                   
                   
                   
               
               
                 199/200 
                 M431V/M507L/I518V/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 L669H/S671N 
                   
                   
                   
               
               
                 201/202 
                 L275V/R377K/S402A/M507L/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 I518V/L669H/S671N/V715G 
                   
                   
                   
               
               
                 203/204 
                 H191R/R414G/E522V/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 G842S/C944S 
                   
                   
                   
               
               
                 205/206 
                 H191R/G280D/R414G/A489D/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 G842S/D928T/C944S 
                   
                   
                   
               
               
                 207/208 
                 L275M/A281V/W610R/V638I/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 S668D/L669H 
                   
                   
                   
               
               
                 209/210 
                 A196V/S402A/M431V/A547G/ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 W610R/V638I 
                   
                   
                   
               
               
                 211/212 
                 H191R/G280D/S402A/R414G/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 A444P/A489D/D500A/C944S 
                   
                   
                   
               
               
                 213/214 
                 L275V/S402A/V638I/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 L669H/S671N 
                   
                   
                   
               
               
                 215/216 
                 L29Q/L240I/A596P/ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 S668D/I869L 
                   
                   
                   
               
               
                 217/218 
                 K106P/G280D/S402A/R414G/ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 A444P/A489D/S727P/C944S 
                   
                   
                   
               
               
                 219/220 
                 L29Q/L240I/A596S/S668D/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 H700F/I744V/I869T 
                   
                   
                   
               
               
                 221/222 
                 L218S/S668D/H700F/I869T 
                 ++ 
                 ++ 
                 + 
               
               
                 223/224 
                 M507L/A547G/W610R 
                 ++ 
                 ++ 
                   
               
               
                 225/226 
                 A281V/M431V/M507L/I518V/ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 A547G/W610R/V638I/S668D 
                   
                   
                   
               
               
                 227/228 
                 H191R/G280D/R414G/A444P/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 A489D/E522V/S727P/C944S 
                   
                   
                   
               
               
                 229/230 
                 L275V/S402A/M431V/I518V/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 W610R/V638I/L669H/ 
                   
                   
                   
               
               
                   
                 S671N/P922L 
                   
                   
                   
               
               
                 231/232 
                 L29V/L218S/L240I/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 H700F/I869T 
                   
                   
                   
               
               
                 233/234 
                 A547G/V638I/S668D 
                 ++ 
                 ++ 
                 + 
               
               
                 235/236 
                 H191R/G280D/R414G/C944S 
                 ++ 
                 ++ 
                 + 
               
               
                 237/238 
                 L275V/M431V/M507L/I518V/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 W610R/L669H/S671N 
                   
                   
                   
               
               
                 239/240 
                 L275M/S402A/M431V/M507L/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 A547G/S671N 
                   
                   
                   
               
               
                 241/242 
                 S402A/M431V/A547G/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 V638I/S671N 
                   
                   
                   
               
               
                 243/244 
                 A281V/S402A/M507L/A547G/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 V638I/L669H/S671N 
                   
                   
                   
               
               
                 245/246 
                 L275M/A281V/M507L/A547G/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 L669H/S67IN 
                   
                   
                   
               
               
                 247/248 
                 L275M/M43IV/I518V/A547G/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 V638I/S668D 
                   
                   
                   
               
               
                 249/250 
                 A547G/W610R/V638I/S671N 
                 ++ 
                 ++ 
                 + 
               
               
                 251/252 
                 L275V/M431V/M507L/A547G/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 W610R/V638I/S671N 
                   
                   
                   
               
               
                 253/254 
                 L275M/S402A/M507L/A547G/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 W610R/S671N 
                   
                   
                   
               
               
                 255/256 
                 L275M/A281V/S402AJ1518V/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 A547G/W610R/V638I/S671N 
                   
                   
                   
               
               
                 257/258 
                 A281V/S402A/I518V/A547G/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 W610R/V638I/S668D/L669H 
                   
                   
                   
               
               
                 259/260 
                 L275M/A281V/S402A/A547G/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 W610R/V638I/L669H/S671N 
                   
                   
                   
               
               
                 261/262 
                 L275M/M431V/I518V/W610R/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 V638I/L669H/S671N 
                   
                   
                   
               
               
                 263/264 
                 L29Q/L218S/L240I/S668D/ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 H700F/I744V/I869L 
                   
                   
                   
               
               
                 265/266 
                 A281V/S402A/M507L/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 I518V/A547G/W610R/ 
                   
                   
                   
               
               
                   
                 V638I/L669H/S671N 
                   
                   
                   
               
               
                 267/268 
                 S402A/M431V/I518V/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 A547G/S671N 
                   
                   
                   
               
               
                 269/270 
                 L275V/A281V/S402A/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 M431V/I518V/A547G/ 
                   
                   
                   
               
               
                   
                 W610R/L669H/S671N 
                   
                   
                   
               
               
                 271/272 
                 L224F/S402A/M507L/I518V/ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 A547G/V638I/S668D 
                   
                   
                   
               
               
                 273/274 
                 N180H/S402A/M507L/A547G/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 W610R/S671N 
                   
                   
                   
               
               
                 275/276 
                 L275M/A281V/S402A/M507L/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 I518V/A547G/V638I/ 
                   
                   
                   
               
               
                   
                 L669H/S671N 
                   
                   
                   
               
               
                 277/278 
                 K106P/T150S/T486E/Q749E/ 
                 ++ 
                 +++ 
                 ++ 
               
               
                   
                 E793K/R883H/Q894G 
                   
                   
                   
               
               
                 279/280 
                 L275V/A281V/M431V/I518V/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 A547G/V638I/L669H/S671N 
                   
                   
                   
               
               
                 281/282 
                 L275V/S402A/A547G/W610R/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 V638I/L669H/S67IN 
                   
                   
                   
               
               
                 283/284 
                 L275M/S402A/A547G/V638I/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 L669H/S671N 
                   
                   
                   
               
               
                 285/286 
                 K106P/T150S/T486E/N527D/ 
                 ++ 
                 +++ 
                 ++ 
               
               
                   
                 A750P/E793K 
                   
                   
                   
               
               
                 287/288 
                 S402A/M431V/I518V/A547G/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 W610R/S668D 
                   
                   
                   
               
               
                 289/290 
                 T150S/L218S/N527D/ 
                 ++ 
                 +++ 
                 ++ 
               
               
                   
                 Q749E/E793K 
                   
                   
                   
               
               
                 291/292 
                 L275V/M507L/I518V/A547G/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 V638I/L669H/S671N 
                   
                   
                   
               
               
                 293/294 
                 N180H/S402A/M431V/ 
                 ++ 
                 ++ 
                   
               
               
                   
                 M507L/A547G/W610R/ 
                   
                   
                   
               
               
                   
                 L669H/S671N/E793G 
                   
                   
                   
               
               
                 295/296 
                 L275V/M507L/I518V/A547G/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 W610R/V638I/S668D/L669H 
                   
                   
                   
               
               
                 297/298 
                 L275V/S402A/M507L/A547G/ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 W610R/V638I/S668D/L669H 
                   
                   
                   
               
               
                 299/300 
                 M507L/A547G/V638I/ 
                 +++ 
                 ++ 
                 + 
               
               
                   
                 L669H/S671N 
                   
                   
                   
               
               
                 301/302 
                 K106P/T150S/N169S/L218S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 Q749E/P800A 
                   
                   
                   
               
               
                 303/304 
                 T150S/R414G/T486E/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 Q749E/A750P/E793K 
                   
                   
                   
               
               
                 305/306 
                 K106P/T150S/L218S/R414G/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 T486E/L642F/ 
                   
                   
                   
               
               
                   
                 A750P/E793K/R883H 
                   
                   
                   
               
               
                 307/308 
                 N180H/L275M/S402A/ 
                 +++ 
                 ++ 
                   
               
               
                   
                 I518V/A547G/W610R/ 
                   
                   
                   
               
               
                   
                 V638I/L669H/S671N 
                   
                   
                   
               
               
                 309/310 
                 T150S/L218S/R414G/ 
                 +++ 
                 +++ 
                 + 
               
               
                   
                 Q749E/E793K 
                   
                   
                   
               
               
                 311/312 
                 L275V/M507L/A547G/W610R/ 
                 +++ 
                 ++ 
                 + 
               
               
                   
                 V638I/L669H/S671N 
                   
                   
                   
               
               
                 313/314 
                 T150S/R414G/T486E/N527D/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 A750P/Q894R 
                   
                   
                   
               
               
                 315/316 
                 K106P/T150S/L218S/N527D/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 E793K/Q894G 
                   
                   
                   
               
               
                 317/318 
                 T150S/N169S/L218S/R414G/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 N527D/E793K 
                   
                   
                   
               
               
                 319/320 
                 K106P/T150S/L218S/E793K 
                 +++ 
                 +++ 
                 ++ 
               
               
                 321/322 
                 K106P/T150S/R414G/Q749E/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 A750P/E793K/Q894R 
                   
                   
                   
               
               
                 323/324 
                 K106P/T150S/N169S/N527D/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 Q749E/E793K/R883H 
                   
                   
                   
               
               
                 325/326 
                 L275V/S402A/M507L/A547G/ 
                 +++ 
                 ++ 
                 + 
               
               
                   
                 W610R/V638I/L669H/S671N 
                   
                   
                   
               
               
                 327/328 
                 K106P/T150S/L218S/Q749E/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 A750P/E793K 
                   
                   
                   
               
               
                 329/330 
                 M431V/M507L/I518V/G541E/ 
                 +++ 
                 +++ 
                 + 
               
               
                   
                 A547G/V638I/L669H/S671N 
                   
                   
                   
               
               
                 331/332 
                 T150S/L218S/R414G/T486A/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 A750P/E793K 
                   
                   
                   
               
               
                 333/334 
                 T150S/L218S/Q749E/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 A750P/E793K 
                   
                   
                   
               
               
                 335/336 
                 K106P/T150S/N169S/L218S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 R414G/T486E/Q894R 
                   
                   
                   
               
               
                 337/338 
                 T150S/L218S/R414G/T486E/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 A750P/E793KR883H 
                   
                   
                   
               
               
                 339/340 
                 K106P/T150S/N169S/L218S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 R414G/Q749E/E793K 
                   
                   
                   
               
               
                 341/342 
                 T269N/L275M/M431V/I518V/ 
                 +++ 
                 +++ 
                   
               
               
                   
                 A547G/V638I/S668D/L669H 
                   
                   
                   
               
               
                 343/344 
                 K106P/T150S/R414G/Q749E/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 E793K/Q894R 
                   
                   
                   
               
               
                 345/346 
                 K106P/T150S/L218S/N527D/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 Q749E/A750P/E793K 
                   
                   
                   
               
               
                 347/348 
                 K106P/T150S/N1695/Q749E/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 E793K/R883H/Q894R 
                   
                   
                   
               
               
                 349/350 
                 K106P/T150S/L218S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 E793K/Q894R 
                   
                   
                   
               
               
                 351/352 
                 K106P/T150S/N169S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 L218S/T486E/N527D/ 
                   
                   
                   
               
               
                   
                 Q749E/E793K/Q894R 
                   
                   
                   
               
               
                 353/354 
                 K106P/T150S/L218S/R414G/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 T486E/A750P/E793K/Q894R 
                   
                   
                   
               
               
                 355/356 
                 K106P/T150S/N169S/L2185/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 R414G/T486E/Q749E/ 
                   
                   
                   
               
               
                   
                 E793K/R883H/Q894R 
                   
                   
                   
               
               
                 357/358 
                 K106P/T150S/N1695/L218S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 T486E/R883H 
                   
                   
                   
               
               
                 359/360 
                 K106P/T150S/N169S/L218S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 R414G/T486E/A750P/ 
                   
                   
                   
               
               
                   
                 E793K/R883H/Q894R 
                   
                   
                   
               
               
                 361/362 
                 G36R/K106P/T1505/L218S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 N527D/A750P/R883H/Q894R 
                   
                   
                   
               
               
                 363/364 
                 K106P/T150S/N169S/L218S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 T486E/Q749E/R883H 
                   
                   
                   
               
               
                 365/366 
                 K106P/N169S/V185G/L218S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 R414G/Q749E/A750P/E793K 
                   
                   
                   
               
               
                 367/368 
                 K106P/T150S/P245S/E793K/ 
                 +++ 
                 +++ 
                 +++ 
               
               
                   
                 R883H/Q894R 
                   
                   
                   
               
               
                 369/370 
                 K106P/T150S/N169S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 L218S/R414G/Q749E 
                   
                   
                   
               
               
                   
                 /A750P/E793K/R883H 
                   
                   
                   
               
               
                 373/374 
                 T150S/L2185/Q749E/E793K 
                 +++ 
                 +++ 
                 ++ 
               
               
                 375/376 
                 T150S/L218S/R414G/Q749E/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 A750P/E793K/Q894R 
                   
                   
                   
               
               
                 377/378 
                 K106P/T150S/N169S/R414G/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 T486E/Q749E/A750P/R883H 
                   
                   
                   
               
               
                 379/380 
                 K106P/T150S/N169S/L218S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 R414G/T486E/E793K/R883H 
                   
                   
                   
               
               
                 381/382 
                 K106P/T150S/L218S/T486E/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 N527D/Q749E/Q894R 
                   
                   
                   
               
               
                 383/384 
                 K106P/T150S/N169S/L218S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 R414G/T486E/N527D/Q894R 
                   
                   
                   
               
               
                 385/386 
                 T150S/L218S/R414G/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 T486E/Q749E/A750P 
                   
                   
                   
               
               
                 387/388 
                 K106P/T150S/L218S/R414G/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 Q749E/E793K/R883H 
                   
                   
                   
               
               
                 389/390 
                 K106P/T150S/N169S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 L218S/R414G/T486E/ 
                   
                   
                   
               
               
                   
                 N527D/A750P/Q894R 
                   
                   
                   
               
               
                 391/392 
                 N169S/T486E/A750P/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 E793K/R883H 
                   
                   
                   
               
               
                 7/8 
                 T150S/T486E/A750P/ 
                 +++ 
                 ++++ 
                 +++ 
               
               
                   
                 R883H/Q894G 
                   
                   
                   
               
               
                 393/394 
                 K106P/T150S/L218S/R414G/ 
                 +++ 
                 ++++ 
                 ++ 
               
               
                   
                 N527D/Q749E/A750P/R883H 
                   
                   
                   
               
               
                 395/396 
                 K106P/T150S/L218S/R414G/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 Q749E/A750P/E793K/ 
                   
                   
                   
               
               
                   
                 R883H/Q894R 
                   
                   
                   
               
               
                 397/398 
                 K106P/T150S/N169S/L218S/ 
                 +++ 
                 ++++ 
                 ++ 
               
               
                   
                 R414G/Q749E/E793K/R883H 
                   
                   
                   
               
               
                 399/400 
                 K106P/T150S/L218S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 T486E/E793K/R883H 
                   
                   
                   
               
               
                 401/402 
                 K106P/T150S/L218S/ 
                 +++ 
                 ++++ 
                 ++ 
               
               
                   
                 V331A/R414G/T486E/N527D/ 
                   
                   
                   
               
               
                   
                 D733E/Q749E/E793K 
                   
                   
                   
               
               
                 403/404 
                 L275M/A281V/S402A/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 I518V/A547G/W610R/ 
                   
                   
                   
               
               
                   
                 S668D/L669H/E887D 
                   
                   
                   
               
               
                 405/406 
                 K106P/T150S/L218S/ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 R414G/N527D/Q749E/ 
                   
                   
                   
               
               
                   
                 E793K/R883H/Q894G 
                   
                   
                   
               
               
                 407/408 
                 K106P/T150S/Q749E/ 
                 +++ 
                 ++++ 
                 +++ 
               
               
                   
                 E793K/R883H 
                   
                   
                   
               
               
                 409/410 
                 K106P/A112S/T150S/L218S/ 
                 ++++ 
                 ++++ 
                 +++ 
               
               
                   
                 R414G/N527D/E793K/R883H 
               
               
                   
               
               
                   1 All activities were determined relative to the reference polypeptide of SEQ ID NO: 2. Levels of increased activity are defined as follows: 
               
               
                 ““+”” = 0.9 to 1.1; 
               
               
                 “++” &gt; 1.1; 
               
               
                 “+++” &gt; 2; and 
               
               
                 “++++” &gt; 3.5 
               
            
           
         
       
     
     EXAMPLE 4 
     GAA variants of SEQ ID NO: S 
     In this Example, analysis of GAA variants derived from SEQ ID NO: 8 for improved GAA activity after a series of challenges are described. Directed evolution of the GAA encoded by SEQ ID NO: 8 was carried out by constructing libraries of variant genes. These libraries were then plated, grown, and screened for GAA 4-MUGIu activity after in the unchallenged, no pre-incubation, activity assay (Unchallenged Activity FIOPC), after pH 7 incubation (pH 7 Stability Activity FIOPC), or after pH 3 incubation (pH 3 Stability Activity FIOPC), as described in Example 2. The results are presented in Table 4-1. 
     
       
         
           
               
             
               
                 TABLE 44 
               
             
            
               
                   
               
               
                 Activity of GAA Variants Relative to SEQ ID NO: 8 1   
               
            
           
           
               
               
               
               
               
            
               
                 SEQ 
                   
                 Un- 
                 pH 3 
                 pH 7 
               
               
                 ID 
                   
                 challenged 
                 Stability 
                 Stability 
               
               
                 NO: 
                 Amino Acid Differences 
                 Activity 
                 Activity 
                 Activity 
               
               
                 (nt/aa) 
                 (Relative to SEQ ID NO: 8) 
                 FIOPC 
                 FIOPC 
                 FIOPC 
               
               
                   
               
               
                 411/412 
                 A281V/M431V/A489R/S668D 
                 +++ 
                 +++ 
                 +++ 
               
               
                 413/414 
                 A418E 
                 ++++ 
                 +++++ 
                 ++++ 
               
               
                 415/416 
                 A418E/A489R 
                 + 
                 ++ 
                 + 
               
               
                 417/418 
                 A489R/L934R 
                 + 
                 + 
                   
               
               
                 419/420 
                 A489R/Q749E 
                 + 
                 + 
                   
               
               
                 421/422 
                 A489R/S671N/L934R 
                 + 
                 + 
                   
               
               
                 423/424 
                 A489R/V638I/L934R 
                 ++ 
                 ++ 
                 ++ 
               
               
                 425/426 
                 F27P/A418E/A478T 
                 + 
                 + 
                 +++ 
               
               
                 427/428 
                 F27P/L28S/A489R 
                 + 
                 +++ 
                 ++ 
               
               
                 429/430 
                 F27R 
                 + 
                 + 
                 ++ 
               
               
                 431/432 
                 K106P 
                 ++ 
                 +++ 
                 ++ 
               
               
                 433/434 
                 K106P/A489R/S671N 
                 +++ 
                 ++ 
                 +++ 
               
               
                 435/436 
                 K106P/L218S/A281V 
                 ++ 
                 +++ 
                 ++ 
               
               
                 437/438 
                 K106P/L218S/R455V 
                 +++ 
                 +++ 
                 +++ 
               
               
                 439/440 
                 K106P/L218S/R455V/ 
                 +++ 
                 +++ 
                 +++ 
               
               
                   
                 M507L/Q749E 
                   
                   
                   
               
               
                 441/442 
                 K106P/M138A/L218S/ 
                 +++ 
                   
                 ++ 
               
               
                   
                 M431V/S671N/Q749E 
                   
                   
                   
               
               
                 443/444 
                 K106P/S671N/L934R 
                 + 
                   
                 + 
               
               
                 445/446 
                 K106P/V638I 
                 + 
                 +++ 
                 + 
               
               
                 447/448 
                 L157M 
                 +++ 
                 +++ 
                 +++ 
               
               
                 449/450 
                 L218S 
                 + 
                 ++ 
                 + 
               
               
                 451/452 
                 L218S/A281V 
                 ++ 
                 +++ 
                 ++ 
               
               
                 453/454 
                 L218S/A281V/M43V 
                 +++ 
                 +++ 
                 +++ 
               
               
                 455/456 
                 L218S/A281V/S671N 
                 + 
                   
                   
               
               
                 457/458 
                 L218S/M431V 
                 + 
                 + 
                   
               
               
                 459/460 
                 L218S/M431V/A489R/ 
                 +++ 
                 ++ 
                 +++ 
               
               
                   
                 M507L/Q749E/L934R 
                   
                   
                   
               
               
                 461/462 
                 L218S/M507L/L934R 
                 + 
                 + 
                 + 
               
               
                 463/464 
                 L218S/M507L/Q749E 
                 +++ 
                 ++ 
                 +++ 
               
               
                 465/466 
                 L218S/Q749E 
                 +++ 
                 +++ 
                 +++ 
               
               
                 467/468 
                 L218S/R455V 
                 + 
                 + 
                 + 
               
               
                 469/470 
                 L218S/V638I/S671N 
                 +++ 
                 +++ 
                 +++ 
               
               
                 471/472 
                 L28S 
                 + 
                 ++ 
                 + 
               
               
                 473/474 
                 L28S/L29T 
                 + 
                 + 
                 + 
               
               
                 475/476 
                 L28S/L29T/A418E 
                 ++ 
                 +++ 
                 ++ 
               
               
                 477/478 
                 L28S/L29T/Q113S/ 
                 + 
                 ++++ 
                 +++ 
               
               
                   
                 S135Q/A418E 
                   
                   
                   
               
               
                 479/480 
                 L28S/L29T/Q113S/ 
                 + 
                 + 
                 + 
               
               
                   
                 S135Q/M138A 
                   
                   
                   
               
               
                 13/14 
                 L28S/L29T/S135Q 
                 +++ 
                 ++++ 
                 +++ 
               
               
                 481/482 
                 L29T/A478T 
                 + 
                   
                 + 
               
               
                 483/484 
                 L29T/Q113S/M138A 
                 + 
                 + 
                 + 
               
               
                 485/486 
                 L29T/Q113S/P126Q/ 
                 + 
                 +++ 
                 ++ 
               
               
                   
                 S135Q/H193Q 
                   
                   
                   
               
               
                 487/488 
                 L29T/Q113S/S135Q 
                 ++ 
                 +++ 
                 ++ 
               
               
                 489/490 
                 L29T/Q113S/S135Q/R455V 
                 + 
                 + 
                 + 
               
               
                 491/492 
                 L29T/T148G 
                 +++ 
                 +++ 
                 +++ 
               
               
                 493/494 
                 M138A/L218S/Q749E/L934R 
                 + 
                 + 
                   
               
               
                 495/496 
                 M138A/L218S/S668D/S671N 
                 +++ 
                 ++ 
                 +++ 
               
               
                 497/498 
                 M138A/S671N/Q749E/L934R 
                 +++ 
                 ++ 
                 +++ 
               
               
                 499/500 
                 M431V/S668D/S671N 
                 + 
                 + 
                 + 
               
               
                 501/502 
                 M507L/S668D 
                 + 
                 + 
                 + 
               
               
                 503/504 
                 M507L/S671N/L934R 
                 +++ 
                 +++ 
                 +++ 
               
               
                 505/506 
                 P4H 
                 + 
                 ++ 
                 + 
               
               
                 507/508 
                 Q113S 
                 + 
                 ++ 
                 + 
               
               
                 509/510 
                 Q113S/A418E/A478T/ 
                 + 
                 + 
                 + 
               
               
                   
                 A489R/K581T 
                   
                   
                   
               
               
                 511/512 
                 Q113S/A418E/R455V/ 
                 + 
                 + 
                 + 
               
               
                   
                 A478T/K581T 
                   
                   
                   
               
               
                 513/514 
                 Q113S/S135Q/A418E 
                 ++ 
                 +++ 
                 +++ 
               
               
                 515/516 
                 Q345K/L934R 
                 + 
                 ++ 
                   
               
               
                 517/518 
                 Q749E/A784T 
                 +++ 
                 +++ 
                 ++ 
               
               
                 519/520 
                 S135P/C944Y 
                 +++ 
                 +++ 
                 +++ 
               
               
                 521/522 
                 S135Q 
                 + 
                 ++ 
                 + 
               
               
                 523/524 
                 S135Q/A478T/A489R/K581T 
                 + 
                   
                 + 
               
               
                 525/526 
                 S135Q/A489R 
                 + 
                 +++ 
                 ++ 
               
               
                 527/528 
                 S135Q/T148G/S150G/A418E 
                 + 
                 +++ 
                 + 
               
               
                 529/530 
                 S671N/L934R 
                 +++ 
                 ++ 
                 +++ 
               
               
                 531/532 
                 S671N/Q749E 
                 +++ 
                 +++ 
                 +++ 
               
               
                   
               
               
                   1 All activities were determined relative to the reference polypeptide of SEQ ID NO: 8. Levels of increased activity are defined as follows: 
               
               
                 ““+”” = 0.5-0.9; 
               
               
                 “++” 0.9 to 1.1; 
               
               
                 “+++” &gt; 1.1; 
               
               
                 “++++” &gt; 2; and 
               
               
                 “+++++” &gt; 3.5. 
               
            
           
         
       
     
     EXAMPLE 5 
     High-Throughput Growth of Adherent. Mammalian Cells and GAA Assays Obtained Through Adherent Mammalian Expression 
     High-Throughput (HTP) Growth of GAA and GAA Variants in Adherent Mammalian Cells (HEK293T) 
     HEK 293T cells were transfected with a pcDNA 3.1(+) vector (ThermoFisher Scientific), pDH vector, or PCR-amplified linear DNA (as described in Example 1) encoding a synthetic mouse IG signal peptide (SEQ ID NOS: 3381 and 3382) fusion to wild-type GAA or GAA variants using the lipofection method with LIPOFECTAMINE® 3000 Reagent (ThermoFisher Scientific). HEK 293T cells were cultured in standard complete growth medium (DMEM with 10% fetal bovine serum [both from Corning]) and seeded into NUNC® Edge 2.0 96-well plate (ThermoFisher Scientific), at densities of 0.5×10 5 cells/well 250 μL to adhere and grow for 24 hours at 37° C., and in the presence of 5% CO 2  prior to lipofection-mediated transfection. Following transfection, cells were incubated for 24-96 hours, to allow for expression and secretion of GAA variants into the conditioned media. Conditioned media (20-100 μL) from the HEK293T transfection was then transferred into new 96-well plates for activity, stability or uptake into cell analysis. 
     HTP-Analysis of Supernatants 
     GAA variant activity was determined by measuring the hydrolysis of 4-methylumbelliferyl D-glucopyranoside (4-MUGIu). For the unchallenged assay, 20 μL of HEK 293T conditioned media produced as described above was mixed with 50 μL of 1.5 mM 4-MUGlu in McMaine Buffer (McIlvaine, J. Biol. Chem., 49:183-186 [1921]), pH 4.4, in a 96-well, black, opaque bottom plate. The reactions were incubated at 25-37° C. for 30-60 minutes with agitation at 400 rpm, prior to quenching with 100 μL of 0.5 M sodium carbonate pH 10.5. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader (Molecular Devices) or an ENVISION® microplate reader (Perkin Elmer) monitoring fluorescence (Ex. 355 nm, Em. 460 nm). 
     HTP-Analysis of Supernatants Challenged with Neutral Buffer 
     GAA variants were challenged with neutral buffer to simulate the pH that the variants encounter in the blood following their administration to a patient. First, 20 μL of conditioned media containing GAA variants from HEK 293T expression were combined with 100 μL of DPBS buffer (pH 7.4) in a 96-well plate. The plates were sealed and incubated at 37° C. for 24-96 h. Next, 20 μL of neutral-pH-challenged sample were mixed with 50 μL of 1.5 mM 4-MUGlu in McIlvaine buffer, pH 4.4. The reactions were incubated at 37° C. for 180 minutes with agitation at 400 rpm, prior to quenching with 100 μL of 0.5 M sodium carbonate pH 10.5. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader or an ENVISION® microplate reader (Perkin Elmer) monitoring fluorescence (Ex. 355 nm, Em. 460 nm). 
     HTP-Analysis of Supernatants Challenged with Plasma 
     GAA variants were challenged with plasma to simulate the conditions that the variants encounter in the blood following their administration to a patient. First, 30 μL of conditioned media containing GAA variants from HEK 293T expression were combined with 30 μL of plasma (Innovative Research, Innovative Grade US Origin Monkey Cynomolgus Plasma K2 EDTA) in a 96-well plate. The plates were sealed and incubated at 37° C. for 2-4 h. Next, 10 μL of plasma-challenged sample were mixed with 50 μL of 1.5 mM 4-MUGlu in McIlvaine buffer, pH 4.4. The reactions were incubated at 25-37° C. for 15-60 minutes with agitation at 400 rpm, prior to quenching with 100 μL of 0.5 M sodium carbonate pH 10.5. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader or an ENVISION® microplate reader (Perkin Elmer) monitoring fluorescence (Ex. 355 nm, Em. 460 nm). 
     HTP-Analysis of GAA Activity in Lysates of Pompe Fibroblasts and C2C12 GAA Knockout Myoblasts 
     GAA variants produced in HTP were incubated with target cells and assayed for residual intracellular activity after 24 hours. For these experiments, mammalian cells lacking functional GAA activity were used, namely Pompe patient-derived fibroblasts (Coriell Institute for Medical Research # GM00248) and C2C12 myoblasts whose native GAA gene had been knocked out using Crispr-Cas9 editing. In these experiments, Pompe fibroblasts or C2C12 GAA knockout myoblasts were seeded into black, clear bottom, tissue culture treated COSTAR® 96-well plates (Corning, 3904) and allowed to grow to confluency in standard complete growth medium. Upon confluency, complete growth culture media was removed from the plates using an automated BIOMEK® i5 liquid handling robot. Conditioned media produced by HEK293T cells transiently transfected as described above, were transferred to Pompe patient-derived fibroblasts and C2C12 myoblasts, and allowed to incubate for 4-24 hours at 37° C., 5% CO 2 . Medium was removed from the cultures using an automated BIOMEK® i5 liquid handling robot. The cells were briefly washed with 150 μL 1×DPBS/well, and DPBS was removed using an automated BIOMEK® i5 liquid handling robot. Then, 200 μL standard complete growth culture medium was added to each well, and the plates were returned to the incubator for 0-72 hours. At the conclusion of incubation, standard complete growth media was removed using an automated BIOMEK® i5 liquid handling robot. The cells were washed with 150 μL 1×DPBS/well, and the DPBS removed using an automated BIOMEK® i5 liquid handling. The cells were lysed via addition of 50 μL of McMaine buffer, pH 4.4, supplemented with 0.2-0.5% TRITON X-100™ non-ionic surfactant (Sigma #93443) and agitation at room temperature for 30 minutes. Activity was assessed by addition of 50 μL: of 1.5 mM 4-MUGlu in McMaine buffer, pH 4.4. The plates were sealed, incubated at 37° C. for 300-360 minutes with agitation at 400 rpm, prior to quenching with 100 μL of 0.5 M sodium carbonate, pH 10.5. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader or an ENVISION® microplate reader (Perkin Elmer) monitoring fluorescence (Ex. 355 nm, Em. 460 nm). Cellular uptake FIOPC was calculated by dividing normalized GAA variant intracellular activity by the activity of the reference polypeptide with the indicated SEQ ID NO. 
     EXAMPLE 6 
     GAA Variants of SEQ ID NO: 16 
     In this Example, experiments for evolution and screening of GAA variants derived from SEQ ID NO: 16 for improved GAA activity after a series of challenges are described. The GAA synthetic gene coding for SEQ ID NO: 13 was fused to the synthetic mouse IG signal peptide polynucleotide (SEQ ID NO: 3381) (as described in Example 1) to generate the synthetic gene coding for SEQ ID NO: 15. Directed evolution of the GAA encoded by SEQ ID NO: 16 was carried out by constructing libraries of variant genes. These libraries were then plated, grown, and screened for GAA MU-Glu activity (“Unchallenged Activity FIOPC”), as well as after pH 7.4 pre-incubation (“pH 7.4 Stability and Activity FIOPC”), as described in Example 5. Variants were also tested for 4-MUGlu activity after lysis of Pompe fibroblasts (“Activity from Pompe Fibroblast Lysate FIOPC”) or GAA −/− C 2C12 cells (“Activity from C2C12 GAA−/− Lysate FIOPC”), as described in Example 5. The results of these assays are presented in Table 6-1. 
     
       
         
           
               
             
               
                 TABLE 6-1 
               
             
            
               
                   
               
               
                 Activity of GAA Variants Relative to SEQ ID NO: 16 1   
               
            
           
           
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                 Activ- 
                 Activ- 
               
               
                   
                   
                   
                   
                 ity 
                 ity 
               
               
                   
                   
                   
                 pH 7.4 
                 from 
                 from 
               
               
                 SEQ  
                 Amino Acid  
                 Un- 
                 Stability 
                 Pompe 
                 C2C12 
               
               
                 ID 
                 Differences 
                 challenged 
                 and 
                 Fibroblast 
                 GAA-/- 
               
               
                 NO: 
                 (Relative to 
                 Activity 
                 Activity 
                 Lysate 
                 Lysate 
               
               
                 (nt/aa) 
                 SEQ ID NO: 16) 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
               
               
                   
               
               
                 533/534 
                 V70A/R267K/ 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                   
                 K725E/C944S 
                   
                   
                   
                   
               
               
                 535/536 
                 R267K/A489D/ 
                 +++ 
                 +++ 
                 ++ 
                 ++ 
               
               
                   
                 D500A/K725E/ 
                   
                   
                   
                   
               
               
                   
                 Q830K/C930P 
                   
                   
                   
                   
               
               
                 537/538 
                 L109P/E522V/ 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                   
                 Q830K/C944S 
                   
                   
                   
                   
               
               
                 539/540 
                 V70A/R267K/ 
                 +++ 
                 +++ 
                 +++ 
                 ++ 
               
               
                   
                 C930P/C944S 
                   
                   
                   
                   
               
               
                 541/542 
                 V70A/K725E/Q830K/ 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                   
                 L860F/C930P/C944S 
                   
                   
                   
                   
               
               
                 545/546 
                 P39Q/R58L/A489D/ 
                 ++ 
                 +++ 
                 ++ 
                 ++ 
               
               
                   
                 K725E/Q830K/ 
                   
                   
                   
                   
               
               
                   
                 G842S/C930P/C944S 
                   
                   
                   
                   
               
               
                 547/548 
                 A60V/D500A/S612D 
                 + 
                 + 
                 + 
                 + 
               
               
                 549/550 
                 P39Q/D500A/S612D 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 551/552 
                 E522V/K725E 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 553/554 
                 P39Q/V70A/L109P/ 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                   
                 Q830K/G842S 
                   
                   
                   
                   
               
               
                 555/556 
                 P39Q/V70A/K725E 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 557/558 
                 P39Q/R267K/A489D/ 
                 +++ 
                 +++ 
                 ++ 
                 +++ 
               
               
                   
                 Q830K/C944S 
                   
                   
                   
                   
               
               
                 559/560 
                 C930P 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 561/562 
                 D500A/C930P/C944S 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 563/564 
                 C944S 
                 ++ 
                 +++ 
                 ++ 
                 ++ 
               
               
                 565/566 
                 L109P/E522V/ 
                 +++ 
                 +++ 
                 ++ 
                 ++ 
               
               
                   
                 S612D/K725E 
                   
                   
                   
                   
               
               
                 19/20 
                 P39Q/R267K/ 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                   
                 A489D/E522V/ 
                   
                   
                   
                   
               
               
                   
                 S612D/ 
                   
                   
                   
                   
               
               
                   
                 Q830K/G842S 
                   
                   
                   
                   
               
               
                 567/568 
                 P39Q/R267K 
                 +++ 
                 + 
                 +++ 
                 ++ 
               
               
                 569/570 
                 P39Q/V70A/ 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                   
                 A489D/S612D 
                   
                   
                   
                   
               
               
                 571/572 
                 L109P/S612D 
                 ++ 
                 + 
                 + 
                 + 
               
               
                 573/574 
                 D500A/L860F/C930P 
                 +++ 
                 +++ 
                 ++ 
                 ++ 
               
               
                 575/576 
                 R267K/E522V/K725E 
                 ++ 
                 ++ 
                 +++ 
                 + 
               
               
                 577/578 
                 V70A/A489D/C930P 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 579/580 
                 A489D/Q830K/C944S 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 581/582 
                 D500AJS612D/ 
                 +++ 
                 + 
                 +++ 
                 +++ 
               
               
                   
                 Q830K/L860F 
                   
                   
                   
                   
               
               
                 583/584 
                 P39Q/A489D/ 
                 +++ 
                 + 
                 ++ 
                 + 
               
               
                   
                 D500A/S612D 
                   
                   
                   
                   
               
               
                 585/586 
                 P39Q 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 587/588 
                 N528S/E793K 
                 + 
                   
                 ++ 
                   
               
               
                 589/590 
                 K106R/K154R 
                 +++ 
                 + 
                   
                 ++ 
               
               
                 591/592 
                 A62E/K106R/D523N/ 
                 + 
                   
                 + 
                   
               
               
                   
                 N528S/A696S/ 
                   
                   
                   
                   
               
               
                   
                 E793K/R862Q 
                   
                   
                   
                   
               
               
                 593/594 
                 A196T/N528S/ 
                 + 
                   
                   
                   
               
               
                   
                 E681Q/I790V/E793K 
                   
                   
                   
                   
               
               
                 595/596 
                 A62E/K154R/ 
                 +++ 
                 + 
                 + 
                 ++ 
               
               
                   
                 A696S/E793K/R862Q 
                   
                   
                   
                   
               
               
                 597/598 
                 A62E/Q92R/ 
                 ++ 
                 + 
                   
                 ++ 
               
               
                   
                 I790V/E793K 
                   
                   
                   
                   
               
               
                 599/600 
                 E793K 
                 +++ 
                 ++ 
                 + 
                 +++ 
               
               
                 601/602 
                 S37F/N528S/I790V 
                 + 
                   
                   
                   
               
               
                 603/604 
                 N528S/E681Q 
                 + 
                   
                   
                   
               
               
                 605/606 
                 D523N/I790V/E793K 
                 +++ 
                 ++ 
                 + 
                 ++ 
               
               
                 607/608 
                 D523N 
                 ++ 
                 + 
                 + 
                 ++ 
               
               
                 609/610 
                 N528S/R862Q 
                 ++ 
                   
                   
                   
               
               
                 611/612 
                 S37F/A62E 
                 ++ 
                 + 
                 + 
                 ++ 
               
               
                 613/614 
                 A753S 
                 +++ 
                 +++ 
                   
                 ++ 
               
               
                 615/616 
                 A62E/N79S/ 
                 +++ 
                   
                   
                 ++ 
               
               
                   
                 K154R/R862Q 
                   
                   
                   
                   
               
               
                 617/618 
                 A62E/N79S/ 
                 +++ 
                 + 
                   
                 +++ 
               
               
                   
                 I790V/E793K 
                   
                   
                   
                   
               
               
                 619/620 
                 A62E/N79S/R862Q 
                 +++ 
                 + 
                 +++ 
                 +++ 
               
               
                 621/622 
                 A62E/N79S/D523N/ 
                 +++ 
                   
                 + 
                   
               
               
                   
                 N528S/I790V 
                   
                   
                   
                   
               
               
                 623/624 
                 A62E/N79S/A196T/ 
                 ++ 
                   
                 + 
                 + 
               
               
                   
                 E681Q/R862Q 
                   
                   
                   
                   
               
               
                 625/626 
                 S37F/A196T 
                 + 
                   
                   
                 + 
               
               
                 627/628 
                 S37F/A62E/D523N 
                 +++ 
                 + 
                 ++ 
                 ++ 
               
               
                 629/630 
                 S37F/N79S/K154R/ 
                 +++ 
                 ++ 
                   
                 ++ 
               
               
                   
                 E793K 
                   
                   
                   
                   
               
               
                 631/632 
                 S37F/P64Q/R66G/ 
                 + 
                   
                 + 
                   
               
               
                   
                 N79S/K154R/D523N/ 
                   
                   
                   
                   
               
               
                   
                 E681Q/E793K/R862Q 
                   
                   
                   
                   
               
               
                 633/634 
                 S37F/A62E/N795/ 
                 +++ 
                 + 
                 + 
                 + 
               
               
                   
                 A196T/A696S/R862Q 
                   
                   
                   
                   
               
               
                 635/636 
                 S37F/I790V/E793K 
                 + 
                   
                   
                 + 
               
               
                 637/638 
                 N795/R862Q 
                 +++ 
                 + 
                 ++ 
                 ++ 
               
               
                 639/640 
                 N79S/K154R/E681Q 
                 +++ 
                   
                 ++ 
                 + 
               
               
                 641/642 
                 S37F/A62E/D523N/ 
                 ++ 
                 + 
                 + 
                 + 
               
               
                   
                 E793K 
                   
                   
                   
                   
               
               
                 643/644 
                 A62E/E793K/R862Q 
                 +++ 
                 +++ 
                 + 
                 +++ 
               
               
                 645/646 
                 S37F/N528S/A696S/ 
                 + 
                   
                   
                   
               
               
                   
                 E793K 
                   
                   
                   
                   
               
               
                 647/648 
                 S37F/N528S/I790V/ 
                 ++ 
                   
                   
                   
               
               
                   
                 E793K/R862Q 
                   
                   
                   
                   
               
               
                 649/650 
                 A62E/Q92R 
                 ++ 
                 + 
                 + 
                 ++ 
               
               
                 651/652 
                 N79S/K154R/ 
                 +++ 
                 + 
                 + 
                 + 
               
               
                   
                 E793K/R862Q 
                   
                   
                   
                   
               
               
                 653/654 
                 R862Q 
                 ++ 
                 + 
                   
                 ++ 
               
               
                 655/656 
                 L34D 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 657/658 
                 Y352K 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 659/660 
                 E207R 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 661/662 
                 Q50L 
                 + 
                 + 
                 ++ 
                 + 
               
               
                 663/664 
                 L672K 
                 ++ 
                 + 
                 ++ 
                 + 
               
               
                 665/666 
                 Q938P 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 667/668 
                 N875D 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 669/670 
                 Q830V 
                 +++ 
                 + 
                 ++ 
                 ++ 
               
               
                 671/672 
                 P178G 
                 ++ 
                   
                 + 
                 + 
               
               
                 673/674 
                 I22R 
                 +++ 
                 ++ 
                 +++ 
                 ++ 
               
               
                 675/676 
                 L24W 
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 677/678 
                 L778Q 
                 +++ 
                 + 
                 + 
                 + 
               
               
                 679/680 
                 E208I 
                 ++ 
                 ++ 
                 ++ 
                 + 
               
               
                 681/682 
                 K925A 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 683/684 
                 A47G 
                 ++ 
                 + 
                 ++ 
                 + 
               
               
                 685/686 
                 Y352V 
                 ++ 
                   
                   
                   
               
               
                 687/688 
                 F27S 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 689/690 
                 P149R 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 691/692 
                 F27K 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 693/694 
                 L672E 
                 +++ 
                 + 
                 ++ 
                 + 
               
               
                 695/696 
                 S932A 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 697/698 
                 L24R 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 699/700 
                 L24E 
                 ++ 
                 ++ 
                 ++ 
                 + 
               
               
                 701/702 
                 C944R 
                 +++ 
                 +++ 
                 ++ 
                 +++ 
               
               
                 703/704 
                 E740G 
                 +++ 
                 ++ 
                 +++ 
                 ++ 
               
               
                 705/706 
                 P55C 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                 707/708 
                 P673R 
                 ++ 
                   
                   
                   
               
               
                 709/710 
                 F27G 
                 ++++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 711/712 
                 Q49A 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                 713/714 
                 L34M 
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 715/716 
                 E207Y 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                 717/718 
                 R68S 
                 +++ 
                 ++ 
                 +++ 
                 +++ 
               
               
                 719/720 
                 P55L 
                 ++ 
                 ++ 
                 ++ 
                 + 
               
               
                 721/722 
                 V70Q 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 723/724 
                 P39H 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 725/726 
                 P922E 
                 +++ 
                 ++ 
                 +++ 
                 ++ 
               
               
                 727/728 
                 R68W 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 729/730 
                 P77W 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 731/732 
                 A774G 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 733/734 
                 Q50G 
                 ++ 
                 ++ 
                 ++ 
                 +++ 
               
               
                 735/736 
                 F27W 
                 ++ 
                 + 
                 + 
                 ++ 
               
               
                 737/738 
                 W118F 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 739/740 
                 F27V 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 741/742 
                 P178V 
                 ++ 
                 + 
                 + 
                 + 
               
               
                 743/744 
                 H424K 
                 +++ 
                   
                   
                   
               
               
                 745/746 
                 R385G 
                 +++ 
                 + 
                 + 
                 + 
               
               
                 747/748 
                 F27G/M165I 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 749/750 
                 V30D 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 751/752 
                 V30L 
                 + 
                 ++ 
                 + 
                 + 
               
               
                 753/754 
                 V40W 
                 ++ 
                 + 
                 ++ 
                 +++ 
               
               
                 755/756 
                 R68N 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 757/758 
                 A179L 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 759/760 
                 A774S 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 761/762 
                 E33G 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 763/764 
                 A902L 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 765/766 
                 L109D 
                 +++ 
                 +++ 
                 +++ 
                 ++ 
               
               
                 767/768 
                 E463A 
                 + 
                 + 
                 + 
                 + 
               
               
                 769/770 
                 F27A 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 771/772 
                 E880R 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 773/774 
                 T44I/L157V 
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 775/776 
                 T158E 
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 777/778 
                 L157Q 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 779/780 
                 K725V 
                 ++ 
                 + 
                 ++ 
                 + 
               
               
                 781/782 
                 Q217A 
                 ++ 
                 +++ 
                 + 
                 + 
               
               
                 783/784 
                 Q938A 
                 +++ 
                 ++ 
                 ++ 
                 + 
               
               
                 785/786 
                 D500A 
                 + 
                 + 
                 ++ 
                 +++ 
               
               
                 787/788 
                 A89R 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 789/790 
                 E844R 
                 ++ 
                 + 
                 ++ 
                 + 
               
               
                 791/792 
                 R448L 
                 + 
                   
                   
                   
               
               
                 793/794 
                 Q107G 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 795/796 
                 E208G 
                 + 
                 + 
                 + 
                 + 
               
               
                 797/798 
                 A47R 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 799/800 
                 E740Q 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 801/802 
                 F27R 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 803/804 
                 L934F 
                 + 
                 + 
                 + 
                 + 
               
               
                 805/806 
                 K725F 
                 ++ 
                 +++ 
                 + 
                 + 
               
               
                 807/808 
                 K925W 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                 809/810 
                 Q49G 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 811/812 
                 Q50V 
                 +++ 
                 ++ 
                 +++ 
                 +++ 
               
               
                 813/814 
                 Q217D 
                 ++ 
                 ++ 
                 ++ 
                 +++ 
               
               
                 815/816 
                 Q892L 
                 ++ 
                 +++ 
                 ++ 
                 ++ 
               
               
                 817/818 
                 L34T 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 819/820 
                 A97G 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 821/822 
                 P673N 
                 + 
                   
                   
                   
               
               
                 823/824 
                 T158F 
                 ++ 
                 + 
                 + 
                 ++ 
               
               
                 825/826 
                 A97D 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 827/828 
                 E33P 
                 ++ 
                 ++ 
                 +++ 
                 ++ 
               
               
                 371/372 
                 P39D 
                 +++ 
                 +++ 
                 +++ 
                 +++ 
               
               
                 543/544 
                 H734K 
                 + 
                 + 
                 ++ 
                 + 
               
               
                   
               
               
                   1 All activities were determined relative to the reference polypeptide of SEQ ID NO: 16. Levels of increased activity are defined as follows; 
               
               
                 ““+”” = 0.5-0.9; 
               
               
                 “++” = 0.9 to 1.1; 
               
               
                 “+++” &gt; 1.1; and 
               
               
                 “++++” &gt; 2. 
               
            
           
         
       
     
     EXAMPLE 7 
     Production of GAA Variants 
     In this Example, production of GAA variants is described. 
     Production of GAA in EXPI293F™ Cells 
     Milligram-scale production of GAA variants was achieved by transient transfection of EXPI293™ cells (ThermoFisher Scientific) using the lipofection method with EXPIFECTAMINE™ 293 Reagent (ThermoFisher Scientific) in EXPI293™ Expression Medium (ThermoFisher Scientific). GAA variants fused to an N-terminal synthetic mammalian signal peptide (SEQ ID NO: 3381) were subcloned into the mammalian expression vectors pLEV113, pcDNA 3.1(+), or pDH as described in Example 1. EXPI293™ cells were transfected with plasmid DNA and grown in suspension for 4-7 days. Conditioned media was then harvested, clarified by centrifugation and filtration and stored at 4° C. until analysis. 
     EXAMPLE 8 
     Purification of GAA Variants 
     In this Example, methods of purifying GAA variants are described. 
     Purification of GAA Variants From Mammalian Cell Supernatants 
     GAA variants (SEQ ID NOS: 4, 6, 10, 12, 16, 18, 20, 946, 1894, 1924, 1950, 1956, 1984, 2034, 2054, 2066, 2074, 2178, 2202, and 2496) produced in EXPI293F™ cells as described in Example 7, were purified from mammalian culture supernatant as described in the literature (Yasuda et al., Prot. Exp. Pur., 37:499-506 [2004]). Concanavalin A resin (Sigma Aldrich) was equilibrated with 0.1 M sodium acetate, 0.1 M NaCl, 1 mM MgCl 2 , CaCl 2 , and MnCl 2 , pH 6.0 (Concanavalin A binding buffer). Supernatant was sterile-filtered with a 0.2 μm bottle-top filter before it was loaded onto the column. After loading, the column was washed with 10 column volumes of Concanavalin A binding buffer and the bound protein was eluted with Concanavalin A binding buffer supplemented with 0.9 M methyl-α-D-mannopyranoside and 0.9 M methyl-α-D-glucopyranoside. Eluted protein was concentrated, and the buffer exchanged into storage buffer (20 mM sodium phosphate, 150 mM sodium chloride, 185 μM TWEEN®-20 non-ionic detergent, pH 6.0) using an AMICON® Ultra 15 mL filtration unit with a 50 kDa molecular weight cut off membrane (Millipore). The GAA in storage buffer was sterile filtered through ANOTOP® 0.2 μm syringe filters (Whatman), and stored at −80° C. Based on BCA quantitation (described below), the purification process produced 2.4-50 ng of purified protein/ml of culture supernatant. 
     Protein Quantification by BCA assay 
     A bicinchoninic acid (BCA) protein assay (Sigma Aldrich) was used to quantify purified GAA variants produced as described above. In a microtiter plate, 25 μL of protein standards and purified GAA with proper dilution were mixed with 200 μL of working reagent containing 50 parts of BCA reagent A and 1 part of BCA reagent B. The plate was thoroughly mixed on a plate shaker for 30 seconds and incubated at 37° C. for 30 minutes. Absorbance was measured at 562 rim on a plate reader. 
     EXAMPLE 9 
     In Vitro Characterization of GAA Variants 
     In this Example, experiments conducted to characterize GAA variants produced as indicated herein are described. 
     Kinetic Characterization of rhGAA and GAA variants 
     GAA variant activity was determined by measuring the hydrolysis of 4-methylumbelliferyl D-glucopyranoside (4-MUGlu). Purified enzyme produced as described above was mixed with 50 of 0-2.5 mM 4-MUGlu in McMaine Buffer (McMaine, J. Biol. Chem., 49:183-186 [1921]), pH 4.5, in a 96-well, black, opaque bottom plate. The reactions were mixed briefly and incubated at 37° C. for 15-30 min, prior to quenching with 100 μL of 0.5 M sodium carbonate pH 10.5. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader monitoring fluorescence (Ex. 355 nm, Em. 460 nm), plotted and analyzed using the Michaelis-Menten equation. The results from this assay are presented in  FIG. 1 . 
     Stability at Neutral pH of rhGAA and GAA Variants 
     GAA variant stability to neutral pH was determined by incubating variants in 100 μL of MEM complete growth medium (pH 7.4) in a 96-well plate. The plates were sealed and incubated at 37° C. for up to 48 h. Next, 10 pt of neutral-pH-challenged sample were mixed with 50 μL of 1.5 mM 4-MUGlu in McMaine buffer, pH 4.4 in a 96-well, black, opaque bottom plate. The reactions were incubated at room temperature for 30 minutes with agitation, prior to quenching with 100 μL of 0.5 M sodium carbonate pH 10.5. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader or an ENVISION® microplate reader (Perkin Elmer) monitoring fluorescence (Ex. 355 nm, Em. 460 nm measuring the hydrolysis of 4-methylumbelliferyl α-D-glucopyranoside (4-MUGlu). The results from this assay are presented in  FIG. 11 . 
     Cellular Uptake in Pompe Fibroblasts or C2C12 GAA Knockout Myoblasts of Purified GAA Variants Expressed in Expi293F Cells 
     The cellular uptake of GAA variants as compared to reference enzymes (SEQ ID NOS: 4 and 6), was determined to assess their overall ability to be endocytosed into cultured cells. Pompe fibroblasts (GM00248, Coriell Institute for Medical Research) or C2C12 GAA knockout cells were seeded into a black walled, clear bottom 96-well plate (Costar, #3603) in standard complete growth medium and allowed to reach confluency (2-3 days at 37° C., 5% CO 2 ). After reaching confluency, standard complete growth medium was removed using an automated BIOMEK®i5 liquid handling robot. Enzymes purified as described in Example 8, were added to cells at 0-10 ug GAA/mL in standard complete growth media and allowed to incubate for acute (1-6 hours) or extended (16-96 hours) treatments at 37′C, 5% CO 2 . Media containing GAA variants were aspirated using an automated BIOMEK® i5 liquid handling robot. The cells were briefly washed with 150 μL 1×DPBS/well, and the DPBS was removed by an automated BIOMEK® i5 liquid handling robot. Then, 200 μL standard complete growth medium was added to each well, and the plates were returned to the incubator for 0-72 hours. At the conclusion of incubation, MEM complete growth media was removed using an automated BIOMEK® i5 liquid handling robot. The cells were washed with 150 μL 1×DPBS/well, and the DPBS was removed using an automated BIOMEK® i5 liquid handling robot. Cells were lysed via addition of 50 μL, of McIlvaine buffer, pH 4.4, supplemented with 0.2-0.5% TRITON X-100™ non-ionic surfactant (Sigma #93443)) and agitation at room temperature for 30 minutes. GAA activity was assessed by addition of 50 μL of 1.5 mM 4-MUGlu in McIlvaine buffer, pH 4.4. The plates were sealed, incubated at 37° C. for 300-360 minutes with agitation at 400 rpm, prior to quenching with 100 μL of 0.5 M sodium carbonate pH 10.5. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader monitoring fluorescence (Ex. 355 nm, Em. 460 nm). Cellular uptake FIOPC was calculated by dividing the normalized GAA variant intracellular activity by the control (WT) activity.  FIGS. 4, 5, 8, 12, 13, 16-18, 22, 24, and 26 , provide graphs showing the cellular uptake in Pompe fibroblasts of purified GAA variants after treatments of 1 to 96 hours.  FIGS. 6, 7, 14, 15, 19-21, 23, 25, and 27  provide graphs showing the cellular uptake in C2C12 GAA KO myoblasts of purified GAA variants after treatments of 1 to 96 hours.  FIG. 8  provides a graph showing the cellular uptake and stability of GAA variants after 1-7 days. 
     Glycogen Degradation Activity of GAA Variants Expressed in EXPI293F™ Cells 
     The relative glycogen hydrolysis activity of GAA variants was assessed using an AMPLEX® Red Glucose/Glucose Oxidase Kit (Invitrogen, #A22189) following the manufacturer&#39;s instructions with the modifications described herein. Briefly, GAA variants were diluted to an appropriate concentration range (0-2 μg/mL) in 50 μL reactions with 10 mM glycogen in McIlvaine buffer pH 4.4, in a COSTAR® black walled, clear bottom 96-well plate (#3603, Corning). The plates were sealed and gently shaken at room temperature for 30 minutes. Reactions were neutralized by addition of 25 μL of 0.5 M sodium carbonate, pH 10.5. 50 μL of the AMPLEX® Red/Horseradish Peroxidase/Glucose oxidase solution prepared as per manufacturer&#39;s instructions, was added to each well. The plates were sealed and gently shaken at room temperature for 30 minutes. Reactions were quantified to a standard curve of free glucose using a SPECTRAMAX® M2 microplate reader monitoring fluorescence (Ex. 530 nm, Em. 590 nm). The results are shown in  FIG. 2 . 
     EXAMPLE 10 
     GAA Variants of SEQ ID NO: 20 
     In this Example, experiments for evolution and screening of GAA variants derived from SEQ ID NO: 20 for improved GAA activity after a series of challenges are described. Libraries of variant genes GAA encoded based off of by SEQ ID NO: 20 were constructed, plated, grown, and screened for GAA MU-Glu activity (“Unchallenged Activity FIOPC”), as well as after plasma challenge (“Plasma Stability and Activity FIOPC”), as described in Example 5. Variants were also tested for 4-MUGlu activity after lysis of Pompe fibroblasts (“Activity from Pompe Fibroblast Lysate FIOPC”) or GAA −/−  C2C12 cells (“Activity from C2C12 GAA−/− Lysate FIOPC”), as described in Example 5. The results of these assays are presented in Table 10-1 and 10-2. 
     
       
         
           
               
             
               
                 TABLE 10-1 
               
             
            
               
                   
               
               
                 Activity of GAA Variants Relative to SEQ ID NO: 20 1   
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 Amino Acid 
                   
                 Plasma 
                 Activity from 
                 Activity 
               
               
                   
                 Differences 
                   
                 Stability 
                 Pompe 
                 from C2C12 
               
               
                 SEQ ID 
                 (Relative  
                 Unchallenged 
                 and 
                 Fibroblast 
                 GAA-/- 
               
               
                 NO: 
                 to SEQ ID 
                 Activity 
                 Activity 
                 Lysate 
                 Lysate 
               
               
                 (nt/aa) 
                 NO: 20) 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
               
               
                   
               
               
                 19/20 
                   
                 + 
                 + 
                 + 
                 + 
               
               
                 829/830 
                 L24R/F27G/A89R/ 
                   
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 D500A/S842G 
                   
                   
                   
                   
               
               
                 831/832 
                 L24R/F27G/D500A/ 
                 + 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 S842G 
                   
                   
                   
                   
               
               
                 833/834 
                 D500A/S932A 
                   
                 + 
                 ++ 
                 + 
               
               
                 835/836 
                 L24R/Q39H/S842G/ 
                   
                 + 
                 + 
                 ++ 
               
               
                   
                 S932A 
                   
                   
                   
                   
               
               
                 837/838 
                 Q39D/A89R/A97G/ 
                   
                 + 
                 ++ 
                 ++ 
               
               
                   
                 D500A 
                   
                   
                   
                   
               
               
                 839/840 
                 D500A/S842G 
                   
                 ++ 
                 ++ 
                 + 
               
               
                 841/842 
                 S842G/S932A 
                   
                   
                 + 
                 ++ 
               
               
                 843/844 
                 A89R/A97G/Q107G 
                   
                 ++ 
                 ++ 
                 ++ 
               
               
                 845/846 
                 A89R/A97G/D500A 
                   
                   
                 ++ 
                 ++ 
               
               
                 847/848 
                 F27G/Q39H/Q49G/ 
                   
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 A97G/D500A/S842G 
                   
                   
                   
                   
               
               
                 849/850 
                 R68N/A89R/A97G/ 
                   
                 + 
                 ++ 
                 + 
               
               
                   
                 S932A 
                   
                   
                   
                   
               
               
                 851/852 
                 A89R/S842G 
                   
                 + 
                 ++ 
                 + 
               
               
                 853/854 
                 L24R/Q39D/R68S/ 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 A89R/Q107G/D500A/ 
                   
                   
                   
                   
               
               
                   
                 S842G 
                   
                   
                   
                   
               
               
                 855/856 
                 L24R/F27G/D500A/ 
                   
                   
                 ++ 
                 ++ 
               
               
                   
                 S842G/S932A 
                   
                   
                   
                   
               
               
                 857/858 
                 L24R/Q39H/Q49G/A 
                   
                   
                 ++ 
                 ++ 
               
               
                   
                 89R/A97G/S842G/ 
                   
                   
                   
                   
               
               
                   
                 S932A 
                   
                   
                   
                   
               
               
                 859/860 
                 L24R/S842G/S932A 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                 861/862 
                 L24R/A89R/D500A 
                   
                 + 
                 ++ 
                 ++ 
               
               
                 863/864 
                 L24R/Q39H/A89R/ 
                   
                   
                 ++ 
                 ++ 
               
               
                   
                 A97D/S842G/S932A 
                   
                   
                   
                   
               
               
                 865/866 
                 L24R 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                 867/868 
                 F27G/Q49G/R68S/ 
                   
                 + 
                 ++ 
                 ++ 
               
               
                   
                 D500A/S842G 
                   
                   
                   
                   
               
               
                 869/870 
                 Q107G/D500A/ 
                   
                 + 
                 ++ 
                 ++ 
               
               
                   
                 S842G 
                   
                   
                   
                   
               
               
                 871/872 
                 L34T/Q39D/D500A/ 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 S932A 
                   
                   
                   
                   
               
               
                 873/874 
                 R68S 
                 + 
                 + 
                 ++ 
                 + 
               
               
                 875/876 
                 L24W/L109D/D612S 
                   
                 + 
                 ++ 
                 ++ 
               
               
                 877/878 
                 L24W/V70A/K267R/ 
                   
                 + 
                 ++ 
                 ++ 
               
               
                   
                 A774S 
                   
                   
                   
                   
               
               
                 879/880 
                 I22R/L24W/D612S/ 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 K725E/C944R 
                   
                   
                   
                   
               
               
                 881/882 
                 L24W 
                   
                   
                 ++ 
                 + 
               
               
                 883/884 
                 I22R/L24W/F27A/ 
                   
                 + 
                 ++ 
                 + 
               
               
                   
                 D489A 
                   
                   
                   
                   
               
               
                 885/886 
                 D489A 
                   
                   
                 + 
                 + 
               
               
                 887/888 
                 I22R/L24W/F27A/ 
                   
                 + 
                 ++ 
                 + 
               
               
                   
                 Q50V/Q107G/L109D/ 
                   
                   
                   
                   
               
               
                   
                 D489A/D612S/ 
                   
                   
                   
                   
               
               
                   
                 K725E 
                   
                   
                   
                   
               
               
                 889/890 
                 Q50V/D612S/C944S 
                 + 
                   
                 ++ 
                 + 
               
               
                 891/892 
                 D612S/K725E/ 
                 ++ 
                 ++ 
                 ++ 
                   
               
               
                   
                 C944S 
                   
                   
                   
                   
               
               
                 893/894 
                 L109D/D612S/ 
                 + 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 A774S/C944S 
                   
                   
                   
                   
               
               
                 895/896 
                 I22R/L24W/F27A/ 
                 + 
                 + 
                 ++ 
                 + 
               
               
                   
                 D612S/C944R 
                   
                   
                   
                   
               
               
                 897/898 
                 Q50V/D489A/A774S 
                   
                   
                 ++ 
                 ++ 
               
               
                 899/900 
                 Q50V/L109D/ 
                   
                   
                 + 
                 + 
               
               
                   
                 D489A/D612S 
                   
                   
                   
                   
               
               
                 901/902 
                 I22R/L24W/Q50V/ 
                   
                 + 
                 ++ 
                 ++ 
               
               
                   
                 L109D/K267R/ 
                   
                   
                   
                   
               
               
                   
                 D489A/A774S/C944R 
                   
                   
                   
                   
               
               
                 903/904 
                 I22R/L24W 
                 + 
                   
                 ++ 
                 ++ 
               
               
                 905/906 
                 L24W/Q50V/D489A/ 
                   
                 + 
                 ++ 
                 ++ 
               
               
                   
                 C944S 
                   
                   
                   
                   
               
               
                 907/908 
                 I22R/Q50V/L109D/ 
                 + 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 K267R/D489A 
                   
                   
                   
                   
               
               
                 909/910 
                 L24W/D489A/ 
                   
                   
                 ++ 
                 ++ 
               
               
                   
                 C944R 
                   
                   
                   
                   
               
               
                 911/912 
                 L24W/K725E 
                   
                   
                 ++ 
                 + 
               
               
                 913/914 
                 L24W/L109D/C944S 
                 + 
                 + 
                 ++ 
                 + 
               
               
                 915/916 
                 D612S/P922E 
                 + 
                 + 
                 + 
                   
               
               
                 917/918 
                 L24W/K267R/ 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 K725E/C944S 
                   
                   
                   
                   
               
               
                 919/920 
                 Q107G/L109D 
                   
                   
                   
                 ++ 
               
               
                 921/922 
                 D489A/C944R 
                 + 
                 + 
                 + 
                 + 
               
               
                 923/924 
                 I22R/L24W/Q50V/ 
                   
                   
                 ++ 
                 ++ 
               
               
                   
                 K267R/D612S/P922E/ 
                   
                   
                   
                   
               
               
                   
                 C944R 
                   
                   
                   
                   
               
               
                 925/926 
                 I22R/L24W/F27A/ 
                 + 
                   
                 +++ 
                 + 
               
               
                   
                 D489A/D612S/A774S 
                   
                   
                   
                   
               
               
                 927/928 
                 L24W/F27A/Q107G/ 
                 + 
                   
                 ++ 
                 + 
               
               
                   
                 K267R/D612S/ 
                   
                   
                   
                   
               
               
                   
                 C944S 
                   
                   
                   
                   
               
               
                 929/930 
                 L24W/F27A/K267R/ 
                   
                   
                 + 
                 + 
               
               
                   
                 C944R 
                   
                   
                   
                   
               
               
                 931/932 
                 I22R/L24W/D489A 
                   
                   
                 ++ 
                 ++ 
               
               
                 933/934 
                 I22R/Q50V/Q107G/ 
                 + 
                 + 
                 ++ 
                 + 
               
               
                   
                 K267R/D489A/ 
                   
                   
                   
                   
               
               
                   
                 D612S/C944S 
                   
                   
                   
                   
               
               
                 935/936 
                 L24W/V70A/Q107G/ 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 L109D/D489A/ 
                   
                   
                   
                   
               
               
                   
                 D612S/K725E 
                   
                   
                   
                   
               
               
                 937/938 
                 I22R/L24W/Q107G/ 
                 + 
                   
                 +++ 
                 ++ 
               
               
                   
                 K267R/D489A/ 
                   
                   
                   
                   
               
               
                   
                 P922E 
                   
                   
                   
                   
               
               
                 939/940 
                 L24W/Q107G/ 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 L109D/K267R/D489A/ 
                   
                   
                   
                   
               
               
                   
                 D612S/K725E/A774S 
                   
                   
                   
                   
               
               
                 941/942 
                 L24W/F27A/C944R 
                 + 
                 + 
                 ++ 
                 + 
               
               
                 943/944 
                 D612S 
                   
                   
                 + 
                 ++ 
               
               
                 945/946 
                 L24W/Q50V/D612S 
                 + 
                   
                 ++ 
                 ++ 
               
               
                 947/948 
                 I22R/K267R/D489A/ 
                   
                 + 
                 ++ 
                 ++ 
               
               
                   
                 D612S 
                   
                   
                   
                   
               
               
                 949/950 
                 L24W/F27A/Q50V/ 
                 + 
                 + 
                 ++ 
                 + 
               
               
                   
                 Q107G/K267R/A774S/ 
                   
                   
                   
                   
               
               
                   
                 C944S 
                   
                   
                   
                   
               
               
                 951/952 
                 L24W/C944S 
                 + 
                   
                 ++ 
                 ++ 
               
               
                 953/954 
                 E614W 
                   
                   
                 ++ 
                 + 
               
               
                 955/956 
                 N527R 
                 + 
                 + 
                 ++ 
                 + 
               
               
                 957/958 
                 E381W 
                   
                   
                 ++ 
                 + 
               
               
                 959/960 
                 R862Y 
                 + 
                   
                 ++ 
                 + 
               
               
                 961/962 
                 D923L 
                   
                   
                 ++ 
                 ++ 
               
               
                 963/964 
                 A62L 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                 965/966 
                 S916R 
                   
                   
                 ++ 
                 + 
               
               
                 967/968 
                 P914G 
                   
                   
                 + 
                 + 
               
               
                 969/970 
                 D523E 
                 + 
                   
                 ++ 
                 + 
               
               
                 971/972 
                 D923W 
                   
                   
                 ++ 
                   
               
               
                 973/974 
                 A62F 
                   
                   
                 +++ 
                 + 
               
               
                 975/976 
                 E188W 
                   
                   
                 ++ 
                 + 
               
               
                 977/978 
                 P71V 
                   
                   
                 + 
                   
               
               
                 979/980 
                 P71W 
                   
                   
                 ++ 
                 + 
               
               
                 981/982 
                 L742V 
                 + 
                 + 
                 ++ 
                 + 
               
               
                 983/984 
                 N527V 
                   
                   
                 + 
                 + 
               
               
                 985/986 
                 P123V 
                   
                   
                 + 
                 + 
               
               
                 987/988 
                 H193P 
                 + 
                 ++ 
                 ++ 
                   
               
               
                 989/990 
                 P123L 
                   
                 ++ 
                 ++ 
                 + 
               
               
                 991/992 
                 P914Q 
                   
                   
                 + 
                 ++ 
               
               
                 993/994 
                 S124V 
                   
                   
                 ++ 
                 + 
               
               
                 995/996 
                 E858C 
                   
                   
                 ++ 
                 + 
               
               
                 997/998 
                 P57M 
                   
                   
                 + 
                 ++ 
               
               
                  999/1000 
                 S264M 
                 + 
                 + 
                 ++ 
                 + 
               
               
                 1001/1002  
                 T148K 
                   
                   
                 + 
                   
               
               
                 1003/1004  
                 P57F 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                 1005/1006  
                 E614Q 
                 + 
                   
                 ++ 
                 ++ 
               
               
                 1007/1008  
                 A112H 
                 ++ 
                 + 
                 ++ 
                 + 
               
               
                 1009/1010  
                 R862Q 
                 + 
                 + 
                 ++ 
                 + 
               
               
                 1011/1012  
                 H48W 
                   
                   
                 ++ 
                 ++ 
               
               
                 1013/1014  
                 P914T 
                   
                   
                 + 
                   
               
               
                 1015/1016  
                 S916G 
                   
                   
                 ++ 
                 + 
               
               
                 1017/1018  
                 K88R 
                   
                 + 
                 ++ 
                 + 
               
               
                 1019/1020  
                 P914K 
                   
                   
                 ++ 
                 ++ 
               
               
                 1021/1022  
                 G820A 
                   
                   
                 ++ 
                 + 
               
               
                 1023/1024  
                 V913W 
                   
                   
                 ++ 
                 + 
               
               
                 1025/1026  
                 D923V 
                   
                 ++ 
                 ++ 
                 ++ 
               
               
                 1027/1028  
                 P832A 
                   
                   
                   
                 + 
               
               
                 1029/1030  
                 P71L 
                 + 
                 ++ 
                 ++ 
                 + 
               
               
                 1031/1032  
                 A253M 
                   
                 ++ 
                 + 
                 ++ 
               
               
                 1033/1034  
                 L823F 
                   
                 + 
                 ++ 
                 + 
               
               
                 1035/1036  
                 L305F 
                   
                   
                 ++ 
                 + 
               
               
                 1037/1038  
                 P914S 
                   
                   
                 + 
                 + 
               
               
                 1039/1040  
                 S727W 
                 + 
                   
                 ++ 
                 ++ 
               
               
                 1041/1042  
                 L940Q 
                 + 
                 + 
                 ++ 
                 + 
               
               
                 1043/1044  
                 E188R 
                   
                   
                 + 
                 + 
               
               
                 1045/1046  
                 H48V 
                 + 
                   
                 + 
                 + 
               
               
                 1047/1048  
                 P832R 
                   
                 + 
                 ++ 
                 ++ 
               
               
                 1049/1050  
                 H48Q 
                 + 
                 + 
                 + 
                   
               
               
                 1051/1052  
                 H193E 
                 + 
                 + 
                 + 
                 + 
               
               
                 1053/1054  
                 T148R 
                 + 
                   
                 +++ 
                 ++ 
               
               
                 1055/1056  
                 G820V 
                   
                   
                 ++ 
                   
               
               
                 1057/1058  
                 E381R 
                   
                   
                 ++ 
                   
               
               
                 1059/1060  
                 S402N 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                 1061/1062  
                 L823V 
                   
                 + 
                 ++ 
                 ++ 
               
               
                 1063/1064  
                 R862M 
                   
                 + 
                 ++ 
                 + 
               
               
                 1065/1066  
                 K88L 
                   
                   
                   
                 + 
               
               
                 1067/1068  
                 A62W 
                   
                 ++ 
                 ++ 
                 ++ 
               
               
                 1069/1070 
                 G108R 
                 + 
                 ++ 
                 + 
                 + 
               
               
                 1071/1072 
                 L748V 
                   
                 + 
                 ++ 
                 + 
               
               
                 1073/1074 
                 E42G 
                   
                 + 
                 ++ 
                 + 
               
               
                 1075/1076 
                 E858W 
                   
                 + 
                 ++ 
                 ++ 
               
               
                 1077/1078 
                 P57L 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                 1079/1080 
                 I333L 
                   
                   
                 + 
                   
               
               
                 1081/1082 
                 V312A 
                   
                   
                 + 
                   
               
               
                 1083/1084 
                 P197G 
                 ++ 
                 ++ 
                 + 
                 + 
               
               
                 1085/1086 
                 S916H 
                 + 
                 ++ 
                 ++ 
                 + 
               
               
                 1087/1088 
                 P914I 
                   
                   
                 ++ 
                   
               
               
                 1089/1090 
                 N911R 
                   
                   
                 ++ 
                   
               
               
                 1091/1092 
                 E381V 
                   
                   
                 ++ 
                 + 
               
               
                 1093/1094 
                 P71Y 
                   
                   
                 ++ 
                 + 
               
               
                 1095/1096 
                 R862I 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1097/1098 
                 S124M 
                 + 
                 + 
                 ++ 
                 + 
               
               
                 1099/1100 
                 P71G 
                 + 
                   
                 + 
                 + 
               
               
                 1101/1102 
                 P914R 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                 1103/1104 
                 S124G 
                   
                   
                 ++ 
                 + 
               
               
                 1105/1106 
                 N911G 
                   
                   
                 + 
                 + 
               
               
                 1107/1108 
                 E614R 
                   
                   
                 ++++ 
                 ++ 
               
               
                 1109/1110 
                 V913R 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1111/1112 
                 E937K 
                   
                 + 
                 +++ 
                 ++ 
               
               
                 1113/1114 
                 E204A 
                   
                 + 
                   
                   
               
               
                 1115/1116 
                 S402V/P781Q 
                 + 
                 ++ 
                 ++ 
                 + 
               
               
                 1117/1118 
                 V913G 
                 + 
                 + 
                 ++ 
                 + 
               
               
                   
               
               
                   1 All activities were determined relative to the reference polypeptide of SEQ ID NO: 20. 
               
               
                 Levels of increased activity are defined as follows: 
               
               
                 “+” = 0.9 to 1.1; 
               
               
                 “++” &gt; 1.1; 
               
               
                 “+++” &gt; 2; and 
               
               
                 “++++” &gt; 3.5. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 10-2 
               
             
            
               
                   
               
               
                 Activity of GAA Variants Relative to SEQ ID NO: 20 1   
               
            
           
           
               
               
               
               
               
            
               
                   
                 Amino Acid  
                   
                 Plasma 
                 Activity from 
               
               
                 SEQ ID 
                 Differences 
                 Unchallenged 
                 Stability and 
                 Pompe 
               
               
                 NO:  
                 (Relative to SEQ  
                 Activity 
                 Activity 
                 Fibroblast 
               
               
                 (nt/aa) 
                 ID NO: 20) 
                 FIOPC 
                 FIOPC 
                 Lysate FIOPC 
               
               
                   
               
               
                 19/20 
                   
                 + 
                 + 
                 + 
               
               
                 1119/1120 
                 K88G 
                 ++ 
                 ++ 
                 + 
               
               
                 1121/1122 
                 L818V 
                 + 
                   
                 ++ 
               
               
                 1123/1124 
                 T148E 
                 + 
                 + 
                 + 
               
               
                 1125/1126 
                 A741D 
                 + 
                   
                 + 
               
               
                 1127/1128 
                 N527P 
                 + 
                 + 
                 ++ 
               
               
                 1129/1130 
                 L737M 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1131/1132 
                 G445L 
                 + 
                   
                   
               
               
                 1133/1134 
                 P197L 
                 + 
                 + 
                 + 
               
               
                 1135/1136 
                 M260V 
                 + 
                 + 
                   
               
               
                 1137/1138 
                 A112W 
                 + 
                   
                 ++ 
               
               
                 1139/1140 
                 H45M 
                 + 
                 + 
                 + 
               
               
                 1141/1142 
                 G108S 
                 + 
                 + 
                 ++ 
               
               
                 1143/1144 
                 L259N 
                   
                   
                 + 
               
               
                 1145/1146 
                 P71Q 
                 + 
                 + 
                 ++ 
               
               
                 1147/1148 
                 E42C 
                   
                   
                 + 
               
               
                 1149/1150 
                 P57T 
                 + 
                 + 
                   
               
               
                 1151/1152 
                 P197I 
                 + 
                 + 
                 + 
               
               
                 1153/1154 
                 L238Q 
                 + 
                   
                   
               
               
                 1155/1156 
                 I816L 
                 + 
                 + 
                 ++ 
               
               
                 1157/1158 
                 E858V 
                 + 
                 + 
                 + 
               
               
                 1159/1160 
                 S916A 
                 + 
                 + 
                 + 
               
               
                 1161/1162 
                 P682A 
                 + 
                 + 
                 + 
               
               
                 1163/1164 
                 M260F 
                 + 
                   
                 + 
               
               
                 1165/1166 
                 H255Q 
                 + 
                   
                 + 
               
               
                 1167/1168 
                 M432C 
                 + 
                 + 
                 ++ 
               
               
                 1169/1170 
                 P71D 
                 + 
                   
                 ++ 
               
               
                 1171/1172 
                 T325A 
                 + 
                   
                   
               
               
                 1173/1174 
                 E188Q/R377Q 
                 + 
                 + 
                   
               
               
                 1175/1176 
                 K106G 
                 + 
                 + 
                   
               
               
                 1177/1178 
                 K106N 
                 ++ 
                 + 
                 + 
               
               
                 1179/1180 
                 L244I 
                 + 
                   
                 + 
               
               
                 1181/1182 
                 A319F 
                   
                   
                 + 
               
               
                 1183/1184 
                 I815M 
                   
                   
                 + 
               
               
                 1185/1186 
                 F237L 
                 + 
                   
                 + 
               
               
                 1187/1188 
                 H63A 
                 ++ 
                 + 
                 + 
               
               
                 1189/1190 
                 P832E 
                 + 
                 + 
                 + 
               
               
                 1191/1192 
                 A741T 
                   
                 + 
                 + 
               
               
                 1193/1194 
                 S124F 
                 ++ 
                 + 
                 ++ 
               
               
                 1195/1196 
                 T325V 
                 + 
                 ++ 
                 ++ 
               
               
                 1197/1198 
                 P832V 
                 ++ 
                 + 
                 + 
               
               
                 1199/1200 
                 P682K 
                 ++ 
                 ++ 
                 + 
               
               
                 1201/1202 
                 H387R 
                 + 
                 + 
                 + 
               
               
                 1203/1204 
                 R862G 
                 + 
                 + 
                 ++ 
               
               
                 1205/1206 
                 H63K 
                 + 
                 + 
                 + 
               
               
                 1207/1208 
                 S243R 
                   
                   
                 + 
               
               
                 1209/1210 
                 H255R 
                 + 
                   
                 + 
               
               
                 1211/1212 
                 E204G 
                 + 
                 + 
                 ++ 
               
               
                 1213/1214 
                 V312F 
                 + 
                   
                 + 
               
               
                 1215/1216 
                 S727T 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1217/1218 
                 L240I 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1219/1220 
                 L261T 
                 + 
                   
                   
               
               
                 1221/1222 
                 S264F 
                 + 
                 + 
                 ++ 
               
               
                 1223/1224 
                 E614V 
                 + 
                   
                 ++ 
               
               
                 1225/1226 
                 T91I 
                   
                   
                 + 
               
               
                 1227/1228 
                 L240M 
                 ++ 
                 + 
                 ++ 
               
               
                 1229/1230 
                 S727A 
                 + 
                 + 
                 + 
               
               
                 1231/1232 
                 V913A 
                 + 
                   
                 + 
               
               
                 1233/1234 
                 P832K 
                   
                 + 
                 ++ 
               
               
                 1235/1236 
                 L940G 
                 + 
                   
                 ++ 
               
               
                 1237/1238 
                 Q61V 
                 + 
                 + 
                 + 
               
               
                 1239/1240 
                 R455T 
                 + 
                 + 
                 + 
               
               
                 1241/1242 
                 H193S 
                 ++ 
                 + 
                 ++ 
               
               
                 1243/1244 
                 M260R 
                 + 
                   
                   
               
               
                 1245/1246 
                 E204Q 
                   
                   
                 + 
               
               
                 1247/1248 
                 S262L 
                 + 
                   
                 + 
               
               
                 1249/1250 
                 T91K 
                 + 
                 + 
                 ++ 
               
               
                 1251/1252 
                 S127G/P914F 
                   
                   
                 + 
               
               
                 1253/1254 
                 R455V 
                 ++ 
                 + 
                   
               
               
                 1255/1256 
                 A62P 
                 + 
                 + 
                   
               
               
                 1257/1258 
                 E42Q 
                 + 
                 + 
                 + 
               
               
                 1259/1260 
                 E614L 
                 + 
                 + 
                 + 
               
               
                 1261/1262 
                 L305Y 
                 + 
                 + 
                 ++ 
               
               
                 1263/1264 
                 S264L 
                 + 
                 + 
                 + 
               
               
                 1265/1266 
                 P186G 
                 + 
                 + 
                   
               
               
                 1267/1268 
                 G820K 
                 + 
                 + 
                 + 
               
               
                 1269/1270 
                 P832M 
                 + 
                 + 
                 ++ 
               
               
                 1271/1272 
                 S264R 
                 + 
                 + 
                 ++ 
               
               
                 1273/1274 
                 H63T 
                 + 
                 + 
                 + 
               
               
                 1275/1276 
                 S262F 
                   
                   
                 + 
               
               
                 1277/1278 
                 F237M 
                 + 
                   
                   
               
               
                 1279/1280 
                 K88V 
                 + 
                 + 
                 + 
               
               
                 1281/1282 
                 S124R 
                 + 
                 + 
                 + 
               
               
                 1283/1284 
                 Q61M 
                 + 
                 + 
                 + 
               
               
                 1285/1286 
                 H193V 
                 + 
                 + 
                 + 
               
               
                 1287/1288 
                 H63C 
                 + 
                   
                 ++ 
               
               
                 1289/1290 
                 T148V 
                 + 
                 + 
                 + 
               
               
                 1291/1292 
                 N911M 
                   
                   
                 + 
               
               
                 1293/1294 
                 N527F 
                 + 
                   
                 ++ 
               
               
                 129S/1296 
                 K88E 
                 + 
                 + 
                   
               
               
                 1297/1298 
                 L305G 
                 + 
                   
                   
               
               
                 1299/1300 
                 Q61G 
                 + 
                 + 
                 ++ 
               
               
                 1301/1302 
                 S124D 
                 + 
                 + 
                 ++ 
               
               
                 1303/1304 
                 F237V 
                 + 
                   
                   
               
               
                 1305/1306 
                 A253L 
                 + 
                 ++ 
                 + 
               
               
                 1307/1308 
                 I815A 
                   
                   
                 + 
               
               
                 1309/1310 
                 R862C 
                 + 
                 + 
                 ++ 
               
               
                 1311/1312 
                 Q421R 
                 + 
                 + 
                 ++ 
               
               
                 1313/1314 
                 H255T 
                 + 
                   
                   
               
               
                 1315/1316 
                 H63D 
                 + 
                 + 
                 + 
               
               
                 1317/1318 
                 P832W 
                 + 
                 + 
                 ++ 
               
               
                 1319/1320 
                 P57R 
                 + 
                 + 
                 ++ 
               
               
                 1321/1322 
                 T148S 
                   
                 + 
                 + 
               
               
                 1323/1324 
                 S262T 
                 + 
                 + 
                 + 
               
               
                 1325/1326 
                 A62G 
                   
                   
                 + 
               
               
                 1327/1328 
                 P914E 
                 + 
                 + 
                 + 
               
               
                 1329/1330 
                 K88M 
                 + 
                 + 
                 + 
               
               
                 1331/1332 
                 R862K 
                 + 
                 + 
                 ++ 
               
               
                 1333/1334 
                 R455G 
                 + 
                   
                   
               
               
                 1335/1336 
                 S264C 
                   
                   
                 + 
               
               
                 1337/1338 
                 K88I 
                 + 
                 + 
                   
               
               
                 1339/1340 
                 Y248A 
                 + 
                   
                   
               
               
                 1341/1342 
                 L305R 
                 + 
                 + 
                 ++ 
               
               
                 1343/1344 
                 P279G 
                 + 
                   
                   
               
               
                 1345/1346 
                 A62S 
                 + 
                 + 
                 ++ 
               
               
                 1347/1348 
                 R455H 
                 + 
                 + 
                 + 
               
               
                 1349/1350 
                 L320M 
                 + 
                 ++ 
                 ++ 
               
               
                 1351/1352 
                 L736V 
                 + 
                 + 
                 + 
               
               
                 1353/1354 
                 A309C 
                 + 
                 + 
                 + 
               
               
                 1355/1356 
                 E204D 
                 + 
                 + 
                 + 
               
               
                 1357/1358 
                 S264A 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1359/1360 
                 H193R 
                 + 
                 + 
                 ++ 
               
               
                 1361/1362 
                 E614G 
                 + 
                 + 
                 ++ 
               
               
                 1363/1364 
                 K154R 
                 + 
                 + 
                 + 
               
               
                 1365/1366 
                 K154E 
                 + 
                 + 
                 + 
               
               
                 1367/1368 
                 T29S 
                 + 
                 + 
                 ++ 
               
               
                 1369/1370 
                 Q421Y 
                   
                   
                 + 
               
               
                 1371/1372 
                 P197V 
                 + 
                 + 
                   
               
               
                 1373/1374 
                 E188G 
                 + 
                 + 
                 ++ 
               
               
                 1375/1376 
                 K88S 
                   
                 + 
                   
               
               
                 1377/1378 
                 Y248F 
                 + 
                 + 
                 + 
               
               
                 1379/1380 
                 K88W 
                   
                 + 
                 + 
               
               
                 1381/1382 
                 H45N 
                 ++ 
                 + 
                 + 
               
               
                 1383/1384 
                 P914M 
                 + 
                 + 
                 ++ 
               
               
                 1385/1386 
                 S727Q 
                 + 
                 + 
                 + 
               
               
                 1387/1388 
                 P71A 
                 + 
                 + 
                 + 
               
               
                 1389/1390 
                 P197T 
                 + 
                 + 
                 + 
               
               
                 1391/1392 
                 T148A 
                 + 
                 + 
                   
               
               
                 1393/1394 
                 E858M 
                 + 
                   
                 + 
               
               
                 1395/1396 
                 L823A 
                 + 
                 + 
                 ++ 
               
               
                 1397/1398 
                 P57S 
                 + 
                 ++ 
                 + 
               
               
                 1399/1400 
                 E204S 
                 + 
                   
                 + 
               
               
                 1401/1402 
                 P186S 
                 + 
                   
                   
               
               
                 1403/1404 
                 K106V 
                 + 
                 + 
                 + 
               
               
                 1405/1406 
                 L736W 
                 + 
                 + 
                   
               
               
                 1407/1408 
                 E614I 
                 + 
                   
                 + 
               
               
                 1409/1410 
                 S916I 
                 + 
                 + 
                 + 
               
               
                 1411/1412 
                 R862A 
                 + 
                 + 
                 + 
               
               
                 1413/1414 
                 V913E 
                 + 
                 + 
                 + 
               
               
                 1415/1416 
                 H63R 
                 + 
                 + 
                 ++ 
               
               
                 1417/1418 
                 E937S 
                 + 
                 + 
                 ++ 
               
               
                 1419/1420 
                 S262A 
                 + 
                 + 
                   
               
               
                 1421/1422 
                 P71R 
                 + 
                 + 
                 ++ 
               
               
                 1423/1424 
                 E858R 
                 + 
                   
                   
               
               
                 1425/1426 
                 H63P 
                 + 
                 + 
                   
               
               
                 1427/1428 
                 L305V 
                 ++ 
                 ++ 
                   
               
               
                 1429/1430 
                 E42W 
                 + 
                 + 
                 ++ 
               
               
                 1431/1432 
                 H48I 
                 + 
                 + 
                 + 
               
               
                 1433/1434 
                 K154A 
                 + 
                 + 
                   
               
               
                 1435/1436 
                 Y248V 
                 + 
                   
                   
               
               
                 1437/1438 
                 A112F 
                 + 
                 + 
                 + 
               
               
                 1439/1440 
                 L818T 
                   
                   
                 + 
               
               
                 1441/1442 
                 A741C 
                 + 
                 + 
                 + 
               
               
                 1443/1444 
                 P123Y 
                 + 
                 + 
                 + 
               
               
                 1445/1446 
                 F556S 
                 + 
                 + 
                 ++ 
               
               
                 1447/1448 
                 D523L 
                 + 
                   
                 + 
               
               
                 1449/1450 
                 R862L 
                 + 
                   
                 + 
               
               
                 1451/1452 
                 A62V 
                 + 
                 + 
                 + 
               
               
                 1453/1454 
                 Q61P 
                 + 
                 + 
                 + 
               
               
                 1455/1456 
                 H193A 
                 + 
                 + 
                   
               
               
                 1457/1458 
                 H255V 
                 + 
                   
                   
               
               
                 1459/1460 
                 L748I 
                 + 
                 + 
                 + 
               
               
                 1461/1462 
                 M260W 
                 ++ 
                   
                 ++ 
               
               
                 1463/1464 
                 R455L 
                 + 
                 + 
                 + 
               
               
                 1465/1466 
                 I249L 
                 + 
                 + 
                 + 
               
               
                 1467/1468 
                 G108N 
                 + 
                 + 
                 ++ 
               
               
                 1469/1470 
                 Q421G 
                 + 
                 + 
                 ++ 
               
               
                 1471/1472 
                 I816V 
                 + 
                 + 
                 + 
               
               
                 1473/1474 
                 L818M 
                 + 
                 + 
                 + 
               
               
                 1475/1476 
                 R195Y 
                 + 
                 + 
                   
               
               
                 1477/1478 
                 P832C 
                   
                   
                 ++ 
               
               
                 1479/1480 
                 L748T 
                 + 
                   
                   
               
               
                 1481/1482 
                 N527W 
                   
                   
                 ++ 
               
               
                 1483/1484 
                 T148R/V772I 
                 + 
                 + 
                 ++ 
               
               
                 1485/1486 
                 K106T 
                 + 
                 + 
                   
               
               
                 1487/1488 
                 L240W/A374T 
                   
                 + 
                   
               
               
                 1489/1490 
                 F556Y 
                   
                 + 
                   
               
               
                 1491/1492 
                 P914F 
                   
                   
                 + 
               
               
                 1493/1494 
                 P57Y 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1495/1496 
                 M432L 
                 + 
                 ++ 
                 ++ 
               
               
                 1497/1498 
                 P123S 
                 + 
                 + 
                 + 
               
               
                 1499/1500 
                 G108V 
                 + 
                 + 
                   
               
               
                 1501/1502 
                 P279R 
                 + 
                   
                   
               
               
                 1503/1504 
                 R195V 
                 + 
                 + 
                   
               
               
                 1505/1506 
                 E42D 
                 + 
                 + 
                   
               
               
                 1507/1508 
                 F205L 
                 + 
                 + 
                   
               
               
                 1509/1510 
                 H45S 
                 + 
                 + 
                 ++ 
               
               
                 1511/1512 
                 Q421M 
                   
                   
                 ++ 
               
               
                 1513/1514 
                 A112R 
                 + 
                 + 
                 ++ 
               
               
                 1515/1516 
                 S916V 
                 + 
                 + 
                 ++ 
               
               
                 1517/I518 
                 E381T 
                 + 
                   
                 ++ 
               
               
                 1519/1520 
                 A253S 
                 + 
                   
                   
               
               
                 1521/1522 
                 F205V 
                 + 
                 + 
                 + 
               
               
                 1523/1524 
                 E858S 
                 + 
                 ++ 
                 + 
               
               
                 1525/1526 
                 E858G 
                 + 
                 ++ 
                 ++ 
               
               
                 1527/1528 
                 E937Q 
                 + 
                 + 
                 + 
               
               
                 1529/1530 
                 P914W 
                   
                   
                 + 
               
               
                 1531/1532 
                 P197R 
                 + 
                 ++ 
                 ++ 
               
               
                 1533/1534 
                 S264V 
                 + 
                 + 
                 ++ 
               
               
                 1535/1536 
                 S727R 
                   
                   
                 + 
               
               
                 1537/1538 
                 E858K 
                   
                 + 
                 + 
               
               
                 1539/1540 
                 P832G 
                 ++ 
                 + 
                 ++ 
               
               
                 1541/1542 
                 V913H 
                   
                   
                 ++ 
               
               
                 1543/1544 
                 T148M 
                 + 
                   
                 ++ 
               
               
                 1545/1546 
                 L252V 
                 + 
                   
                 + 
               
               
                 1547/1548 
                 P123M 
                 + 
                 + 
                 ++ 
               
               
                 1549/1550 
                 E937R 
                   
                   
                 + 
               
               
                 1551/1552 
                 S243G 
                   
                   
                 + 
               
               
                 1553/1554 
                 R455S 
                   
                   
                 + 
               
               
                 1555/1556 
                 A741E 
                   
                   
                 + 
               
               
                 1557/1558 
                 S243V 
                   
                   
                 + 
               
               
                 1559/1560 
                 S402R 
                 + 
                 + 
                 + 
               
               
                 1561/1562 
                 P832I 
                 + 
                 + 
                 ++ 
               
               
                 1563/1564 
                 P57C 
                 + 
                 + 
                 + 
               
               
                 1565/1566 
                 E614P 
                   
                   
                 + 
               
               
                 1567/1568 
                 P279E 
                 + 
                   
                 + 
               
               
                 1569/1570 
                 V913Q 
                 + 
                 + 
                 ++ 
               
               
                 1571/1572 
                 P682W 
                   
                   
                 ++ 
               
               
                 1573/1574 
                 E381G 
                   
                   
                 ++ 
               
               
                 1575/1576 
                 N527S 
                 + 
                 + 
                 + 
               
               
                 1577/1578 
                 E614Y 
                 + 
                 ++ 
                 ++ 
               
               
                 1579/1580 
                 I816M 
                   
                   
                 + 
               
               
                 1581/1582 
                 H45C 
                 + 
                 + 
                 + 
               
               
                 1583/1584 
                 L259G 
                 + 
                   
                   
               
               
                 1585/1586 
                 S243E 
                   
                   
                 + 
               
               
                 1587/1588 
                 E204V 
                 + 
                 + 
                 + 
               
               
                 1589/1590 
                 P57N 
                 + 
                 + 
                 + 
               
               
                 1591/1592 
                 H45Y 
                   
                   
                 + 
               
               
                 1593/1594 
                 F237A 
                   
                   
                 + 
               
               
                 1595/1596 
                 P71C 
                 + 
                   
                 ++ 
               
               
                 1597/1598 
                 H48G 
                 + 
                 + 
                 ++ 
               
               
                 1599/1600 
                 A253G 
                 + 
                   
                 ++ 
               
               
                 1601/1602 
                 L736M 
                 ++ 
                 + 
                 ++ 
               
               
                 1603/1604 
                 L940W 
                 + 
                   
                 ++ 
               
               
                 1605/1606 
                 L823G 
                   
                   
                 ++ 
               
               
                 1607/1608 
                 S262E 
                 ++ 
                 ++ 
                 + 
               
               
                 1609/1610 
                 E188S 
                 + 
                 ++ 
                 + 
               
               
                 1611/1612 
                 T325L 
                 + 
                 + 
                 ++ 
               
               
                 1613/1614 
                 N527G 
                   
                   
                 + 
               
               
                 1615/1616 
                 P197A 
                 + 
                 + 
                 + 
               
               
                 1617/1618 
                 H193L 
                 + 
                 + 
                   
               
               
                 1619/1620 
                 S727G 
                 + 
                 + 
                 ++ 
               
               
                 1621/1622 
                 F556R 
                 + 
                 + 
                 ++ 
               
               
                 1623/1624 
                 L261E 
                 + 
                   
                 + 
               
               
                 1625/1626 
                 A309G 
                 ++ 
                   
                 ++ 
               
               
                 1627/1628 
                 E42Y 
                   
                   
                 + 
               
               
                 1629/1630 
                 K154L 
                 + 
                   
                 + 
               
               
                 1631/1632 
                 F556H 
                 + 
                 + 
                 + 
               
               
                 1633/1634 
                 K106A 
                 + 
                 + 
                   
               
               
                 1635/1636 
                 S402G 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1637/1638 
                 H45T 
                 ++ 
                 ++ 
                 + 
               
               
                 1639/1640 
                 E858P 
                 + 
                 + 
                 ++ 
               
               
                 1641/1642 
                 S262P 
                 + 
                 ++ 
                 + 
               
               
                 1643/1644 
                 P914H 
                   
                 + 
                 ++ 
               
               
                 1645/1646 
                 P71E 
                 ++ 
                 ++ 
                 + 
               
               
                 1647/1648 
                 P682L 
                 + 
                 + 
                 + 
               
               
                 1649/1650 
                 E188T 
                 + 
                 ++ 
                 + 
               
               
                 1651/1652 
                 L329F 
                 + 
                 ++ 
                 ++ 
               
               
                 1653/1654 
                 S246G 
                   
                   
                 + 
               
               
                 1655/1656 
                 H63M 
                 + 
                 ++ 
                 + 
               
               
                 1657/1658 
                 H63L 
                 + 
                 + 
                 + 
               
               
                 1659/1660 
                 R323A 
                   
                   
                 + 
               
               
                 1661/1662 
                 T148G 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1663/1664 
                 S124C 
                   
                   
                 ++ 
               
               
                 1665/1666 
                 R323L 
                   
                   
                 + 
               
               
                 1667/1668 
                 P682V 
                 + 
                 ++ 
                 ++ 
               
               
                 1669/1670 
                 G445Y 
                 + 
                   
                 ++ 
               
               
                 1671/1672 
                 E858Y 
                 + 
                 ++ 
                 ++ 
               
               
                 1673/1674 
                 P279L 
                 + 
                   
                 ++ 
               
               
                 1675/1676 
                 R862N 
                 ++ 
                 ++ 
                 + 
               
               
                 1677/1678 
                 P186A 
                 + 
                 + 
                   
               
               
                 1679/1680 
                 S262M 
                 + 
                 + 
                 ++ 
               
               
                 1681/1682 
                 E937F 
                   
                   
                 ++ 
               
               
                 1683/1684 
                 A741G 
                 ++ 
                 ++ 
                 + 
               
               
                 1685/1686 
                 P123G 
                 + 
                 + 
                 ++ 
               
               
                 1687/1688 
                 H45L 
                   
                 + 
                 ++ 
               
               
                 1689/1690 
                 H63W 
                 + 
                 ++ 
                 ++ 
               
               
                 1691/1692 
                 S246A 
                 + 
                   
                 + 
               
               
                 1693/1694 
                 L940T 
                 ++ 
                 ++ 
                 + 
               
               
                 1695/1696 
                 P57E 
                 + 
                 ++ 
                 + 
               
               
                 1697/1698 
                 P123A 
                 + 
                 + 
                 ++ 
               
               
                 1699/1700 
                 H63V 
                 + 
                 + 
                 + 
               
               
                 1701/1702 
                 H255S 
                 + 
                   
                   
               
               
                 1703/1704 
                 H387L 
                 + 
                 ++ 
                 + 
               
               
                 1705/1706 
                 K106W 
                   
                   
                 + 
               
               
                 1707/1708 
                 P832S 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1709/1710 
                 S727C 
                 ++ 
                 + 
                 + 
               
               
                 1711/1712 
                 S124L 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1713/1714 
                 P914V 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1715/1716 
                 S124N 
                 + 
                 + 
                 + 
               
               
                 1717/1718 
                 L244V 
                 + 
                   
                 ++ 
               
               
                 1719/1720 
                 R323M 
                 + 
                   
                 ++ 
               
               
                 1721/1722 
                 S402D 
                 + 
                 + 
                 + 
               
               
                 1723/1724 
                 S402M 
                 + 
                 + 
                 ++ 
               
               
                 1725/1726 
                 L259M 
                 + 
                 + 
                 ++ 
               
               
                 1727/1728 
                 D523W 
                 + 
                 + 
                 + 
               
               
                 1729/1730 
                 R195G 
                 ++ 
                 ++ 
                 + 
               
               
                 1731/1732 
                 Q421F 
                   
                   
                 ++ 
               
               
                 1733/1734 
                 T148H 
                 + 
                 ++ 
                 ++ 
               
               
                 1735/1736 
                 Y248R 
                 + 
                   
                   
               
               
                 1737/1738 
                 A62T 
                 + 
                 + 
                 + 
               
               
                 1739/1740 
                 P279A 
                 + 
                   
                 + 
               
               
                 1741/1742 
                 R455E 
                   
                 + 
                   
               
               
                 1743/1744 
                 P682G 
                 ++ 
                 ++ 
                 + 
               
               
                 1745/1746 
                 E188M 
                 + 
                 ++ 
                 ++ 
               
               
                 1747/1748 
                 P57Q 
                 + 
                 + 
                 + 
               
               
                 1749/1750 
                 H193Y 
                 + 
                 + 
                 + 
               
               
                 1751/1752 
                 Q421A 
                 + 
                 + 
                 ++ 
               
               
                 1753/1754 
                 R195P 
                 + 
                 + 
                 + 
               
               
                 1755/1756 
                 L320V 
                 ++ 
                 + 
                 + 
               
               
                 1757/1758 
                 A253P 
                 + 
                 ++ 
                 + 
               
               
                 1759/1760 
                 S298P/Q421R 
                   
                   
                 ++ 
               
               
                 1761/1762 
                 H63G 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1763/1764 
                 A319M 
                   
                   
                 ++ 
               
               
                 1765/1766 
                 P682F 
                 + 
                 + 
                 ++ 
               
               
                 1767/1768 
                 H48R 
                 + 
                 + 
                 ++ 
               
               
                 1769/1770 
                 I333V 
                 + 
                 + 
                 ++ 
               
               
                 1771/1772 
                 A112P 
                   
                 + 
                 + 
               
               
                 1773/1774 
                 Q61D 
                 + 
                   
                   
               
               
                 1775/1776 
                 R323K 
                   
                 + 
                 + 
               
               
                 1777/1778 
                 P71F 
                 + 
                 + 
                 + 
               
               
                 1779/1780 
                 V913L 
                 + 
                 + 
                 + 
               
               
                 1781/1782 
                 E614S 
                 + 
                 ++ 
                 + 
               
               
                 1783/1784 
                 M260L 
                   
                   
                 ++ 
               
               
                 1785/1786 
                 L259S 
                   
                   
                 + 
               
               
                 1787/1788 
                 L823R 
                   
                   
                 ++ 
               
               
                 1789/1790 
                 L240Y 
                   
                   
                 + 
               
               
                 1791/1792 
                 S402W 
                 + 
                   
                 ++ 
               
               
                 1793/1794 
                 E937G 
                   
                   
                 + 
               
               
                 1795/1796 
                 H63Y 
                   
                 + 
                 ++ 
               
               
                 1797/1798 
                 I249V/S777N 
                 + 
                   
                 ++ 
               
               
                 1799/1800 
                 E42M 
                   
                   
                 + 
               
               
                 1801/1802 
                 E188V 
                 + 
                 + 
                 + 
               
               
                 1803/1804 
                 S402L 
                 + 
                 + 
                 + 
               
               
                 1805/1806 
                 A112V 
                 ++ 
                 ++ 
                 ++ 
               
               
                 1807/1808 
                 G108H 
                 + 
                 ++ 
                 ++ 
               
               
                 1809/1810 
                 P682R 
                 ++ 
                 + 
                 + 
               
               
                 1811/1812 
                 M432I 
                   
                   
                 + 
               
               
                 1813/1814 
                 Q61S 
                 + 
                 + 
                 + 
               
               
                 1815/1816 
                 N527A 
                 + 
                 + 
                 + 
               
               
                 1817/1818 
                 A741I 
                   
                   
                 + 
               
               
                 1819/1820 
                 G251C 
                   
                   
                 + 
               
               
                 1821/1822 
                 H63E 
                 ++ 
                 ++ 
                 + 
               
               
                 1823/1824 
                 T91V 
                   
                   
                 + 
               
               
                 1825/1826 
                 Q421P 
                   
                   
                 + 
               
               
                 1827/1828 
                 E937L 
                   
                   
                 + 
               
               
                   
               
               
                   1 All activities were determined relative to the reference polypeptide of SEQ ID NO: 20. 
               
               
                 Levels of increased activity are defined as follows: 
               
               
                 “+” = 0.9 to 1.1; and 
               
               
                 “++” &gt; 1.1. 
               
            
           
         
       
     
     EXAMPLE 11 
     High-Throughput Growth of Suspension Mammalian Cells and GAA Assays Obtained Through Suspension Mammalian Expression 
     High-Throughput (HTP) Growth of GAA and GAA Variants in Suspension Mammalian Cells (Expi293F) 
     EXPI293F™ cells (ThermoFisher Scientific) were transfected with pDH or PCR-amplified linear DNA (as described in Example 1) encoding a synthetic mouse IG signal peptide (SEQ ID NOS: 3381 and 3382) fusion to wild-type GAA or GAA variants using the lipofection method with EXPIFECTAMINE™ 293 Reagent (ThermoFisher Scientific) in EXPI293™ Expression Medium (ThermoFisher Scientific). EXPI293F™ cells (ThermoFisher Scientific) were cultured in EXPI293™ Expression Medium (ThermoFisher Scientific) and seeded into Axygen 1.1 mL deep well plate (Corning, P-DW-11-C-S), at densities of 1×10 6 cells/well/400 μL. Cells were subjected to lipofection-mediated transfection and returned to a shaking incubator with 8% CO 2  and 70% humidity for 3-4 days to allow for expression and secretion of GAA variants into the conditioned media. Conditioned media was harvested by centrifugation of expression plates and transfer of conditioned media into a BioRad Hardshell PCR Plate (BioRad, HSP9601). Plates were centrifuged again and clarified conditioned media was transferred into new 96-well plates for activity, stability or uptake into cell analysis. 
     HTP-Analysis of Supernatants 
     GAA variant activity was determined by measuring the hydrolysis of 4-methylumbelliferyl α-D-glucopyranoside (4-MUGlu). For the unchallenged assay, 5-10 μL of EXPI293™ clarified conditioned media produced as described above was mixed with 50 μL of 1.5 mM 4-MUGlu in McMaine Buffer (McIlvaine, J. Biol. Chem., 49:183-186 [1921]), pH 4.4, in a 96-well, black, opaque bottom plate. The reactions were incubated at 25-37° C. for 10-60 minutes with agitation at 400 rpm, prior to quenching with 100 μL of 0.5 M sodium carbonate pH 10.5. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader (Molecular Devices) or an ENVISION® microplate reader (Perkin Elmer) monitoring fluorescence (Ex. 355 nm, Em. 460 nm). Unchallenged activity FIOPC was calculated by dividing normalized GAA variant by the activity of the reference polypeptide with the indicated SEQ ID NO. 
     HTP-Analysis of Supernatants Challenged with Plasma 
     GAA variants were challenged with plasma to simulate the conditions that the variants encounter in the blood following their administration to a patient. First, 30 μL of GAA variants in EXPI293F™ clarified conditioned media were combined with 30 μL of plasma (Innovative Research, Innovative Grade US Origin Monkey Cynomolgus Plasma K2 EDTA) in a 96-well plate. The plates were sealed and incubated at 37° C. for 2-4 h. Next, 10 μL of plasma-challenged sample were mixed with 50 μL of 1.5 mM 4-MUGlu in McIlvaine buffer, pH 4.4. The reactions were incubated at 25-37° C, for 15-60 minutes with agitation at 400 rpm, prior to quenching with 100 μL of 0.5 M sodium carbonate pH 10.5. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader or an ENVISION® microplate reader (Perkin Elmer) monitoring fluorescence (Ex. 355 nm, Em. 460 nm). Plasma stability FIOPC was calculated by dividing normalized GAA variant activity following challenge by the activity of the reference polypeptide with the indicated SEQ ID NO following challenge. 
     HTP-Analysis of GAA Activity in Lysates of Pompe Fibroblasts and C2C12 GAA Knockout Myoblasts 
     GAA variants from HTP EXPI293F™ expression in clarified conditioned media were incubated with target cells and assayed for residual intracellular activity after 24-72 hours. For these experiments, mammalian cells lacking functional GAA activity were used, namely Pompe patient-derived fibroblasts (Coriell Institute for Medical Research # GM00248) and C2C12 myoblasts whose native GAA gene had been knocked out using Crispr-Cas9 editing. In these experiments, Pompe fibroblasts or C2C12 GAA knockout myoblasts were seeded into 96-well plates COSTAR® (3904, Corning) and allowed to grow to confluency in standard complete growth medium. Upon confluency, complete growth culture media was removed from the plates using an automated BIOMEK® i5 liquid handling robot. Clarified conditioned media from transient HPT transfections in EXPI293F™, were transferred to Pompe patient-derived fibroblasts and C2C12 myoblasts, and allowed to incubate for 4-24 hours at 37° C., 5% CO 2 . Medium was removed from the cultures using an automated BIOMEK® i5 liquid handling robot. The cells were briefly washed with 150 μL 1×DPBS/well, and DPBS was removed using an automated BIOMEK® i5 liquid handling robot. Then, 200 μL standard complete growth culture medium was added to each well, and the plates were returned to the incubator for 0-72 hours. At the conclusion of incubation, standard complete growth media was removed using an automated BIOMEK® i5 liquid handling robot. The cells were washed with 150 μL. 1×DPBS/well, and the DPBS removed using an automated BIOMEK® iS liquid handling. The cells were lysed via addition of 50 μL of McIlvaine buffer, pH 4.4, supplemented with 0.2-0.5% TRITON X-100™ non-ionic surfactant (Sigma #93443) and agitation at room temperature for 30 minutes. Activity was assessed by addition of 50 μL of 1.5 mM 4-MUGlu in McIlvaine buffer, pH 4.4. The plates were sealed, incubated at 37° C. for 300-360 minutes with agitation at 400 rpm, prior to quenching with 100 μL of 0.5 M sodium carbonate, pH 10.5. Hydrolysis was analyzed using a SPECTRAMAX® M2 microplate reader or an ENVISION® microplate reader (Perkin Elmer) monitoring fluorescence (Ex. 355 nm, Em. 460 nm). Cellular uptake FIOPC was calculated by dividing normalized GAA variant intracellular activity by the activity of the reference polypeptide with the indicated SEQ ID NO. 
     EXAMPLE 12 
     GAA Variants of SEQ ID NO: 946 
     In this Example, experiments for evolution and screening of GAA variants derived from SEQ ID NO: 946 for improved GAA activity after a series of challenges are described. Libraries of variant genes GAA encoded based off of by SEQ ID NO: 946 were constructed, plated, grown, and screened for GAA MU-Glu activity (“Unchallenged Activity FIOPC”), as well as after plasma challenge (“Plasma Stability and Activity FIOPC”), as described in Example 11. Variants were also tested for 4-MUGlu activity after lysis of Pompe fibroblasts treated for 24 hours (“Lysate Activity from Extended Treatment of Pompe Fibroblast FIOPC”) or GAA −/−  C2C12 cells (“Lysate Activity from Extended Treatment C2C12 GAA−/− FIOPC”) or 6 hour treatments hours (“Lysate Activity from Acute Treatment of Pompe Fibroblast FIOPC”) or (“Lysate Activity from Acute Treatment C2C12 GAA−/− FIOPC”), as described in Example 11. The results of these assays are presented in Table 12-1. 
     
       
         
           
               
             
               
                 TABLE 12-1 
               
             
            
               
                   
               
               
                 Activity of GAA Variants Relative to SEQ ID NO: 946 1   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                 Lysate 
                 Lysate 
                 Lysate 
                 Lysate 
               
               
                   
                   
                   
                   
                 Activity  
                 Activity 
                 Activity 
                 Activity 
               
               
                   
                   
                   
                   
                 from  
                 from 
                 from 
                 from 
               
               
                   
                 Amino Acid  
                   
                   
                 Extended 
                 Extended 
                 Acute 
                 Acute 
               
               
                   
                 Differences 
                   
                 Plasma  
                 Treatment 
                 Treatment  
                 Treatment 
                 Treatment 
               
               
                   
                 (Relative to  
                 Unchallenged 
                 Stability 
                 of Pompe 
                 C2C12 
                 of Pompe 
                 C2C12 
               
               
                 SEQ ID NO: 
                 SEQ ID NO: 
                 Activity 
                 and Activity 
                 Fibroblast 
                 GAA−/− 
                 Fibroblast 
                 GAA−/− 
               
               
                 (nt/aa) 
                 946) 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
               
               
                   
               
               
                 945/946 
                   
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                 1829/1830 
                 A62W/A89R/ 
                   
                   
                 +++ 
                 ++ 
                 +++ 
                   
               
               
                   
                 E188W/D489A/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 D500A/S727W/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 L823F 
                   
                   
                   
                   
                   
                   
               
               
                 1831/1832 
                 S124V/D500A/ 
                 + 
                   
                 ++ 
                 ++ 
                 ++ 
                   
               
               
                   
                 S842G/R862Q 
                   
                   
                   
                   
                   
                   
               
               
                 1833/1834 
                 W24R/D489A/ 
                 + 
                 + 
                   
                 ++ 
                 + 
                 ++ 
               
               
                   
                 D500A/S842G 
                   
                   
                   
                   
                   
                   
               
               
                 1835/1836 
                 W24R/Q39H/ 
                 ++ 
                 + 
                 ++ 
                   
                   
                   
               
               
                   
                 D489A/R862Q 
                   
                   
                   
                   
                   
                   
               
               
                 1837/1838 
                 W24R/P57L/ 
                 + 
                 + 
                 + 
                 + 
                 ++ 
                   
               
               
                   
                 L823F/R862Q 
                   
                   
                   
                   
                   
                   
               
               
                 1839/1840 
                 P57L 
                 + 
                 + 
                 ++ 
                 + 
                 ++ 
                   
               
               
                 1841/1842 
                 W24R/A89R/ 
                 + 
                 + 
                   
                 + 
                   
                   
               
               
                   
                 D489A 
                   
                   
                   
                   
                   
                   
               
               
                 1843/1844 
                 W24R/A89R/ 
                 + 
                 + 
                 ++ 
                 ++ 
                 + 
                   
               
               
                   
                 D489A/S727W/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 R862Q 
                   
                   
                   
                   
                   
                   
               
               
                 1845/1846 
                 Q39H/P57L/ 
                   
                   
                 +++ 
                 ++ 
                 +++ 
                   
               
               
                   
                 A62W/E188W/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 D500A/S842G 
                   
                   
                   
                   
                   
                   
               
               
                 1847/1848 
                 W24R/P57L/ 
                 + 
                   
                 ++ 
                 ++ 
                 ++ 
                   
               
               
                   
                 A62W/A89R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 D489A/L823F/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 R862Q 
                   
                   
                   
                   
                   
                   
               
               
                 1849/1850 
                 W24R/A62W/ 
                   
                   
                 + 
                   
                 ++ 
                   
               
               
                   
                 A89R/E188W/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 L823V/S842G/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 R862Q 
                   
                   
                   
                   
                   
                   
               
               
                 1851/1852 
                 P57L/E188W/ 
                   
                   
                 ++ 
                 ++ 
                 +++ 
                   
               
               
                   
                 D489A/L823F/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 R862Q 
                   
                   
                   
                   
                   
                   
               
               
                 1853/1854 
                 Q39H/P57L/ 
                 + 
                 + 
                 ++ 
                 ++ 
                 ++ 
                   
               
               
                   
                 D500A/R862Q 
                   
                   
                   
                   
                   
                   
               
               
                 1855/1856 
                 A62W/S124V/ 
                   
                   
                 ++ 
                 ++ 
                 +++ 
                   
               
               
                   
                 E188W/L823F/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S842G/R862Q 
                   
                   
                   
                   
                   
                   
               
               
                 1857/1858 
                 P57F/A62L/ 
                   
                   
                 +++ 
                 ++ 
                 +++ 
                   
               
               
                   
                 L305F/D500A/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 V913R/S916G 
                   
                   
                   
                   
                   
                   
               
               
                 1859/1860 
                 P57F/E614Q/ 
                   
                   
                 ++ 
                   
                 ++ 
                   
               
               
                   
                 S916G/S932A 
                   
                   
                   
                   
                   
                   
               
               
                 1861/1862 
                 P57F/A62L/ 
                   
                   
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 L305F/V913R 
                   
                   
                   
                   
                   
                   
               
               
                 1863/1864 
                 P57F/A62L/ 
                   
                 + 
                 +++ 
                 ++ 
                 + 
                   
               
               
                   
                 A437G/D500A/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 L761F/P914K/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S916R 
                   
                   
                   
                   
                   
                   
               
               
                 1865/1866 
                 A62L/A437G/ 
                   
                 + 
                 ++ 
                 ++ 
                   
                   
               
               
                   
                 V913R/S916R 
                   
                   
                   
                   
                   
                   
               
               
                 1867/1868 
                 A62L/D489A/ 
                   
                   
                 ++ 
                 + 
                 ++ 
                   
               
               
                   
                 E614Q/S916R 
                   
                   
                   
                   
                   
                   
               
               
                 1869/1870 
                 P57F/A62L/ 
                   
                   
                 +++ 
                 ++ 
                 ++ 
                   
               
               
                   
                 V913R/S916R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S932A 
                   
                   
                   
                   
                   
                   
               
               
                 1871/1872 
                 A62L/N527R/ 
                   
                   
                 +++ 
                   
                   
                   
               
               
                   
                 S727W/S916G 
                   
                   
                   
                   
                   
                   
               
               
                 1873/1874 
                 P57F/A62W/ 
                   
                   
                 +++ 
                 +++ 
                 ++ 
                   
               
               
                   
                 L305F/A437G/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 D500A/S727W/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 V913R/S916R 
                   
                   
                   
                   
                   
                   
               
               
                 1875/1876 
                 P57F/A437G/ 
                   
                   
                 +++ 
                 ++ 
                   
                   
               
               
                   
                 D500A/E614Q/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S727W/P914R 
                   
                   
                   
                   
                   
                   
               
               
                 1877/1878 
                 D500A/S727W/ 
                   
                   
                 +++ 
                 ++ 
                 + 
                   
               
               
                   
                 V913R/S916R 
                   
                   
                   
                   
                   
                   
               
               
                 1879/1880 
                 E381V 
                   
                   
                 ++ 
                 + 
                 + 
                   
               
               
                 1881/1882 
                 S124V/T148R/ 
                   
                   
                 +++ 
                   
                 ++ 
                   
               
               
                   
                 E381W/S727W/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 E858W/E937K 
                   
                   
                   
                   
                   
                   
               
               
                 1883/1884 
                 E381W/E858C/ 
                   
                   
                 +++ 
                 ++ 
                 ++ 
                   
               
               
                   
                 E937K 
                   
                   
                   
                   
                   
                   
               
               
                 1885/1886 
                 A62F/E614R 
                   
                   
                 +++ 
                 ++ 
                 +++ 
                 ++ 
               
               
                 1887/1888 
                 A89R/T148R/ 
                 + 
                   
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 P149R/E381W 
                   
                   
                   
                   
                   
                   
               
               
                 1889/1890 
                 A62F/P149R/ 
                   
                   
                 +++ 
                 ++ 
                 +++ 
                   
               
               
                   
                 E381V/E858W/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 E937K 
                   
                   
                   
                   
                   
                   
               
               
                 1891/1892 
                 A62F/P149R/ 
                   
                   
                 +++ 
                 ++ 
                 +++ 
                 ++ 
               
               
                   
                 S727W 
                   
                   
                   
                   
                   
                   
               
               
                 1893/1894 
                 A89R/T148R/ 
                 + 
                 + 
                 +++ 
                 ++ 
                 +++ 
                 +++ 
               
               
                   
                 P149R 
                   
                   
                   
                   
                   
                   
               
               
                 1895/1896 
                 A62F/A89R/ 
                   
                   
                 ++++ 
                 ++ 
                 +++ 
                 ++ 
               
               
                   
                 S124V/T148R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 E381W/E858W 
                   
                   
                   
                   
                   
                   
               
               
                 1897/1898 
                 A62F/A89R/ 
                   
                   
                 +++ 
                 ++ 
                 +++ 
                 ++ 
               
               
                   
                 T148R/E38IV/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 E614R/E858W 
                   
                   
                   
                   
                   
                   
               
               
                 1899/1900 
                 A62W/S124V/ 
                   
                   
                 +++ 
                 + 
                 ++ 
                   
               
               
                   
                 P149R/E381V/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 P832R/E858C/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 E937K 
                   
                   
                   
                   
                   
                   
               
               
                 1901/1902 
                 S124V/P832R/ 
                   
                   
                 +++ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 E937K 
                   
                   
                   
                   
                   
                   
               
               
                 1903/1904 
                 A62W/A89R/ 
                 + 
                 + 
                 +++ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 E381V 
                   
                   
                   
                   
                   
                   
               
               
                 1905/1906 
                 A62W/P149R/ 
                   
                   
                 +++ 
                 ++ 
                 +++ 
                 + 
               
               
                   
                 E381W/E614R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 E937K 
                   
                   
                   
                   
                   
                   
               
               
                 1907/1908 
                 S124V/E381W/ 
                   
                   
                 +++ 
                 + 
                 ++ 
                 + 
               
               
                   
                 E614R 
                   
                   
                   
                   
                   
                   
               
               
                 1909/1910 
                 A62F/E96K/ 
                   
                   
                 +++ 
                 + 
                 ++ 
                   
               
               
                   
                 E614R 
                   
                   
                   
                   
                   
                   
               
               
                 1911/1912 
                 T148R/P832R/ 
                   
                   
                 +++ 
                 ++ 
                 +++ 
                   
               
               
                   
                 E858W/E937K 
                   
                   
                   
                   
                   
                   
               
               
                 1913/1914 
                 A62F/A89R/ 
                   
                   
                 +++ 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 E381V/D923W 
                   
                   
                   
                   
                   
                   
               
               
                 1915/1916 
                 A62F/E381V 
                   
                   
                 +++ 
                 + 
                 + 
                   
               
               
                 1917/1918 
                 A62W/T148R/ 
                   
                   
                 ++++ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 P149R/E381V/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 E858C/E937K 
                   
                   
                   
                   
                   
                   
               
               
                 1919/1920 
                 A62W/T148R/ 
                   
                   
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 E381W/E858C 
                   
                   
                   
                   
                   
                   
               
               
                 1921/1922 
                 A62F/A89R/ 
                   
                   
                 ++++ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 P149R/E381W/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 P832R 
                   
                   
                   
                   
                   
                   
               
               
                 1923/1924 
                 A62W/A89R/ 
                 + 
                   
                 +++ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 P149R/E381W 
                   
                   
                   
                   
                   
                   
               
               
                 1925/1926 
                 D923W 
                   
                   
                 ++ 
                   
                   
                   
               
               
                 1927/1928 
                 A62W/A89R/ 
                   
                   
                 +++ 
                 ++ 
                 ++ 
                   
               
               
                   
                 S124V/E381W/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 E858C 
                   
                   
                   
                   
                   
                   
               
               
                 1929/1930 
                 E381V/E614R/ 
                   
                   
                 +++ 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 P832R 
                   
                   
                   
                   
                   
                   
               
               
                 1931/1932 
                 A62W/A89R/ 
                   
                   
                 +++ 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 E381W/E858C 
                   
                   
                   
                   
                   
                   
               
               
                 1933/1934 
                 A89R/E381W 
                 + 
                 + 
                 ++ 
                 ++ 
                 ++ 
                   
               
               
                 1935/1936 
                 A62W/S124V/ 
                   
                   
                 +++ 
                 + 
                 ++ 
                 +++ 
               
               
                   
                 T148R/P149R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 E381W/E614R 
                   
                   
                   
                   
                   
                   
               
               
                 1937/1938 
                 A62F/S124V/ 
                   
                   
                 +++ 
                 + 
                 ++ 
                   
               
               
                   
                 E381W/P832R 
                   
                   
                   
                   
                   
                   
               
               
                 1939/1940 
                 S19T/S124V/ 
                   
                   
                 +++ 
                 + 
                 ++ 
                   
               
               
                   
                 P149R/E381V/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S727W 
                   
                   
                   
                   
                   
                   
               
               
                 1941/1942 
                 A62W/T148R/ 
                   
                   
                 +++ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 E381W/E614R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 E937K 
                   
                   
                   
                   
                   
                   
               
               
                 1943/1944 
                 A62F/A89R/ 
                   
                   
                 +++ 
                 ++ 
                 +++ 
                 ++++ 
               
               
                   
                 T148R/D923W 
                   
                   
                   
                   
                   
                   
               
               
                 1945/1946 
                 A62W/T148R/ 
                   
                   
                 ++++ 
                 ++ 
                 ++ 
                 +++ 
               
               
                   
                 E381W/S727W 
                   
                   
                   
                   
                   
                   
               
               
                 1947/1948 
                 A62W/E381V 
                   
                   
                 ++ 
                 + 
                   
                   
               
               
                 1949/1950 
                 A62F/A89R 
                 + 
                 + 
                 +++ 
                 ++ 
                 + 
                 ++ 
               
               
                 1951/1952 
                 A62F/A89R/ 
                   
                   
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 E858C 
                   
                   
                   
                   
                   
                   
               
               
                 1953/1954 
                 A62W/A437G/ 
                   
                   
                 ++ 
                 ++ 
                 + 
                   
               
               
                   
                 D489A/E614Q/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S727W/V913R 
                   
                   
                   
                   
                   
                   
               
               
                 1955/1956 
                 A62L/A437G/ 
                   
                   
                 +++ 
                 +++ 
                 ++ 
                 + 
               
               
                   
                 D489A/N527R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S727W/V913R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S932A 
                   
                   
                   
                   
                   
                   
               
               
                 1957/1958 
                 P57F/A62W/ 
                   
                   
                 +++ 
                 ++ 
                 +++ 
                 ++ 
               
               
                   
                 L305F/D489A/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 Q907K/V913R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S916G 
                   
                   
                   
                   
                   
                   
               
               
                 1959/1960 
                 P57F/A62W/ 
                   
                   
                 ++ 
                 ++ 
                 +++ 
                 ++ 
               
               
                   
                 L305F/S916R 
                   
                   
                   
                   
                   
                   
               
               
                 1961/1962 
                 P57F/A437G/ 
                   
                   
                 +++ 
                 +++ 
                 ++ 
                 ++ 
               
               
                   
                 D500A/N527R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S727W/S916R 
                   
                   
                   
                   
                   
                   
               
               
                 1963/1964 
                 A62L/L305F/ 
                   
                   
                 ++ 
                   
                 +++ 
                 ++ 
               
               
                   
                 S727W 
                   
                   
                   
                   
                   
                   
               
               
                 1965/1966 
                 P57F/A62L/ 
                   
                   
                 +++ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 L305F/A437G/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 E614Q/A683S/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 V913R/S916R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S932A 
                   
                   
                   
                   
                   
                   
               
               
                 1967/1968 
                 P57F/L305F 
                   
                 + 
                 ++ 
                 + 
                 ++ 
                 + 
               
               
                 1969/1970 
                 D489A/E614Q/ 
                   
                   
                 ++ 
                 + 
                 ++ 
                   
               
               
                   
                 S916G 
                   
                   
                   
                   
                   
                   
               
               
                 1971/1972 
                 D489A/D500A 
                 + 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                   
               
               
                 1973/1974 
                 P57F/A62W/ 
                   
                   
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 A437G/V913R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S916G 
                   
                   
                   
                   
                   
                   
               
               
                 1975/1976 
                 P57F/A62W/ 
                   
                   
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 L305F/D489A/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 V913R/S916G 
                   
                   
                   
                   
                   
                   
               
               
                 1977/1978 
                 A62W/S727W 
                   
                   
                 ++ 
                   
                 ++ 
                 ++ 
               
               
                 1979/1980 
                 A62L/N527R 
                   
                   
                 ++ 
                 + 
                 ++ 
                 + 
               
               
                 1981/1982 
                 P57F/L305F/ 
                   
                 + 
                 +++ 
                 ++ 
                   
                   
               
               
                   
                 A437G/S916G 
                   
                   
                   
                   
                   
                   
               
               
                 1983/1984 
                 A62L/A437G/ 
                 + 
                 + 
                 ++++ 
                 +++ 
                   
                   
               
               
                   
                 N527R/S727W 
                   
                   
                   
                   
                   
                   
               
               
                 1985/1986 
                 P57F/A62L/ 
                 + 
                 ++++ 
                 +++ 
                   
                   
                   
               
               
                   
                 A437G/N527R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S727W 
                   
                   
                   
                   
                   
                   
               
               
                 1987/1988 
                 A62W/D489A/ 
                   
                   
                 +++ 
                 +++ 
                   
                   
               
               
                   
                 N527R/S916R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S932A 
                   
                   
                   
                   
                   
                   
               
               
                 1989/1990 
                 A62L/D489A/ 
                 + 
                 ++ 
                 ++ 
                 ++ 
                   
                   
               
               
                   
                 D500A/S932A 
                   
                   
                   
                   
                   
                   
               
               
                 1991/1992 
                 D500A/P9 
                   
                 + 
                 +++ 
                 ++ 
                   
                   
               
               
                   
                 14R/S916G 
                   
                   
                   
                   
                   
                   
               
               
                 1993/1994 
                 A62W/D500A 
                   
                 + 
                 ++ 
                 ++ 
                   
                   
               
               
                 1995/1996 
                 A62L/L305F/ 
                   
                   
                 +++ 
                 ++ 
                 ++ 
                   
               
               
                   
                 A437G/D500A/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S727W/V913R 
                   
                   
                   
                   
                   
                   
               
               
                 1997/1998 
                 A437G 
                 + 
                 + 
                 + 
                 + 
                   
                   
               
               
                 1999/2000 
                 P57F/A62L/ 
                 + 
                 ++ 
                 +++ 
                 ++ 
                   
                   
               
               
                   
                 S916G 
                   
                   
                   
                   
                   
                   
               
               
                 2001/2002 
                 P57F/A62L/ 
                   
                   
                 ++++ 
                 +++ 
                 ++ 
                 +++ 
               
               
                   
                 L305F/A437G/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 D500A/E614Q/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S727W/S916R 
                   
                   
                   
                   
                   
                   
               
               
                 2003/2004 
                 A437G/D489A/ 
                 + 
                 + 
                 ++ 
                 ++ 
                   
                   
               
               
                   
                 P914R/S916R 
                   
                   
                   
                   
                   
                   
               
               
                 2005/2006 
                 P57F/A62W/ 
                   
                   
                 ++ 
                   
                 ++ 
                 ++ 
               
               
                   
                 F120I/N527R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 V913R/S916R 
                   
                   
                   
                   
                   
                   
               
               
                 2007/2008 
                 A62L/A437G/ 
                   
                 + 
                 +++ 
                 ++ 
                   
                 ++ 
               
               
                   
                 N527R/S916G/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S932A 
                   
                   
                   
                   
                   
                   
               
               
                 2009/2010 
                 A437G/S727W/ 
                   
                 + 
                 +++ 
                 ++ 
                   
                   
               
               
                   
                 P914K 
                   
                   
                   
                   
                   
                   
               
               
                 2011/2012 
                 P57F/A437G/ 
                 + 
                 ++ 
                 ++ 
                 +++ 
                   
                 ++ 
               
               
                   
                 V913R/P914R 
                   
                   
                   
                   
                   
                   
               
               
                 2013/2014 
                 A62W/S916G 
                 + 
                 ++ 
                 ++ 
                 + 
                   
                   
               
               
                 2015/2016 
                 P57F/D489A/ 
                   
                   
                 +++ 
                 ++ 
                   
                   
               
               
                   
                 N527R/P914R/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S916G 
                   
                   
                   
                   
                   
                   
               
               
                 2017/2018 
                 A437G/P914R/ 
                   
                 + 
                 ++ 
                 ++ 
                   
                   
               
               
                   
                 S916G 
               
               
                   
               
               
                   1 All activities were determined relative to the reference polypeptide of SEQ ID NO: 946. 
               
               
                 Levels of increased activity are defined as follows: 
               
               
                 “+” = 0.9 to 1.1; 
               
               
                 “++” &gt; 1.1; 
               
               
                 “+++” &gt; 2; and 
               
               
                 “++++” &gt; 3.5. 
               
            
           
         
       
     
     EXAMPLE 13 
     GAA Variants of SEQ ID NO: 1956 
     In this Example, experiments for evolution and screening of GAA variants derived from SEQ ID NO: 1956 for improved GAA activity after a series of challenges are described. Libraries of variant genes GAA encoded based off of by SEQ ID NO: 1956 were constructed, plated, grown, and screened for GAA MU-Glu activity (“Unchallenged Activity FIOPC”), as well as after plasma challenge (“Plasma Stability and Activity HOPC”), as described in Example 11. Variants were also tested for 4-MUGlu activity after lysis of Pompe fibroblasts treated for 24 hours (“Lysate Activity from Extended Treatment of Pompe Fibroblast FIOPC”) or GAA −/−  C2C12 cells (“Lysate Activity from Extended Treatment C2C12 GAA−/− FIOPC”) or 6 hour treatments hours (“Lysate Activity from Acute Treatment of Pompe Fibroblast HOPC”) or (“Lysate Activity from Acute Treatment C2C12 GAA−/− FIOPC”), as described in Example 11. The results of these assays are presented in Tables 13-1 and 13-2. 
     
       
         
           
               
             
               
                 TABLE 13-1 
               
             
            
               
                   
               
               
                 Activity of GAA Variants Relative to SEQ ID NO: 1956 1   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                 Lysate 
                 Lysate 
                 Lysate 
                 Lysate 
               
               
                   
                   
                   
                   
                 Activity 
                 Activity 
                 Activity 
                 Activity 
               
               
                   
                   
                   
                   
                 from 
                 from 
                 from 
                 from 
               
               
                   
                 Amino Acid 
                   
                 Plasma 
                 Extended 
                 Extended 
                 Acute 
                 Acute 
               
               
                   
                 Differences  
                   
                 Stability 
                 Treatment 
                 Treatment 
                 Treatment 
                 Treatment 
               
               
                 SEQ ID 
                 (Relative to 
                 Unchallenged 
                 and 
                 of Pompe 
                 C2C12 
                 of Pompe 
                 C2C12 
               
               
                 NO: 
                 SEQ ID 
                 Activity 
                 Activity 
                 Fibroblast 
                 GAA-/- 
                 Fibroblast 
                 GAA-/- 
               
               
                 (nt/aa) 
                 NO: 1956) 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
               
               
                   
               
               
                 1955/1956 
                   
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                 2019/2020 
                 Q795E 
                 + 
                   
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                 2021/2022 
                 P78E/S372T/ 
                   
                   
                   
                 ++ 
                   
                   
               
               
                   
                 L390Q 
                   
                   
                   
                   
                   
                   
               
               
                 2023/2024 
                 D87E/T266N/ 
                   
                 ++ 
                 ++ 
                 ++ 
                   
                 ++ 
               
               
                   
                 S372T/T483S 
                   
                   
                   
                   
                   
                   
               
               
                 2025/2026 
                 D87E/Q795E 
                 + 
                 + 
                 +++ 
                 ++ 
                 ++ 
                 +++ 
               
               
                 2027/2028 
                 T266N/S372T/ 
                   
                 ++ 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 T924N 
                   
                   
                   
                   
                   
                   
               
               
                 2029/2030 
                 P78E 
                 + 
                 ++ 
                 ++ 
                 + 
                 + 
                   
               
               
                 2031/2032 
                 P78E/D87E/ 
                 ++ 
                 ++ 
                 ++ 
                 +++ 
                   
                   
               
               
                   
                 V536T 
                   
                   
                   
                   
                   
                   
               
               
                 2033/2034 
                 D87E/T266N/ 
                 + 
                 ++ 
                 ++ 
                 +++ 
                 + 
                 ++ 
               
               
                   
                 T483S 
                   
                   
                   
                   
                   
                   
               
               
                 2035/2036 
                 D87E 
                 + 
                 + 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                 2037/2038 
                 P78E/D87E/ 
                 + 
                 ++ 
                 + 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 K176T/T266N/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 V536T/Q615D 
                   
                   
                   
                   
                   
                   
               
               
                 2039/2040 
                 P78E/D87E/ 
                   
                 ++ 
                 ++ 
                 +++ 
                   
                 ++ 
               
               
                   
                 T266N/T483S/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 T924N 
                   
                   
                   
                   
                   
                   
               
               
                 2041/2042 
                 D87E/S372T/ 
                 + 
                   
                 + 
                   
                 ++ 
                 + 
               
               
                   
                 S777G 
                   
                   
                   
                   
                   
                   
               
               
                 2043/2044 
                 T266N/S372T/ 
                   
                   
                   
                   
                   
                 + 
               
               
                   
                 V536T/Q615D/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 T763L/S777G 
                   
                   
                   
                   
                   
                   
               
               
                 2045/2046 
                 P78E/V536T/ 
                 + 
                   
                 ++ 
                   
                   
                   
               
               
                   
                 Q615D 
                   
                   
                   
                   
                   
                   
               
               
                 2047/2048 
                 P78E/T266N/ 
                 + 
                 + 
                   
                 ++ 
                   
                   
               
               
                   
                 T483S/V536T/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 Q615D 
                   
                   
                   
                   
                   
                   
               
               
                 2049/2050 
                 T266N 
                 + 
                 ++ 
                 ++ 
                 +++ 
                 + 
                 ++ 
               
               
                 2051/2052 
                 D87E/Q615D 
                   
                   
                 ++ 
                 +++ 
                 ++ 
                 + 
               
               
                 2053/2054 
                 P78E/T266N/ 
                 + 
                 ++ 
                 ++ 
                 +++ 
                   
                   
               
               
                   
                 T763L 
                   
                   
                   
                   
                   
                   
               
               
                 2055/2056 
                 P78E/D87E/ 
                 + 
                 +++ 
                 ++ 
                 ++ 
                   
                 + 
               
               
                   
                 T266N/S372T/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 A386Y/S777G 
                   
                   
                   
                   
                   
                   
               
               
                 2057/2058 
                 D87E/V536T/ 
                 + 
                 + 
                 ++ 
                   
                 + 
                 + 
               
               
                   
                 S777G 
                   
                   
                   
                   
                   
                   
               
               
                 2059/2060 
                 L390Q/Q615D 
                 + 
                   
                 + 
                   
                 ++ 
                   
               
               
                 2061/2062 
                 P78E/T266N/ 
                 + 
                 +++ 
                 ++ 
                 +++ 
                   
                 ++ 
               
               
                   
                 T483S/Q795E 
                   
                   
                   
                   
                   
                   
               
               
                 2063/2064 
                 P78E/D87E/ 
                 + 
                 + 
                   
                   
                   
                 ++ 
               
               
                   
                 T483S/S777G 
                   
                   
                   
                   
                   
                   
               
               
                 2065/2066 
                 D87E/T266N 
                 + 
                 +++ 
                 +++ 
                 +++ 
                 ++ 
                 +++ 
               
               
                 2067/2068 
                 P78E/L390Q 
                 + 
                   
                 ++ 
                 + 
                   
                   
               
               
                 2069/2070 
                 T266N/V536T/ 
                 + 
                 + 
                 ++ 
                 +++ 
                 + 
                 + 
               
               
                   
                 Q615D/Q795E 
                   
                   
                   
                   
                   
                   
               
               
                 2071/2072 
                 D87E/T266N/ 
                   
                 ++ 
                 ++ 
                 ++ 
                   
                 + 
               
               
                   
                 T924N 
                   
                   
                   
                   
                   
                   
               
               
                 2073/2074 
                 P78E/D87E/ 
                 + 
                 +++ 
                 ++ 
                 +++ 
                 + 
                 ++ 
               
               
                   
                 T266N/S372T/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 V536T 
                   
                   
                   
                   
                   
                   
               
               
                 2075/2076 
                 S202K 
                 + 
                   
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 2077/2078 
                 T44G 
                 + 
                   
                 + 
                 ++ 
                   
                 ++ 
               
               
                 2079/2080 
                 S446T 
                 + 
                 + 
                 ++ 
                   
                 ++ 
                 ++ 
               
               
                 2081/2082 
                 Q344M 
                 + 
                 ++ 
                 ++ 
                 + 
                 ++ 
                 +++ 
               
               
                 2083/2084 
                 L41I/S53M 
                 + 
                 + 
                   
                 ++ 
                   
                 ++ 
               
               
                 2085/2086 
                 L488M 
                 + 
                 + 
                 + 
                 ++ 
                 + 
                 ++ 
               
               
                 2087/2088 
                 Q615G 
                   
                   
                 + 
                 ++ 
                 + 
                 ++ 
               
               
                 2089/2090 
                 P779E 
                 + 
                   
                 + 
                   
                 ++ 
                 ++ 
               
               
                 2091/2092 
                 S777G 
                 ++ 
                 + 
                 ++ 
                   
                 ++ 
                 ++ 
               
               
                 2093/2094 
                 T141W 
                 + 
                   
                   
                   
                 + 
                 + 
               
               
                 2095/2096 
                 G65L 
                 + 
                   
                   
                 + 
                 ++ 
                 ++ 
               
               
                 2097/2098 
                 L857T 
                 + 
                   
                   
                   
                 + 
                 + 
               
               
                 2099/2100 
                 P779R 
                 + 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2101/2102 
                 S202N 
                 + 
                   
                 + 
                   
                 ++ 
                 ++ 
               
               
                 2103/2104 
                 S678H 
                 + 
                 ++ 
                   
                   
                 + 
                 + 
               
               
                 2105/2106 
                 Q425R/S678I/ 
                   
                   
                 ++ 
                 + 
                 ++ 
                 +++ 
               
               
                   
                 G894C 
                   
                   
                   
                   
                   
                   
               
               
                 2107/2108 
                 T543C 
                 + 
                   
                 + 
                 + 
                 + 
                 + 
               
               
                 2109/2110 
                 T543S 
                 + 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2111/2112 
                 V859Y 
                   
                   
                   
                   
                 + 
                 + 
               
               
                 2113/2114 
                 P199V 
                 + 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2115/2116 
                 G412Y 
                 + 
                   
                   
                   
                 + 
                 + 
               
               
                 2117/2118 
                 L909F 
                 + 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2119/2120 
                 F679W 
                 + 
                 + 
                   
                   
                   
                   
               
               
                 2121/2122 
                 G65V 
                 + 
                   
                   
                   
                 + 
                 + 
               
               
                 2123/2124 
                 P503S 
                 + 
                 + 
                   
                   
                 ++ 
                 ++ 
               
               
                 2125/2126 
                 G56L 
                 + 
                 ++ 
                 + 
                 ++ 
                 ++ 
                 + 
               
               
                 2127/2128 
                 G56A 
                 + 
                 + 
                 + 
                   
                 ++ 
                 + 
               
               
                 2129/2130 
                 L423V 
                 + 
                 + 
                   
                   
                 + 
                   
               
               
                 2131/2132 
                 S777I 
                 + 
                   
                 + 
                 + 
                 + 
                 + 
               
               
                 2133/2134 
                 V797L 
                   
                   
                   
                 ++ 
                   
                 ++ 
               
               
                 2135/2136 
                 S678Y 
                 ++ 
                 ++ 
                 + 
                 + 
                 + 
                 ++ 
               
               
                 2137/2138 
                 N484L 
                   
                   
                   
                   
                   
                 ++ 
               
               
                 2139/2140 
                 Q768S 
                 + 
                   
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2141/2142 
                 T145R 
                 + 
                 + 
                 ++ 
                   
                 ++ 
                 ++ 
               
               
                 2143/2144 
                 I156L 
                   
                   
                   
                   
                 + 
                 ++ 
               
               
                 2145/2146 
                 V797M 
                   
                   
                   
                 + 
                 + 
                 + 
               
               
                 2147/2148 
                 T44P/L347I 
                   
                   
                   
                   
                 + 
                   
               
               
                 2149/2150 
                 E773V 
                 ++ 
                   
                 ++ 
                   
                 ++ 
                 ++ 
               
               
                 2151/2152 
                 A105T 
                 + 
                 ++ 
                   
                 + 
                 + 
                 + 
               
               
                 2153/2154 
                 L530V 
                   
                   
                   
                   
                 + 
                 ++ 
               
               
                 2155/2156 
                 T543Q 
                 ++ 
                   
                 ++ 
                   
                 ++ 
                 + 
               
               
                 2157/2158 
                 T543V 
                 + 
                   
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2159/2160 
                 L488K 
                 + 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2161/2162 
                 T826G 
                   
                   
                   
                   
                   
                 + 
               
               
                 2163/2164 
                 V859T 
                 + 
                   
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                 2165/2166 
                 T141S 
                 ++ 
                   
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 2167/2168 
                 S202L 
                 + 
                   
                 + 
                 ++ 
                   
                 ++ 
               
               
                 2169/2170 
                 S202R 
                 + 
                   
                 + 
                 + 
                   
                 + 
               
               
                 2171/2172 
                 A834H 
                 + 
                   
                   
                   
                   
                 + 
               
               
                 2173/2174 
                 L488G 
                   
                 ++ 
                   
                   
                   
                   
               
               
                 2175/2176 
                 S777R 
                 + 
                   
                 + 
                 + 
                   
                 + 
               
               
                 2177/2178 
                 T44R 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 2179/2180 
                 S136G 
                   
                   
                   
                   
                 + 
                 + 
               
               
                 2181/2182 
                 T44E 
                 ++ 
                 + 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2183/2184 
                 T145I 
                 + 
                   
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                 2185/2186 
                 D726E 
                   
                   
                   
                   
                   
                 + 
               
               
                 2187/2188 
                 S202T 
                 + 
                   
                 + 
                 + 
                 + 
                 ++ 
               
               
                 2189/2190 
                 P779H 
                   
                   
                   
                   
                 ++ 
                 + 
               
               
                 2191/2192 
                 A496G 
                 + 
                   
                 + 
                 + 
                   
                 + 
               
               
                 2193/2194 
                 S678L 
                 + 
                 ++ 
                   
                   
                 ++ 
                 +++ 
               
               
                 2195/2196 
                 G56R 
                 + 
                 ++ 
                 + 
                 ++ 
                 ++ 
                 + 
               
               
                 2197/2198 
                 D348G 
                 + 
                   
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2199/2200 
                 Q344G 
                   
                 + 
                   
                   
                   
                 + 
               
               
                 2201/2202 
                 S678T 
                 ++ 
                 ++ 
                 ++ 
                 +++ 
                 ++ 
                 ++ 
               
               
                 2203/2204 
                 T44L 
                 ++ 
                   
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 2205/2206 
                 L656V 
                   
                 + 
                   
                 ++ 
                   
                 + 
               
               
                 2207/2208 
                 L693F 
                   
                   
                   
                   
                   
                 + 
               
               
                 2209/2210 
                 V710N 
                   
                   
                   
                   
                   
                 + 
               
               
                 2211/2212 
                 V710L 
                   
                 + 
                   
                   
                   
                   
               
               
                 2213/2214 
                 M663A 
                   
                   
                   
                   
                   
                 + 
               
               
                 2215/2216 
                 V710M 
                 + 
                   
                   
                   
                   
                   
               
               
                 2217/2218 
                 L670I 
                 + 
                   
                 ++ 
                 + 
                   
                 + 
               
               
                 2219/2220 
                 L670F 
                 + 
                 ++ 
                 + 
                 ++ 
                   
                 + 
               
               
                 2221/2222 
                 L670R 
                 + 
                 + 
                 ++ 
                   
                 + 
                 ++ 
               
               
                 2223/2224 
                 V710S 
                   
                   
                   
                   
                   
                 + 
               
               
                 2225/2226 
                 F588L 
                 + 
                   
                   
                   
                   
                   
               
               
                 2227/2228 
                 F705M 
                   
                 + 
                   
                   
                   
                 + 
               
               
                 2229/2230 
                 L670Q 
                 + 
                 + 
                 + 
                 + 
                   
                   
               
               
                 2231/2232 
                 L670T 
                 + 
                 ++ 
                 + 
                 ++ 
                   
                 ++ 
               
               
                 2233/2234 
                 K154R/F588L 
                 + 
                   
                   
                   
                   
                 + 
               
               
                 2235/2236 
                 L693Y 
                   
                   
                 + 
                   
                   
                   
               
               
                 2237/2238 
                 V710K 
                   
                 + 
                 + 
                   
                   
                 + 
               
               
                 2239/2240 
                 A708C 
                   
                   
                 + 
                 + 
                   
                 ++ 
               
               
                 2241/2242 
                 Y430F 
                   
                   
                 + 
                   
                   
                 + 
               
               
                 2243/2244 
                 I816L 
                   
                   
                 ++ 
                   
                   
                   
               
               
                 2245/2246 
                 L656M 
                   
                   
                 ++ 
                   
                   
                   
               
               
                 2247/2248 
                 L670W 
                   
                   
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                 2249/2250 
                 L670V 
                 + 
                   
                   
                   
                 + 
                   
               
               
                 2251/2252 
                 L693I 
                   
                   
                 ++ 
                 + 
                   
                 ++ 
               
               
                 2253/2254 
                 V589I/M663F 
                 + 
                 + 
                   
                 + 
                 ++ 
                 ++ 
               
               
                 2255/2256 
                 F588V 
                   
                   
                 ++ 
                   
                   
                   
               
               
                 2257/2258 
                 M663F 
                 + 
                 + 
                 ++ 
                   
                 + 
                 + 
               
               
                 2259/2260 
                 M687L 
                   
                   
                 ++ 
                   
                 + 
                 ++ 
               
               
                 2261/2262 
                 L670E 
                 + 
                   
                 + 
                   
                   
                 + 
               
               
                 2263/2264 
                 L670S 
                 ++ 
                 ++ 
                 ++ 
                   
                   
                 + 
               
               
                 2265/2266 
                 L628M 
                 + 
                 + 
                 + 
                 ++ 
                 + 
                 + 
               
               
                 2267/2268 
                 V580I 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2269/2270 
                 V580L 
                 + 
                   
                 + 
                   
                   
                   
               
               
                 2271/2272 
                 R583L 
                 + 
                   
                 + 
                   
                 + 
                 + 
               
               
                 2273/2274 
                 W3L/L569F 
                 + 
                 + 
                   
                   
                 + 
                 + 
               
               
                 2275/2276 
                 L629I 
                 + 
                   
                   
                   
                 ++ 
                 ++ 
               
               
                 2277/2278 
                 T692L 
                 + 
                 + 
                 + 
                   
                 + 
                   
               
               
                 2279/2280 
                 A711C 
                   
                   
                   
                   
                   
                 + 
               
               
                 2281/2282 
                 R577T 
                 + 
                   
                   
                   
                   
                   
               
               
                 2283/2284 
                 H499Y/A711F 
                   
                   
                   
                   
                 + 
                   
               
               
                 2285/2286 
                 P503T 
                 + 
                 ++ 
                   
                   
                   
                 + 
               
               
                 2287/2288 
                 A690V 
                   
                   
                 + 
                   
                   
                 ++ 
               
               
                 2289/2290 
                 L628V 
                   
                   
                   
                   
                   
                 + 
               
               
                 2291/2292 
                 L569I 
                 + 
                 + 
                   
                   
                   
                 + 
               
               
                 2293/2294 
                 L69IV 
                   
                 ++ 
                   
                   
                   
                   
               
               
                 2295/2296 
                 T692V 
                   
                 ++ 
                 ++ 
                   
                   
                   
               
               
                 2297/2298 
                 L569Y 
                 + 
                 ++ 
                 ++ 
                 + 
                   
                 ++ 
               
               
                 2299/2300 
                 I573Q 
                 + 
                 ++ 
                   
                   
                   
                 ++ 
               
               
                 2301/2302 
                 A711F 
                   
                 + 
                 + 
                 + 
                   
                 + 
               
               
                 2303/2304 
                 T692Y 
                 + 
                 + 
                 + 
                 ++ 
                   
                 ++ 
               
               
                 2305/2306 
                 L629C 
                   
                   
                   
                   
                   
                 + 
               
               
                 2307/2308 
                 T692I 
                   
                   
                 + 
                   
                   
                   
               
               
                 2309/2310 
                 L157S 
                   
                   
                 + 
                   
                   
                   
               
               
                 2311/2312 
                 S671A 
                   
                 + 
                   
                   
                   
                 + 
               
               
                 2313/2314 
                 R577M 
                   
                 + 
                   
                   
                   
                 + 
               
               
                 2315/2316 
                 L569S 
                   
                 ++ 
                   
                   
                   
                 + 
               
               
                 2317/2318 
                 I573M 
                 + 
                 ++ 
                   
                   
                   
                 + 
               
               
                 2319/2320 
                 R577V 
                 + 
                   
                   
                   
                   
                   
               
               
                 2321/2322 
                 T692C 
                 + 
                 + 
                   
                   
                   
                   
               
               
                 2323/2324 
                 I573H 
                 + 
                   
                   
                   
                   
                   
               
               
                 2325/2326 
                 S671T 
                 ++ 
                 ++ 
                   
                   
                   
                 ++ 
               
               
                 2327/2328 
                 I573D 
                 ++ 
                   
                   
                   
                   
                   
               
               
                 2329/2330 
                 S671M 
                 + 
                 ++ 
                   
                   
                   
                   
               
               
                 2331/2332 
                 R577D 
                 + 
                 + 
                   
                   
                   
                 + 
               
               
                 2333/2334 
                 L629A 
                   
                 + 
                   
                   
                 + 
                 + 
               
               
                 2335/2336 
                 T692G 
                 + 
                 + 
                 + 
                   
                 ++ 
                 ++ 
               
               
                 2337/2338 
                 A711R 
                 + 
                 ++ 
                 ++ 
                 + 
                   
                 ++ 
               
               
                 2339/2340 
                 R577A 
                 + 
                 + 
                   
                   
                   
                   
               
               
                 2341/2342 
                 L628I 
                 + 
                 ++ 
                 ++ 
                 + 
                 + 
                 ++ 
               
               
                 2343/2344 
                 T692F 
                 + 
                 + 
                 + 
                   
                   
                 ++ 
               
               
                 2345/2346 
                 R583G 
                   
                   
                   
                   
                   
                 + 
               
               
                 2347/2348 
                 R583K 
                 + 
                 + 
                 + 
                   
                   
                 + 
               
               
                 2349/2350 
                 V580Y 
                   
                   
                   
                   
                   
                 + 
               
               
                 2351/2352 
                 A572G 
                   
                   
                   
                   
                   
                 + 
               
               
                 2353/2354 
                 A711W 
                   
                   
                 + 
                   
                   
                   
               
               
                 2355/2356 
                 L629G 
                   
                   
                   
                   
                   
                 + 
               
               
                 2357/2358 
                 I573C 
                 + 
                   
                   
                   
                   
                 + 
               
               
                 2359/2360 
                 L569V 
                   
                   
                   
                   
                   
                 + 
               
               
                 2361/2362 
                 L669R 
                   
                   
                 ++ 
                   
                   
                   
               
               
                 2363/2364 
                 L579V 
                   
                   
                   
                   
                   
                 + 
               
               
                 2365/2366 
                 A572S 
                 ++ 
                 ++ 
                 + 
                   
                   
                 ++ 
               
               
                 2367/2368 
                 T692S 
                 + 
                 ++ 
                 ++ 
                   
                   
                 + 
               
               
                 2369/2370 
                 T692R 
                 + 
                 + 
                 ++ 
                   
                   
                 ++ 
               
               
                 2371/2372 
                 V580E 
                 + 
                 + 
                 + 
                   
                   
                 ++ 
               
               
                 2373/2374 
                 A574S 
                   
                 + 
                   
                   
                   
                 + 
               
               
                 2375/2376 
                 V631I 
                   
                 + 
                 + 
                   
                   
                 + 
               
               
                 2377/2378 
                 A711H 
                 + 
                 ++ 
                   
                   
                 + 
                 ++ 
               
               
                 2379/2380 
                 L691F 
                 + 
                   
                 + 
                 + 
                   
                 ++ 
               
               
                 2381/2382 
                 V580G 
                 + 
                   
                   
                   
                   
                 + 
               
               
                 2383/2384 
                 V580W 
                 + 
                   
                   
                   
                   
                   
               
               
                 2385/2386 
                 R577E 
                 ++ 
                   
                   
                   
                   
                 + 
               
               
                 2387/2388 
                 R583C 
                   
                   
                   
                   
                   
                 + 
               
               
                 2389/2390 
                 A711L 
                 + 
                   
                 + 
                   
                   
                   
               
               
                 2391/2392 
                 S671G 
                   
                   
                 + 
                   
                   
                   
               
               
                 2393/2394 
                 A711G 
                   
                   
                   
                 + 
                   
                 + 
               
               
                 2395/2396 
                 V631L 
                   
                   
                 ++ 
                   
                   
                 + 
               
               
                 2397/2398 
                 L569T 
                 + 
                 ++ 
                 ++ 
                 + 
                   
                 ++ 
               
               
                 2399/2400 
                 L569H 
                 ++ 
                   
                   
                   
                 + 
                 + 
               
               
                 2401/2402 
                 L569Q 
                 + 
                   
                   
                   
                   
                   
               
               
                 2403/2404 
                 V631M 
                   
                   
                 ++ 
                   
                   
                 + 
               
               
                 2405/2406 
                 H709S 
                 + 
                   
                 + 
                   
                   
                 ++ 
               
               
                 2407/2408 
                 T227A 
                   
                   
                 + 
                   
                   
                 + 
               
               
                 2409/2410 
                 V878R 
                 + 
                 + 
                 ++ 
                 + 
                   
                   
               
               
                 2411/2412 
                 A578S 
                 + 
                   
                   
                   
                   
                   
               
               
                 2413/2414 
                 T585L 
                 + 
                   
                 ++ 
                 + 
                 + 
                 + 
               
               
                 2415/2416 
                 L871E 
                 + 
                 + 
                 + 
                 + 
                   
                   
               
               
                 2417/2418 
                 V222C 
                 + 
                   
                 ++ 
                 + 
                   
                 + 
               
               
                 2419/2420 
                 K581Y 
                   
                   
                   
                   
                   
                 + 
               
               
                 2421/2422 
                 V878G 
                   
                   
                   
                   
                   
                 ++ 
               
               
                 2423/2424 
                 T585V 
                   
                 + 
                   
                   
                   
                   
               
               
                 2425/2426 
                 K581H 
                   
                   
                   
                   
                   
                 ++ 
               
               
                 2427/2428 
                 I877L 
                   
                 + 
                 + 
                   
                   
                 + 
               
               
                 2429/2430 
                 V868L 
                   
                 + 
                   
                   
                   
                 + 
               
               
                 2431/2432 
                 V878A 
                 + 
                 + 
                   
                 ++ 
                 + 
                 + 
               
               
                 2433/2434 
                 R873Y 
                   
                 + 
                 + 
                 + 
                   
                 + 
               
               
                 2435/2436 
                 H706V 
                   
                   
                   
                   
                   
                 + 
               
               
                 2437/2438 
                 K581G 
                   
                   
                   
                   
                   
                 + 
               
               
                 2439/2440 
                 V222P 
                   
                 + 
                   
                   
                   
                 + 
               
               
                 2441/2442 
                 T585M 
                   
                   
                 + 
                 + 
                   
                 ++ 
               
               
                 2443/2444 
                 T585Q 
                   
                 + 
                   
                 + 
                   
                 + 
               
               
                 2445/2446 
                 L633V 
                   
                   
                 + 
                   
                   
                   
               
               
                 2447/2448 
                 A229C 
                   
                   
                 ++ 
                   
                   
                   
               
               
                 2449/2450 
                 L871R 
                   
                   
                   
                   
                   
                 + 
               
               
                 2451/2452 
                 V878L 
                 + 
                 ++ 
                 + 
                   
                   
                 + 
               
               
                 2453/2454 
                 V868I 
                   
                 + 
                 ++ 
                   
                   
                 + 
               
               
                 2455/2456 
                 K581V 
                   
                   
                   
                   
                   
                 + 
               
               
                 2457/2458 
                 K581F 
                   
                   
                   
                   
                   
                 + 
               
               
                 2459/2460 
                 T585F 
                   
                 + 
                   
                   
                   
                 + 
               
               
                 2461/2462 
                 V878K 
                   
                   
                 ++ 
                   
                   
                 + 
               
               
                 2463/2464 
                 R873A 
                 + 
                 + 
                 + 
                   
                   
                   
               
               
                 2465/2466 
                 K581L 
                 + 
                 ++ 
                   
                   
                   
                 + 
               
               
                 2467/2468 
                 K581T 
                 + 
                 + 
                   
                   
                   
                   
               
               
                 2469/2470 
                 I869L 
                 + 
                 + 
                 ++ 
                 + 
                   
                 + 
               
               
                 2471/2472 
                 K581S 
                 + 
                 ++ 
                   
                   
                   
                 + 
               
               
                 2473/2474 
                 V878S 
                 ++ 
                 ++ 
                   
                 ++ 
                 ++ 
                 ++ 
               
               
                 2475/2476 
                 H706M 
                   
                 ++ 
                   
                   
                   
                 + 
               
               
                 2477/2478 
                 V878Q 
                 ++ 
                 ++ 
                 ++ 
                   
                   
                   
               
               
                 2479/2480 
                 R873F 
                   
                   
                 + 
                   
                   
                   
               
               
                 2481/2482 
                 I877V 
                 + 
                 ++ 
                 + 
                   
                   
                   
               
               
                 2483/2484 
                 V878F 
                 ++ 
                 ++ 
                 + 
                 + 
                   
                 + 
               
               
                 2485/2486 
                 I869S 
                 + 
                 ++ 
                 + 
                   
                   
                   
               
               
                 2487/2488 
                 V878W 
                 ++ 
                 ++ 
                   
                   
                   
                 + 
               
               
                 2489/2490 
                 H706F 
                 + 
                 + 
                 ++ 
                   
                   
                   
               
               
                 2491/2492 
                 N225D 
                   
                 + 
                 ++ 
                   
                   
                   
               
               
                 2493/2494 
                 L871K 
                 ++ 
                 ++ 
                   
                 + 
                 ++ 
                 + 
               
               
                 2495/2496 
                 P78E/D87E/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 T266N 
               
               
                   
               
               
                   1 All activities were determined relative to the reference polypeptide of SEQ ID NO: 1956. Levels of increased activity are defined as follows: “+” = 0.9 to 1.1; “++” &gt; 1.1; and “+++” &gt; 2. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 13-2 
               
             
            
               
                   
               
               
                 Activity of GAA Variants Relative to SEQ ID NO: 1956 1   
               
            
           
           
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                 Lysate Activity 
                 Lysate 
               
               
                   
                   
                   
                 Plasma 
                 from Extended  
                 Activity from 
               
               
                   
                 Amino Acid 
                   
                 Stability 
                 Treatment of 
                 Extended 
               
               
                 SEQ ID 
                 Differences 
                 Unchallenged 
                 and 
                 Pompe 
                 Treatment 
               
               
                 NO: 
                 (Relative to SEQ ID  
                 Activity 
                 Activity 
                 Fibroblast 
                 C2C12 GAA-/-  
               
               
                 (nt/aa) 
                 NO: 1956) 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
               
               
                   
               
               
                 2497/2498 
                 A142G 
                 + 
                   
                 + 
                 + 
               
               
                 2499/2500 
                 P788N 
                   
                 + 
                   
                 + 
               
               
                 2501/2502 
                 D493L 
                   
                 ++ 
                 ++ 
                 ++ 
               
               
                 2503/2504 
                 P788L 
                   
                 ++ 
                   
                   
               
               
                 2505/2506 
                 S612T 
                 + 
                 ++ 
                 + 
                 + 
               
               
                 2507/2508 
                 W265H 
                   
                   
                   
                 + 
               
               
                 2509/2510 
                 K129E 
                   
                   
                   
                 + 
               
               
                 2511/2512 
                 K752N 
                 + 
                 +++ 
                   
                   
               
               
                 2513/2514 
                 H499E 
                 + 
                   
                   
                 ++ 
               
               
                 2515/2516 
                 V185L 
                   
                 ++ 
                   
                   
               
               
                 2517/2518 
                 L857E 
                 + 
                   
                   
                   
               
               
                 2519/2520 
                 K752S 
                 + 
                 + 
                   
                   
               
               
                 2521/2522 
                 G56S 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 2523/2524 
                 T145L 
                   
                 ++ 
                   
                 + 
               
               
                 2525/2526 
                 T44F 
                 + 
                   
                   
                 + 
               
               
                 2527/2528 
                 T543K 
                 + 
                   
                   
                 ++ 
               
               
                 2529/2530 
                 P788T 
                   
                 + 
                   
                 + 
               
               
                 2531/2532 
                 K176R 
                 + 
                 ++ 
                   
                   
               
               
                 2533/2534 
                 V859A 
                 ++ 
                 + 
                   
                 + 
               
               
                 2535/2536 
                 K129V 
                 ++ 
                 ++ 
                   
                 ++ 
               
               
                 2537/2538 
                 T44A 
                 ++ 
                   
                 ++ 
                   
               
               
                 2539/2540 
                 P779S 
                 + 
                   
                 ++ 
                   
               
               
                 2541/2542 
                 L857A 
                 + 
                   
                   
                 ++ 
               
               
                 2543/2544 
                 S202Q 
                 + 
                 + 
                 + 
                   
               
               
                 2545/2546 
                 F354S 
                 ++ 
                 ++ 
                   
                   
               
               
                 2547/2548 
                 H499I 
                   
                   
                   
                 + 
               
               
                 2549/2550 
                 S446K 
                 + 
                   
                   
                   
               
               
                 2551/2552 
                 K752G 
                 + 
                 ++ 
                   
                   
               
               
                 2553/2554 
                 G65F 
                   
                 + 
                   
                   
               
               
                 2555/2556 
                 P503N 
                 + 
                 ++ 
                   
                 + 
               
               
                 2557/2558 
                 T44W 
                 + 
                   
                 ++ 
                 + 
               
               
                 2559/2560 
                 A834S 
                 + 
                 + 
                 ++ 
                 + 
               
               
                 2561/2562 
                 S446D 
                 + 
                   
                   
                   
               
               
                 2563/2564 
                 Q615M 
                 + 
                 + 
                 + 
                   
               
               
                 2565/2566 
                 L857V 
                 ++ 
                   
                   
                   
               
               
                 2567/2568 
                 F152W 
                 + 
                 + 
                 + 
                   
               
               
                 2569/2570 
                 F152S 
                   
                   
                   
                 + 
               
               
                 2571/2572 
                 S136K 
                   
                 ++ 
                   
                   
               
               
                 2573/2574 
                 K129S 
                 + 
                 ++ 
                   
                   
               
               
                 2575/2576 
                 T373S 
                 + 
                 ++ 
                   
                   
               
               
                 2577/2578 
                 G822R 
                 + 
                 ++ 
                   
                 + 
               
               
                 2579/2580 
                 T826M 
                 + 
                   
                   
                   
               
               
                 2581/2582 
                 G936S 
                 + 
                   
                   
                 +++ 
               
               
                 2583/2584 
                 F679Y 
                 + 
                 ++ 
                   
                   
               
               
                 2585/2586 
                 H63N 
                 ++ 
                 + 
                   
                   
               
               
                 2587/2588 
                 V931L 
                 + 
                 + 
                   
                   
               
               
                 2589/2590 
                 I156C 
                 + 
                 ++ 
                   
                   
               
               
                 2591/2592 
                 H499V 
                   
                   
                   
                 ++ 
               
               
                 2593/2594 
                 P788A 
                 + 
                 + 
                   
                   
               
               
                 2595/2596 
                 K752W 
                   
                   
                   
                 ++ 
               
               
                 2597/2598 
                 W730L 
                   
                   
                 ++ 
                 +++++ 
               
               
                 2599/2600 
                 P788Q 
                   
                 + 
                   
                   
               
               
                 2601/2602 
                 H499M 
                 + 
                   
                 ++ 
                   
               
               
                 2603/2604 
                 S202D 
                 + 
                 ++ 
                   
                   
               
               
                 2605/2606 
                 T543L 
                 ++ 
                 ++ 
                 ++ 
                   
               
               
                 2607/2608 
                 P199A 
                 ++ 
                 + 
                 ++ 
                   
               
               
                 2609/2610 
                 S612G 
                   
                   
                   
                 +++ 
               
               
                 2611/2612 
                 S856A 
                 ++ 
                   
                 + 
                   
               
               
                 2613/2614 
                 K129W 
                   
                   
                 ++ 
                 ++ 
               
               
                 2615/2616 
                 I156R 
                 + 
                 + 
                   
                   
               
               
                 2617/2618 
                 S136V 
                 ++ 
                   
                 ++ 
                   
               
               
                 2619/2620 
                 F354L 
                 ++ 
                   
                 ++ 
                   
               
               
                 2621/2622 
                 P186H 
                 + 
                   
                   
                   
               
               
                 2623/2624 
                 Y677T 
                 + 
                   
                   
                   
               
               
                 2625/2626 
                 P199W 
                 ++ 
                   
                 + 
                   
               
               
                 2627/2628 
                 S136R 
                 + 
                 ++ 
                 + 
                   
               
               
                 2629/2630 
                 K129T 
                 ++ 
                 ++ 
                 + 
                   
               
               
                 2631/2632 
                 P337H 
                   
                   
                   
                 +++ 
               
               
                 2633/2634 
                 I469M 
                 ++ 
                   
                 ++ 
                   
               
               
                 2635/2636 
                 H499A 
                 + 
                   
                   
                 +++ 
               
               
                 2637/2638 
                 Q344C 
                   
                   
                 ++ 
                 ++++ 
               
               
                 2639/2640 
                 D177Q 
                   
                   
                 + 
                 ++ 
               
               
                 2641/2642 
                 S202Y 
                   
                 ++ 
                   
                   
               
               
                 2643/2644 
                 A105V 
                 + 
                 ++ 
                   
                   
               
               
                 2645/2646 
                 E773P 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2647/2648 
                 W730K 
                   
                   
                   
                 + 
               
               
                 2649/2650 
                 L857R 
                 + 
                   
                   
                 + 
               
               
                 2651/2652 
                 A834W 
                   
                 ++ 
                   
                   
               
               
                 2653/2654 
                 L488C 
                 + 
                 +++ 
                 + 
                 + 
               
               
                 2655/2656 
                 L860S 
                 + 
                   
                 ++ 
                 ++ 
               
               
                 2657/2658 
                 L488E 
                 + 
                 +++ 
                   
                   
               
               
                 2659/2660 
                 L649M 
                   
                 + 
                   
                   
               
               
                 2661/2662 
                 K267E 
                   
                   
                   
                 + 
               
               
                 2663/2664 
                 K752L 
                 ++ 
                 ++ 
                   
                   
               
               
                 2665/2666 
                 S678R 
                   
                 + 
                   
                   
               
               
                 2667/2668 
                 E855G 
                 + 
                   
                   
                   
               
               
                 2669/2670 
                 N484A 
                   
                 ++ 
                   
                   
               
               
                 2671/2672 
                 P788I 
                 + 
                 + 
                   
                 ++ 
               
               
                 2673/2674 
                 D348E 
                 ++ 
                 ++ 
                 + 
                   
               
               
                 2675/2676 
                 L488S 
                 ++ 
                 +++ 
                   
                 + 
               
               
                 2677/2678 
                 Q615S 
                 + 
                 + 
                   
                   
               
               
                 2679/2680 
                 V859G 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                 2681/2682 
                 T141K 
                   
                   
                 + 
                   
               
               
                 2683/2684 
                 Q768I 
                   
                 ++ 
                 ++ 
                 +++ 
               
               
                 2685/2686 
                 V926T 
                 + 
                 + 
                 + 
                   
               
               
                 2687/2688 
                 P788H 
                 + 
                 ++ 
                 + 
                 + 
               
               
                 2689/2690 
                 S446C 
                 + 
                 ++ 
                 + 
                   
               
               
                 2691/2692 
                 P779I 
                 + 
                 ++ 
                 + 
                   
               
               
                 2693/2694 
                 V797F 
                 + 
                 ++ 
                 ++ 
                   
               
               
                 2695/2696 
                 S372D 
                 + 
                   
                   
                 ++ 
               
               
                 2697/2698 
                 V350F 
                   
                   
                   
                 + 
               
               
                 2699/2700 
                 Y765W 
                   
                   
                   
                 ++ 
               
               
                 2701/2702 
                 T44V 
                 ++ 
                   
                 ++ 
                 ++ 
               
               
                 2703/2704 
                 T373A 
                 + 
                   
                   
                   
               
               
                 2705/2706 
                 G936N 
                 ++ 
                   
                   
                 + 
               
               
                 2707/2708 
                 S446I 
                 + 
                   
                   
                   
               
               
                 2709/2710 
                 S678Q 
                 + 
                   
                 + 
                 ++ 
               
               
                 2711/2712 
                 P526L 
                   
                   
                 ++ 
                   
               
               
                 2713/2714 
                 P199G 
                 + 
                 ++ 
                 + 
                   
               
               
                 2715/2716 
                 P199R 
                 + 
                   
                 + 
                   
               
               
                 2717/2718 
                 L187I 
                 + 
                   
                 + 
                   
               
               
                 2719/2720 
                 K267R 
                 + 
                   
                 ++ 
                 ++ 
               
               
                 2721/2722 
                 I469T 
                 ++ 
                   
                   
                   
               
               
                 2723/2724 
                 T826I 
                 ++ 
                 ++ 
                 ++ 
                 +++ 
               
               
                 2725/2726 
                 S856G 
                 ++ 
                 + 
                 ++ 
                 +++ 
               
               
                 2727/2728 
                 P503C 
                 + 
                 ++ 
                 ++ 
                   
               
               
                 2729/2730 
                 V797I 
                 + 
                 ++ 
                   
                   
               
               
                 2731/2732 
                 G412W 
                 + 
                   
                 + 
                 ++ 
               
               
                 2733/2734 
                 S202A 
                 ++ 
                 ++ 
                 ++ 
                 + 
               
               
                 2735/2736 
                 T145A 
                 + 
                 + 
                 + 
                   
               
               
                 2737/2738 
                 S777W 
                 + 
                   
                 ++ 
                 ++ 
               
               
                 2739/2740 
                 G412R 
                 + 
                   
                 + 
                 ++ 
               
               
                 2741/2742 
                 D348W 
                   
                   
                   
                 ++ 
               
               
                 2743/2744 
                 P199T 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 2745/2746 
                 W265D 
                   
                   
                   
                 +++ 
               
               
                 2747/2748 
                 K267G 
                   
                   
                 + 
                 ++++ 
               
               
                 2749/2750 
                 W265F 
                 + 
                 + 
                   
                   
               
               
                 2751/2752 
                 H499Q 
                 ++ 
                 + 
                   
                 + 
               
               
                 2753/2754 
                 E855L 
                 + 
                   
                   
                 ++ 
               
               
                 2755/2756 
                 A496M 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                 2757/2758 
                 S202G 
                 ++ 
                   
                 ++ 
                 ++ 
               
               
                 2759/2760 
                 Q768V 
                   
                   
                   
                 ++ 
               
               
                 2761/2762 
                 T543H 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2763/2764 
                 Y I25W 
                   
                 ++ 
                   
                   
               
               
                 2765/2766 
                 N484K 
                 + 
                 + 
                 ++ 
                   
               
               
                 2767/2768 
                 N484R 
                   
                   
                   
                 ++ 
               
               
                 2769/2770 
                 Q768K 
                   
                   
                 + 
                 ++ 
               
               
                 2771/2772 
                 S612L 
                   
                   
                   
                 +++ 
               
               
                 2773/2774 
                 A834V 
                 + 
                   
                   
                 ++ 
               
               
                 2775/2776 
                 S678V 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2777/2778 
                 V926M 
                 + 
                 ++ 
                 + 
                 ++ 
               
               
                 2779/2780 
                 G139E 
                   
                   
                   
                 ++ 
               
               
                 2781/2782 
                 Y125H 
                   
                   
                 ++ 
                 ++ 
               
               
                 2783/2784 
                 P503H 
                 + 
                   
                 + 
                 ++ 
               
               
                 2785/2786 
                 V797R 
                   
                   
                 + 
                 +++ 
               
               
                 2787/2788 
                 F152L 
                 ++ 
                   
                 ++ 
                   
               
               
                 2789/2790 
                 W730R 
                   
                   
                 ++ 
                 + 
               
               
                 2791/2792 
                 T924A 
                 + 
                   
                 ++ 
                 + 
               
               
                 2793/2794 
                 V797W 
                   
                   
                   
                 ++ 
               
               
                 2795/2796 
                 V797E 
                   
                 ++ 
                   
                 + 
               
               
                 2797/2798 
                 T141R 
                 + 
                 + 
                 + 
                 ++ 
               
               
                 2799/2800 
                 S678W 
                 ++ 
                   
                 ++ 
                 ++ 
               
               
                 2801/2802 
                 G65Y 
                 + 
                   
                 ++ 
                 + 
               
               
                 2803/2804 
                 G936R 
                 ++ 
                   
                   
                   
               
               
                 2805/2806 
                 T44Y 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 2807/2808 
                 P788S 
                 + 
                   
                 + 
                   
               
               
                 2809/2810 
                 PI99V/L775I 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 2811/2812 
                 S777M 
                   
                 + 
                 ++ 
                 ++ 
               
               
                 2813/2814 
                 I156K 
                   
                   
                   
                 ++ 
               
               
                 2815/2816 
                 P526V 
                 + 
                 + 
                   
                   
               
               
                 2817/2818 
                 G56W 
                 ++ 
                 ++ 
                 ++ 
                   
               
               
                 2819/2820 
                 P199I 
                 + 
                 + 
                 + 
                   
               
               
                 2821/2822 
                 D40IG 
                 + 
                   
                   
                   
               
               
                 2823/2824 
                 G412S 
                 ++ 
                   
                 ++ 
                   
               
               
                 2825/2826 
                 A834G 
                 + 
                   
                 ++ 
                 ++ 
               
               
                 2827/2828 
                 P788Y 
                 + 
                 ++ 
                 + 
                 +++ 
               
               
                 2829/2830 
                 S612R 
                 + 
                   
                   
                 ++ 
               
               
                 2831/2832 
                 S202H 
                 + 
                 + 
                   
                 + 
               
               
                 2833/2834 
                 K129I 
                 + 
                 ++ 
                   
                 ++ 
               
               
                 2835/2836 
                 D401S 
                 + 
                   
                   
                 + 
               
               
                 2837/2838 
                 A496W 
                   
                 ++ 
                 + 
                   
               
               
                 2839/2840 
                 T543R 
                 + 
                   
                 + 
                 +++ 
               
               
                 2841/2842 
                 S446G 
                 + 
                   
                   
                 + 
               
               
                 2843/2844 
                 I156S 
                   
                 + 
                   
                 ++ 
               
               
                 2845/2846 
                 G65R 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2847/2848 
                 G65A 
                 + 
                   
                 + 
                 ++ 
               
               
                 2849/2850 
                 P779M 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 2851/2852 
                 K752F 
                 ++ 
                 ++ 
                   
                   
               
               
                 2853/2854 
                 D162T 
                   
                 + 
                   
                   
               
               
                 2855/2856 
                 I469V 
                 ++ 
                   
                 + 
                 ++ 
               
               
                 2857/2858 
                 S53I 
                 + 
                   
                 + 
                 ++ 
               
               
                 2859/2860 
                 A105W 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 2861/2862 
                 L857S 
                 + 
                   
                   
                   
               
               
                 2863/2864 
                 T543G 
                 ++ 
                   
                   
                 ++ 
               
               
                 2865/2866 
                 V350I 
                 ++ 
                   
                 + 
                 ++ 
               
               
                   
               
               
                   1 All activities were determined relative to the reference polypeptide of SEQ ID NO: 1956. 
               
               
                 Levels of increased activity are defined as follows: 
               
               
                 “+” = 0.9 to 1.1; 
               
               
                 “++” &gt; 1.1; 
               
               
                 “+++” &gt; 2; 
               
               
                 “++++” &gt; 3.5; and 
               
               
                 “+++++” &gt; 5. 
               
            
           
         
       
     
     EXAMPLE 14 
     GAA Variants of SEQ ID NO: 2496 
     In this Example, experiments for evolution and screening of GAA variants derived from SEQ ID NO: 2496 for improved GAA activity after a series of challenges are described. Libraries of variant genes GAA encoded based off of by SEQ ID NO: 2496 were constructed, plated, grown, and screened for GAA MU-Glu activity (“Unchallenged Activity FIOPC”), as well as after plasma challenge (“Plasma Stability and Activity FIOPC”), as described in Example 11. Variants were also tested for 4-MUGlu activity after lysis of Pompe fibroblasts treated for 24 hours (“Lysate Activity from Extended Treatment of Pompe Fibroblast FIOPC”) or GAA −/−  C2C12 cells (“Lysate Activity from Extended Treatment C2C12 GAA−/− FIOPC”) or 6 hour treatments hours (“Lysate Activity from Acute Treatment of Pompe Fibroblast FIOPC”) or (“Lysate Activity from Acute Treatment C2C12 GAA−/− FIOPC”), as described in Example 11. The results of these assays are presented in Table 14-1 and Table 14-2. 
     
       
         
           
               
             
               
                 TABLE 14-1 
               
             
            
               
                   
               
               
                 Activity of GAA Variants Relative to SEQ ID NO: 2496 1   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                 Lysate 
                 Lysate 
                 Lysate 
                 Lysate 
               
               
                   
                 Amino 
                   
                   
                 Activity 
                 Activity 
                 Activity 
                 Activity 
               
               
                   
                 Acid 
                   
                   
                 from 
                 from 
                 from 
                 from 
               
               
                   
                 Differences 
                   
                 Plasma 
                 Extended 
                 Extended 
                 Acute 
                 Acute 
               
               
                   
                 (Relative 
                   
                 Stability 
                 Treatment 
                 Treatment 
                 Treatment 
                 Treatment 
               
               
                 SEQ ID 
                 to SEQ 
                 Unchallenged 
                 and 
                 of pompe 
                 C2C12 
                 of Pompe 
                 C2C12 
               
               
                 NO: 
                 ID NO: 
                 Activity 
                 Activity 
                 Fibroblast 
                 GAA-/- 
                 Fibroblast 
                 GAA-/- 
               
               
                 (nt/aa) 
                 2496) 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
               
               
                   
               
               
                 2495/2496 
                   
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                 2867/2868 
                 L569T/L628M/ 
                 ++ 
                 + 
                   
                 ++ 
                 ++ 
                 + 
               
               
                   
                 T692Y 
                   
                   
                   
                   
                   
                   
               
               
                 2869/2870 
                 L569Y/L670T/ 
                 ++ 
                   
                 + 
                 ++ 
                 + 
                 + 
               
               
                   
                 A711H 
                   
                   
                   
                   
                   
                   
               
               
                 2871/2872 
                 L569Y/L628M/ 
                 ++ 
                 + 
                 + 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 L670T/T692Y/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 A711H/L871S 
                   
                   
                   
                   
                   
                   
               
               
                 2873/2874 
                 V589I/L670T/ 
                   
                   
                   
                 + 
                 + 
                 + 
               
               
                   
                 Q795E/L871S 
                   
                   
                   
                   
                   
                   
               
               
                 2875/2876 
                 L628M/L670F 
                 + 
                   
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2877/2878 
                 L569H/L628M/ 
                 ++ 
                 + 
                 + 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 L670T 
                   
                   
                   
                   
                   
                   
               
               
                 2879/2880 
                 L569T/L670T/ 
                 ++ 
                 + 
                   
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 A711H/L871E 
                   
                   
                   
                   
                   
                   
               
               
                 2881/2882 
                 L628M/L670T/ 
                 ++ 
                   
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 T692G/A711H/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 Q795E 
                   
                   
                   
                   
                   
                   
               
               
                 2883/2884 
                 L569Y/L628M/ 
                 ++ 
                 + 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 L670T/A711H 
                   
                   
                   
                   
                   
                   
               
               
                 2885/2886 
                 L569Y/V589I/ 
                 + 
                 + 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 L628M/T692G/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 A711H/Q795E 
                   
                   
                   
                   
                   
                   
               
               
                 2887/2888 
                 L569H/T692G 
                 + 
                   
                   
                 + 
                 + 
                 + 
               
               
                 2889/2890 
                 L569Y/V589I/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 L670T/S678T/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 T692G/A711H/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 Q795E 
                   
                   
                   
                   
                   
                   
               
               
                 2891/2892 
                 L569T/L871K 
                 ++ 
                 ++ 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2893/2894 
                 L569Y/V589I/ 
                 ++ 
                 ++ 
                 + 
                 + 
                 ++ 
                 + 
               
               
                   
                 L628M/L670T/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 T692Y/A711H 
                   
                   
                   
                   
                   
                   
               
               
                 2895/2896 
                 V589I/L871E 
                 + 
                   
                   
                   
                 + 
                   
               
               
                 2897/2898 
                 L670T/S678T/ 
                   
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                   
                 T692Y/L871S 
                   
                   
                   
                   
                   
                   
               
               
                 2899/2900 
                 L628M/A711H/ 
                 ++ 
                   
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 Q795E 
                   
                   
                   
                   
                   
                   
               
               
                 2901/2902 
                 T692G/A711H 
                 + 
                   
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                 2903/2904 
                 V589I/L670T/ 
                   
                   
                 + 
                 + 
                 + 
                 ++ 
               
               
                   
                 T692G/Q795E/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 L871K 
                   
                   
                   
                   
                   
                   
               
               
                 2905/2906 
                 L569Y/V589I/ 
                 + 
                 + 
                   
                 ++ 
                 + 
                 ++ 
               
               
                   
                 A711H/L871K 
                   
                   
                   
                   
                   
                   
               
               
                 2907/2908 
                 L670T/T692G/ 
                 ++ 
                   
                 + 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 L871K 
                   
                   
                   
                   
                   
                   
               
               
                 2909/2910 
                 L569H/T692Y 
                 + 
                   
                   
                 + 
                 + 
                 + 
               
               
                 2911/2912 
                 L569H/L628M/ 
                 ++ 
                 + 
                 ++ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 L670T/T692Y/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 A711H/L871K 
                   
                   
                   
                   
                   
                   
               
               
                 2913/2914 
                 L670T/S678T 
                 ++ 
                   
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2915/2916 
                 L569T/L670T/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 S678T/T692G/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 L871K 
                   
                   
                   
                   
                   
                   
               
               
                 2917/2918 
                 V589I 
                   
                   
                   
                   
                   
                 ++ 
               
               
                 2919/2920 
                 L569H/V589I/ 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 L628M/L670T/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S678T/T692G/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 A711H/Q795E/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 L871S 
                   
                   
                   
                   
                   
                   
               
               
                 2921/2922 
                 L569H/L670F/ 
                 + 
                 ++ 
                 + 
                 + 
                 + 
                 ++ 
               
               
                   
                 S678T/T692G/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 L871S 
                   
                   
                   
                   
                   
                   
               
               
                 2923/2924 
                 L569T/V589I/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 L628M/L670F/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 T692G/A711H 
                   
                   
                   
                   
                   
                   
               
               
                 2925/2926 
                 L569H/L670T/ 
                 ++ 
                 + 
                   
                   
                   
                 + 
               
               
                   
                 T692G 
                   
                   
                   
                   
                   
                   
               
               
                 2927/2928 
                 L569Y/L871E 
                 ++ 
                 + 
                   
                   
                   
                 + 
               
               
                 2929/2930 
                 L569H/L628M/ 
                 ++ 
                 + 
                 + 
                   
                 + 
                 ++ 
               
               
                   
                 L670F/S678T 
                   
                   
                   
                   
                   
                   
               
               
                 2931/2932 
                 L569Y/L670F/ 
                 + 
                 ++ 
                   
                   
                   
                 ++ 
               
               
                   
                 S678T 
                   
                   
                   
                   
                   
                   
               
               
                 2933/2934 
                 L569Y/V589I/ 
                 ++ 
                 ++ 
                   
                 + 
                 + 
                 ++ 
               
               
                   
                 L670F 
                   
                   
                   
                   
                   
                   
               
               
                 2935/2936 
                 L569Y/V589I/ 
                 ++ 
                 ++ 
                 + 
                 + 
                 + 
                 ++ 
               
               
                   
                 L670T/L871K 
                   
                   
                   
                   
                   
                   
               
               
                 2937/2938 
                 L569T/L871S 
                 + 
                 ++ 
                   
                   
                 + 
                 + 
               
               
                 2939/2940 
                 L871K 
                 + 
                   
                 + 
                   
                 ++ 
                 ++ 
               
               
                 2941/2942 
                 L569Y/L670T 
                   
                   
                   
                 ++ 
                 + 
                 ++ 
               
               
                 2943/2944 
                 L569Y/T692Y/ 
                 ++ 
                 ++ 
                 + 
                 + 
                   
                   
               
               
                   
                 A711H 
                   
                   
                   
                   
                   
                   
               
               
                 2945/2946 
                 L871S 
                 + 
                   
                   
                   
                 + 
                 ++ 
               
               
                 2947/2948 
                 L569Y/A711H 
                 ++ 
                 ++ 
                   
                   
                   
                 ++ 
               
               
                 2949/2950 
                 L628M/L871S 
                 + 
                   
                   
                 + 
                 ++ 
                 ++ 
               
               
                 2951/2952 
                 L569T/V589I/ 
                 ++ 
                 + 
                   
                 + 
                 + 
                 ++ 
               
               
                   
                 L871S 
                   
                   
                   
                   
                   
                   
               
               
                 2953/2954 
                 T692G/A711H/ 
                 ++ 
                   
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 I869L/V878S 
                   
                   
                   
                   
                   
                   
               
               
                 2955/2956 
                 A572S/F588L/ 
                 + 
                   
                   
                 + 
                 + 
                 + 
               
               
                   
                 S678T/T692G/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 I869L/V878A 
                   
                   
                   
                   
                   
                   
               
               
                 2957/2958 
                 A711H 
                 ++ 
                   
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                 2959/2960 
                 T692G/I869S 
                   
                   
                   
                 + 
                 ++ 
                 + 
               
               
                 2961/2962 
                 A572S/T692L/ 
                 + 
                 + 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 I869S/V878S 
                   
                   
                   
                   
                   
                   
               
               
                 2963/2964 
                 L629I/I869L/ 
                   
                   
                 + 
                   
                 ++ 
                 + 
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
                   
               
               
                 2965/2966 
                 A572S/F588L/ 
                   
                   
                   
                   
                   
                 + 
               
               
                   
                 Q795E 
                   
                   
                   
                   
                   
                   
               
               
                 2967/2968 
                 A711H/I869S/ 
                 + 
                   
                   
                   
                 + 
                 + 
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
                   
               
               
                 2969/2970 
                 V878S 
                 ++ 
                 + 
                   
                 ++ 
                 + 
                 + 
               
               
                 2971/2972 
                 S678T/T692G/ 
                 ++ 
                 + 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 A711H/I869S 
                   
                   
                   
                   
                   
                   
               
               
                 2973/2974 
                 A572S/T692G/ 
                 + 
                   
                   
                   
                 + 
                   
               
               
                   
                 I869S/V878S 
                   
                   
                   
                   
                   
                   
               
               
                 2975/2976 
                 A572S/T692G/ 
                 + 
                   
                   
                 + 
                 ++ 
                 ++ 
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
                   
               
               
                 2977/2978 
                 A711H/Q795E/ 
                 + 
                   
                   
                   
                 + 
                 ++ 
               
               
                   
                 I869S/V878S 
                   
                   
                   
                   
                   
                   
               
               
                 2979/2980 
                 Q795E/V878S 
                 + 
                 + 
                   
                   
                 + 
                   
               
               
                 2981/2982 
                 T692G/A711H/ 
                 + 
                   
                 + 
                   
                 + 
                 + 
               
               
                   
                 Q795E/I869S 
                   
                   
                   
                   
                   
                   
               
               
                 2983/2984 
                 S678T/T692G/ 
                   
                   
                   
                 + 
                 ++ 
                 ++ 
               
               
                   
                 Q795E/I869S 
                   
                   
                   
                   
                   
                   
               
               
                 2985/2986 
                 T692G/A711H/ 
                   
                   
                   
                 + 
                 ++ 
                   
               
               
                   
                 I869S/V878A 
                   
                   
                   
                   
                   
                   
               
               
                 2987/2988 
                 L569T/A711H 
                 ++ 
                   
                   
                 + 
                 + 
                   
               
               
                 2989/2990 
                 L569T/L628M/ 
                 + 
                 + 
                   
                   
                 + 
                 + 
               
               
                   
                 S678T/A711H 
                   
                   
                   
                   
                   
                   
               
               
                 2991/2992 
                 L569T/V589I/ 
                 ++ 
                 ++ 
                   
                 ++ 
                 ++ 
                   
               
               
                   
                 T692G/Q795E/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 L871K/V878S 
                   
                   
                   
                   
                   
                   
               
               
                 2993/2994 
                 L569T/V589I/ 
                 ++ 
                 ++ 
                   
                 ++ 
                 ++ 
                 + 
               
               
                   
                 S678T/L871K/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
                   
               
               
                 2995/2996 
                 L569H/A711H/ 
                 + 
                   
                   
                   
                 ++ 
                   
               
               
                   
                 I869S/V878S 
                   
                   
                   
                   
                   
                   
               
               
                 2997/2998 
                 S678T/Q795E/ 
                 + 
                   
                   
                   
                 + 
                 ++ 
               
               
                   
                 L871K/V878A 
                   
                   
                   
                   
                   
                   
               
               
                 2999/3000 
                 L569H/S678T/ 
                 + 
                   
                   
                 + 
                 + 
                   
               
               
                   
                 T692G/Q795E 
                   
                   
                   
                   
                   
                   
               
               
                 3001/3002 
                 F588L/V589I/ 
                 ++ 
                   
                   
                 + 
                 + 
                 + 
               
               
                   
                 L628M/S678T 
                   
                   
                   
                   
                   
                   
               
               
                 3003/3004 
                 T692Y 
                 ++ 
                 + 
                 + 
                 + 
                 ++ 
                 + 
               
               
                 3005/3006 
                 L569T 
                 ++ 
                 + 
                   
                 + 
                 ++ 
                 + 
               
               
                 3007/3008 
                 T692G/L871K 
                 + 
                   
                 + 
                 + 
                 ++ 
                   
               
               
                 3009/3010 
                 L569T/F588L/ 
                 ++ 
                 ++ 
                 + 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
                   
               
               
                 3011/3012 
                 L569H/A711H/ 
                 ++ 
                   
                   
                 ++ 
                 + 
                   
               
               
                   
                 L871K 
                   
                   
                   
                   
                   
                   
               
               
                 3013/3014 
                 L569T/F588L/ 
                 ++ 
                 ++ 
                   
                 + 
                 + 
                 + 
               
               
                   
                 S678T/T692Y 
                   
                   
                   
                   
                   
                   
               
               
                 3015/3016 
                 L569T/F588L/ 
                 + 
                   
                   
                 + 
                 ++ 
                   
               
               
                   
                 A711H/I869L/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 L871K/V878S 
                   
                   
                   
                   
                   
                   
               
               
                 3017/3018 
                 L569T/F588L 
                 ++ 
                 ++ 
                   
                   
                 + 
                 ++ 
               
               
                 3019/3020 
                 L569T/T692Y 
                 + 
                 ++ 
                 + 
                 ++ 
                 ++ 
                 + 
               
               
                 3021/3022 
                 L569T/S678T/ 
                 ++ 
                 + 
                   
                 ++ 
                 + 
                 ++ 
               
               
                   
                 I869S/V878S 
                   
                   
                   
                   
                   
                   
               
               
                 3023/3024 
                 L628M/L629I/ 
                 + 
                   
                   
                 + 
                 ++ 
                 + 
               
               
                   
                 T692Y/L871S/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
                   
               
               
                 3025/3026 
                 L569T/S678T/ 
                 ++ 
                 ++ 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
                   
               
               
                 3027/3028 
                 L569H/A711H/ 
                 ++ 
                 ++ 
                   
                 + 
                 ++ 
                 ++ 
               
               
                   
                 Q795E/L871S/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
                   
               
               
                 3029/3030 
                 A711H/L871K 
                 ++ 
                   
                   
                   
                 + 
                 + 
               
               
                 3031/3032 
                 T692G/A711H/ 
                 + 
                   
                   
                 + 
                 ++ 
                 + 
               
               
                   
                 Q795E/I869L/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 L871K/V878A 
                   
                   
                   
                   
                   
                   
               
               
                 3033/3034 
                 L569T/F588L/ 
                   
                 + 
                 + 
                 + 
                   
                 ++ 
               
               
                   
                 V589I/L628M/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 L629I/T692Y/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 A711H 
                   
                   
                   
                   
                   
                   
               
               
                 3035/3036 
                 S678T/T692G/ 
                 ++ 
                   
                   
                 + 
                 ++ 
                 + 
               
               
                   
                 I869S 
                   
                   
                   
                   
                   
                   
               
               
                 3037/3038 
                 T692G/I869L/ 
                 + 
                   
                   
                 + 
                 ++ 
                 + 
               
               
                   
                 L871K/V878S/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 S916R 
                   
                   
                   
                   
                   
                   
               
               
                 3039/3040 
                 L569H/L628M 
                 ++ 
                 + 
                   
                   
                 + 
                 + 
               
               
                 3041/3042 
                 L628M/V878S 
                 ++ 
                   
                   
                 + 
                 + 
                 + 
               
               
                 3043/3044 
                 T692G/A711H/ 
                 ++ 
                   
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 L871S/V878A 
                   
                   
                   
                   
                   
                   
               
               
                 3045/3046 
                 L569T/Q795E 
                 ++ 
                 ++ 
                   
                 + 
                 + 
                 ++ 
               
               
                 3047/3048 
                 L569T/T692Y/ 
                 ++ 
                 ++ 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 A711H/I869L/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 L871K/V878A 
                   
                   
                   
                   
                   
                   
               
               
                 3049/3050 
                 S246T 
                 ++ 
                   
                   
                 + 
                 + 
                 + 
               
               
                 3051/3052 
                 T585K 
                 ++ 
                   
                   
                   
                 + 
                 ++ 
               
               
                 3053/3054 
                 G584E 
                 + 
                   
                   
                   
                 + 
                   
               
               
                 3055/3056 
                 A812E 
                 ++ 
                 + 
                   
                 + 
                 + 
                 + 
               
               
                 3057/3058 
                 V313L 
                 + 
                   
                   
                   
                 + 
                   
               
               
                 3059/3060 
                 L304M 
                 ++ 
                   
                   
                 + 
                 ++ 
                 ++ 
               
               
                 3061/3062 
                 V313I 
                 ++ 
                   
                   
                 + 
                 ++ 
                 ++ 
               
               
                 3063/3064 
                 A582T 
                 ++ 
                   
                   
                 ++ 
                 ++ 
                 ++ 
               
               
                   
               
               
                   1 All activities were determined relative to the reference polypeptide of SEQ ID NO: 2496. Levels of increased activity are defined as follows: “+” = 0.9 to 1.1; and “++” &gt; 1.1. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 14-2 
               
             
            
               
                   
               
               
                 Activity of GAA Variants Relative to SEQ ID NO: 2496 1   
               
            
           
           
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                 Lysate Activity 
                 Lysate 
               
               
                   
                   
                   
                 Plasma 
                 from Extended 
                 Activity from 
               
               
                   
                 Amino Acid 
                   
                 Stability 
                 Treatment of 
                 Extended 
               
               
                 SEQ ID 
                 Differences 
                 Unchallenged 
                 and 
                 Pompe 
                 rfreatment 
               
               
                 NO: 
                 (Relative to SEQ ID  
                 Activity 
                 Activity 
                 Fibroblast 
                 C2C12 GAA-/- 
               
               
                 (nt/aa) 
                 NO: 2496) 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
               
               
                   
               
               
                 2495/2496 
                   
                 + 
                 + 
                 + 
                 + 
               
               
                 3065/3066 
                 L810V 
                   
                 ++ 
                   
                   
               
               
                 3067/3068 
                 A60V/V589A 
                   
                   
                   
                 + 
               
               
                 3069/3070 
                 S307T 
                   
                   
                   
                 + 
               
               
                 3071/3072 
                 V313T 
                   
                   
                 + 
                   
               
               
                 3073/3074 
                 G584C 
                   
                   
                   
                 + 
               
               
                   
               
               
                   1 All activities were determined relative to the reference polypeptide of SEQ ID NO: 2496. 
               
               
                 Levels of increased activity are defined as follows: 
               
               
                 “+” = 0.9 to 1.1; and 
               
               
                 “++” &gt; 1.1. 
               
            
           
         
       
     
     EXAMPLE 15 
     GAA Variants of SEQ ID NO: 2880 
     In this Example, experiments for evolution and screening of GAA variants derived from SEQ ID NO: 2880 for improved GAA activity after a series of challenges are described. Libraries of variant genes GAA encoded based off of by SEQ ID NO: 2880 were constructed, plated, grown, and screened for GAA MU-Glu activity (“Unchallenged Activity FIOPC”), as well as after plasma challenge (“Plasma Stability and Activity FIOPC”), as described in Example 11. Variants were also tested for 4-MUGlu activity after lysis of GAA −/−  C2C12 cells (“Lysate Activity from Extended Treatment C2C12 GAA−/− FIOPC”) or 6 hour treatments hours of Pompe fibroblasts (“Lysate Activity from Acute Treatment of Pompe Fibroblast FIOPC”) or GAA −/−  C2C12 cells (“Lysate Activity from Acute Treatment C2C12 GAA−/− FIOPC”), as described in Example 11. The results of these assays are presented in Table 15-1. 
     
       
         
           
               
             
               
                 TABLE 15-1 
               
             
            
               
                   
               
               
                 Activity of GAA Variants Relative to SEQ ID NO: 2880 1   
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                 Lysate 
                 Lysate 
                 Lysate 
               
               
                   
                   
                   
                   
                 Activity 
                 Activity 
                 Activity 
               
               
                   
                   
                   
                   
                 from 
                 from 
                 from 
               
               
                   
                 Amino Acid 
                   
                 Plasma 
                 Extended 
                 Acute 
                 Acute 
               
               
                   
                 Differences 
                   
                 Stability 
                 Treatment 
                 Treatment 
                 Treatment 
               
               
                 SEQ ID 
                 (Relative to 
                 Unchallenged 
                 and 
                 C2C12 
                 of Pompe 
                 C2C12 
               
               
                 NO: 
                 SEQ ID NO: 
                 Activity 
                 Activity 
                 GAA-/- 
                 Fibroblast 
                 GAA-/- 
               
               
                 (nt/aa) 
                 2880) 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
               
               
                   
               
               
                 2879/2880 
                   
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                 3075/3076 
                 R527N/L736M/ 
                 ++ 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
               
               
                 3077/3078 
                 L109D/S678T/ 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 A812E 
                   
                   
                   
                   
                   
               
               
                 3079/3080 
                 A89R/S842G/ 
                 ++ 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
               
               
                 3081/3082 
                 R403H/R527N/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 S678T/T692G/ 
                   
                   
                   
                   
                   
               
               
                   
                 L736M/A812E/ 
                   
                   
                   
                   
                   
               
               
                   
                 S842G/L860F 
                   
                   
                   
                   
                   
               
               
                 3083/3084 
                 S678T/T692G/ 
                 ++ 
                 ++ 
                 + 
                 + 
                 ++ 
               
               
                   
                 A812E 
                   
                   
                   
                   
                   
               
               
                 3085/3086 
                 L109D/W727S/ 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 L860F/V878S 
                   
                   
                   
                   
                   
               
               
                 3087/3088 
                 A89R/R527N/ 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 W727S/A812E/ 
                   
                   
                   
                   
                   
               
               
                   
                 L860F 
                   
                   
                   
                   
                   
               
               
                 3089/3090 
                 A89R/S678T/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 T692G/L736M/ 
                   
                   
                   
                   
                   
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
               
               
                 3091/3092 
                 L109D/R527N/ 
                 ++ 
                 ++ 
                 + 
                 + 
                 ++ 
               
               
                   
                 S678T/A812E 
                   
                   
                   
                   
                   
               
               
                 3093/3094 
                 S678T/L860F/ 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
               
               
                 3095/3096 
                 L109D/A812E 
                 ++ 
                 ++ 
                 + 
                   
                 ++ 
               
               
                 3097/3098 
                 T692G/W727S/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 L736M/S842G/ 
                   
                   
                   
                   
                   
               
               
                   
                 R913V 
                   
                   
                   
                   
                   
               
               
                 3099/3100 
                 A89R/L109D/ 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 W727S/A932S 
                   
                   
                   
                   
                   
               
               
                 3101/3102 
                 R527N/S678T/ 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 T692G/W727S/ 
                   
                   
                   
                   
                   
               
               
                   
                 L736M/V878S 
                   
                   
                   
                   
                   
               
               
                 3103/3104 
                 R527N/T692G/ 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 W727S/L736M/ 
                   
                   
                   
                   
                   
               
               
                   
                 A812E 
                   
                   
                   
                   
                   
               
               
                 3105/3106 
                 A89R/R527N 
                 ++ 
                 ++ 
                 + 
                   
                 + 
               
               
                 3107/3108 
                 A89R/L109D/ 
                 ++ 
                 ++ 
                 + 
                   
                 + 
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
               
               
                 3109/3110 
                 L109D/S842G 
                 + 
                 + 
                 + 
                 ++ 
                   
               
               
                 3111/3112 
                 S678T/R913V 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 3113/3114 
                 A89R/L109D/ 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 S678T/W727S/ 
                   
                   
                   
                   
                   
               
               
                   
                 L736M/A812E/ 
                   
                   
                   
                   
                   
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
               
               
                 3115/3116 
                 L109D/T692G/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 W727S/A812E/ 
                   
                   
                   
                   
                   
               
               
                   
                 S842G/L860F 
                   
                   
                   
                   
                   
               
               
                 3117/3118 
                 T692G/A812E 
                 ++ 
                 + 
                 ++ 
                 + 
                 + 
               
               
                 3119/3120 
                 S678T/A932S 
                 ++ 
                 + 
                 ++ 
                 + 
                 ++ 
               
               
                 3121/3122 
                 L109D/S678T/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 L736M/A812E/ 
                   
                   
                   
                   
                   
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
               
               
                 3123/3124 
                 L109D/A932S 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                 3125/3126 
                 R527N/T692G/ 
                 ++ 
                 ++ 
                 + 
                 + 
                 ++ 
               
               
                   
                 W727S/L736M/ 
                   
                   
                   
                   
                   
               
               
                   
                 S842G/L860F/ 
                   
                   
                   
                   
                   
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
               
               
                 3127/3128 
                 R527N/W727S/ 
                 ++ 
                 ++ 
                 + 
                   
                 ++ 
               
               
                   
                 L736M 
                   
                   
                   
                   
                   
               
               
                 3129/3130 
                 L109D/S678T/ 
                 ++ 
                 + 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 S842G/V878S 
                   
                   
                   
                   
                   
               
               
                 3131/3132 
                 L109D/S678T/ 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 W727S/L860F 
                   
                   
                   
                   
                   
               
               
                 3133/3134 
                 R527N/S678T/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 +++ 
               
               
                   
                 T692G/A812E/ 
                   
                   
                   
                   
                   
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
               
               
                 3135/3136 
                 A89R/S678T/ 
                 ++ 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 A812E/V878S 
                   
                   
                   
                   
                   
               
               
                 3137/3138 
                 R527N/A812E 
                 ++ 
                 ++ 
                 + 
                   
                 ++ 
               
               
                 3139/3140 
                 S678T/T692G/ 
                 ++ 
                 + 
                 + 
                   
                 ++ 
               
               
                   
                 W727S/A812E/ 
                   
                   
                   
                   
                   
               
               
                   
                 S842G 
                   
                   
                   
                   
                   
               
               
                 3141/3142 
                 L109D/L736M/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
               
               
                 3143/3144 
                 A89R/L109D/ 
                 ++ 
                 ++ 
                 ++ 
                   
                 ++ 
               
               
                   
                 R527N/S678T/ 
                   
                   
                   
                   
                   
               
               
                   
                 W727S/S842G 
                   
                   
                   
                   
                   
               
               
                 3145/3146 
                 W727S 
                 ++ 
                 + 
                 ++ 
                 + 
                 ++ 
               
               
                 3147/3148 
                 A89R/R527N/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 +++ 
               
               
                   
                 S678T/A932S 
                   
                   
                   
                   
                   
               
               
                 3149/3150 
                 L109D/S678T/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 +++ 
               
               
                   
                 T692G/S842G/ 
                   
                   
                   
                   
                   
               
               
                   
                 L860F/V878S/ 
                   
                   
                   
                   
                   
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
               
               
                 3151/3152 
                 A89R/R527N/ 
                 ++ 
                 + 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 S678T/T692G/ 
                   
                   
                   
                   
                   
               
               
                   
                 L736M/S842G/ 
                   
                   
                   
                   
                   
               
               
                   
                 V878S/A932S 
                   
                   
                   
                   
                   
               
               
                 3153/3154 
                 R527N 
                 ++ 
                   
                 + 
                   
                 + 
               
               
                 3155/3156 
                 L109D/T692G/ 
                 ++ 
                 ++ 
                 + 
                 + 
                 ++ 
               
               
                   
                 W727S/L736M/ 
                   
                   
                   
                   
                   
               
               
                   
                 A812E 
                   
                   
                   
                   
                   
               
               
                 3157/3158 
                 W727S/A932S 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                 3159/3160 
                 V878S/A932S 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                 3161/3162 
                 S678T/A812E 
                 ++ 
                 + 
                 ++ 
                 ++ 
                 +++ 
               
               
                 3163/3164 
                 W24L/S28L/ 
                 ++ 
                 ++ 
                 + 
                   
                 ++ 
               
               
                   
                 T29L/Q39P/ 
                   
                   
                   
                   
                   
               
               
                   
                 V50Q/L62A/ 
                   
                   
                   
                   
                   
               
               
                   
                 E78P/E87D/ 
                   
                   
                   
                   
                   
               
               
                   
                 Q135S/S150T/ 
                   
                   
                   
                   
                   
               
               
                   
                 N266T/K267R/ 
                   
                   
                   
                   
                   
               
               
                   
                 V522E/R527N/ 
                   
                   
                   
                   
                   
               
               
                   
                 A551V/T670L/ 
                   
                   
                   
                   
                   
               
               
                   
                 W727S/P750A/ 
                   
                   
                   
                   
                   
               
               
                   
                 K830Q/S842G/ 
                   
                   
                   
                   
                   
               
               
                   
                 E871L/H883R/ 
                   
                   
                   
                   
                   
               
               
                   
                 G894Q/A932S 
                   
                   
                   
                   
                   
               
               
                 3165/3166 
                 S28L/V50Q/ 
                 ++ 
                 ++ 
                 + 
                   
                 + 
               
               
                   
                 E78P/E87D/ 
                   
                   
                   
                   
                   
               
               
                   
                 Q135S/N266T/ 
                   
                   
                   
                   
                   
               
               
                   
                 K267R/G437A/ 
                   
                   
                   
                   
                   
               
               
                   
                 E486T/R527N/ 
                   
                   
                   
                   
                   
               
               
                   
                 A551V/T670L/ 
                   
                   
                   
                   
                   
               
               
                   
                 W727S/P750A/ 
                   
                   
                   
                   
                   
               
               
                   
                 K830Q/S842G/ 
                   
                   
                   
                   
                   
               
               
                   
                 E871L/H883R/ 
                   
                   
                   
                   
                   
               
               
                   
                 G894Q/R913V/ 
                   
                   
                   
                   
                   
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
               
               
                 3167/3168 
                 W24L/S28L/ 
                 ++ 
                 + 
                   
                   
                 + 
               
               
                   
                 Q39P/V50Q/ 
                   
                   
                   
                   
                   
               
               
                   
                 L62A/E78P/ 
                   
                   
                   
                   
                   
               
               
                   
                 E87D/Q135S/ 
                   
                   
                   
                   
                   
               
               
                   
                 S150T/N266T/ 
                   
                   
                   
                   
                   
               
               
                   
                 K267R/V522E/ 
                   
                   
                   
                   
                   
               
               
                   
                 R527N/A551V/ 
                   
                   
                   
                   
                   
               
               
                   
                 T569L/W727S/ 
                   
                   
                   
                   
                   
               
               
                   
                 K830Q/S842G/ 
                   
                   
                   
                   
                   
               
               
                   
                 E871L/H883R/ 
                   
                   
                   
                   
                   
               
               
                   
                 G894Q/R913V 
                   
                   
                   
                   
                   
               
               
                 3169/3170 
                 T29L/Q39P/ 
                 ++ 
                 + 
                 ++ 
                   
                   
               
               
                   
                 V50Q/L62A/ 
                   
                   
                   
                   
                   
               
               
                   
                 G65R/E78P/ 
                   
                   
                   
                   
                   
               
               
                   
                 E87D/Q135S/ 
                   
                   
                   
                   
                   
               
               
                   
                 S150T/G437A/ 
                   
                   
                   
                   
                   
               
               
                   
                 A551V/T569L/ 
                   
                   
                   
                   
                   
               
               
                   
                 T670L/W727S/ 
                   
                   
                   
                   
                   
               
               
                   
                 P750A/K830Q/ 
                   
                   
                   
                   
                   
               
               
                   
                 S842G/H883R/ 
                   
                   
                   
                   
                   
               
               
                   
                 G894Q/A932S 
                   
                   
                   
                   
                   
               
               
                 3171/3172 
                 W24L/V50Q/ 
                 ++ 
                 ++ 
                 ++ 
                   
                 ++ 
               
               
                   
                 E78P/E87D/ 
                   
                   
                   
                   
                   
               
               
                   
                 Q135S/S150T/ 
                   
                   
                   
                   
                   
               
               
                   
                 K267R/E486T/ 
                   
                   
                   
                   
                   
               
               
                   
                 V522E/R527N/ 
                   
                   
                   
                   
                   
               
               
                   
                 A551V/T670L/ 
                   
                   
                   
                   
                   
               
               
                   
                 W727S/P750A/ 
                   
                   
                   
                   
                   
               
               
                   
                 K830Q/S842G/ 
                   
                   
                   
                   
                   
               
               
                   
                 E871L/H883R/ 
                   
                   
                   
                   
                   
               
               
                   
                 G894Q/R913V/ 
                   
                   
                   
                   
                   
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
               
               
                 3173/3174 
                 W24L/T29L/ 
                 ++ 
                 ++ 
                 + 
                   
                 ++ 
               
               
                   
                 Q39P/V50Q/ 
                   
                   
                   
                   
                   
               
               
                   
                 L62A/E78P/ 
                   
                   
                   
                   
                   
               
               
                   
                 E87D/Q135S/ 
                   
                   
                   
                   
                   
               
               
                   
                 S150T/K267R/ 
                   
                   
                   
                   
                   
               
               
                   
                 G437A/E486T/ 
                   
                   
                   
                   
                   
               
               
                   
                 V522E/R527N/ 
                   
                   
                   
                   
                   
               
               
                   
                 A551V/H711A/ 
                   
                   
                   
                   
                   
               
               
                   
                 W727S/P750A/ 
                   
                   
                   
                   
                   
               
               
                   
                 K830Q/S842G/ 
                   
                   
                   
                   
                   
               
               
                   
                 E871L/H883R/ 
                   
                   
                   
                   
                   
               
               
                   
                 G894Q/R913V/ 
                   
                   
                   
                   
                   
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
               
               
                 3175/3176 
                 L62A/Q135S/ 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 V522E/H711A/ 
                   
                   
                   
                   
                   
               
               
                   
                 W727S/P750A/ 
                   
                   
                   
                   
                   
               
               
                   
                 S842G/E871L/ 
                   
                   
                   
                   
                   
               
               
                   
                 G894Q 
                   
                   
                   
                   
                   
               
               
                 3177/3178 
                 E87D/P750A 
                 + 
                 ++ 
                 ++ 
                   
                 ++ 
               
               
                 3179/3180 
                 Q135S/H711A/ 
                 + 
                 + 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 P750A/A932S 
                   
                   
                   
                   
                   
               
               
                 3181/3182 
                 V522E/K830Q 
                 ++ 
                 ++ 
                 ++ 
                   
                 ++ 
               
               
                 3183/3184 
                 S28L/G437A/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 R527N/E871L 
                   
                   
                   
                   
                   
               
               
                 3185/3186 
                 L62A/G437A 
                 ++ 
                 ++ 
                 + 
                   
                 ++ 
               
               
                 3187/3188 
                 G437A/P750A/ 
                 ++ 
                 ++ 
                 + 
                 ++ 
                 ++ 
               
               
                   
                 K830Q/A932S 
                   
                   
                   
                   
                   
               
               
                 3189/3190 
                 T29L/E78P/ 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 Q135S/W727S/ 
                   
                   
                   
                   
                   
               
               
                   
                 K830Q 
                   
                   
                   
                   
                   
               
               
                 3191/3192 
                 L62A 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 3193/3194 
                 V50Q/H711A 
                 + 
                 + 
                 ++ 
                 + 
                 ++ 
               
               
                 3195/3196 
                 S150T/E871L/ 
                 + 
                 ++ 
                 + 
                 ++ 
                 + 
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
               
               
                 3197/3198 
                 Q39P/V50Q 
                 + 
                 + 
                 ++ 
                 + 
                 ++ 
               
               
                 3199/3200 
                 E78P/E87D/ 
                 + 
                 + 
                 ++ 
                   
                 ++ 
               
               
                   
                 E486T/R527N/ 
                   
                   
                   
                   
                   
               
               
                   
                 T670L/W727S/ 
                   
                   
                   
                   
                   
               
               
                   
                 P750A/K830Q/ 
                   
                   
                   
                   
                   
               
               
                   
                 S842G/E871L/ 
                   
                   
                   
                   
                   
               
               
                   
                 R913V/A932S 
                   
                   
                   
                   
                   
               
               
                 3201/3202 
                 W24L/R527N/ 
                 ++ 
                 ++ 
                 ++ 
                   
                 +++ 
               
               
                   
                 W727S/S842G/ 
                   
                   
                   
                   
                   
               
               
                   
                 E871L/H883R/ 
                   
                   
                   
                   
                   
               
               
                   
                 R913V/A932S 
                   
                   
                   
                   
                   
               
               
                 3203/3204 
                 W24L/T670L/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 W727S/P750A/ 
                   
                   
                   
                   
                   
               
               
                   
                 S842G/E871L 
                   
                   
                   
                   
                   
               
               
                 3205/3206 
                 V50Q/W727S/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 P750A/H883R/ 
                   
                   
                   
                   
                   
               
               
                   
                 G894Q 
                   
                   
                   
                   
                   
               
               
                 3207/3208 
                 T29L/Q135S/ 
                 + 
                 + 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 S150T/R527N/ 
                   
                   
                   
                   
                   
               
               
                   
                 T670L/W727S/ 
                   
                   
                   
                   
                   
               
               
                   
                 H883R 
                   
                   
                   
                   
                   
               
               
                 3209/3210 
                 Q39P/W727S/ 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 P750A/A932S 
                   
                   
                   
                   
                   
               
               
                 3211/3212 
                 S150T/H883R/ 
                 + 
                 + 
                 + 
                 + 
                   
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
               
               
                 3213/3214 
                 Q1355/T670L/ 
                 + 
                 + 
                 +++ 
                 ++ 
                 ++ 
               
               
                   
                 W727S 
                   
                   
                   
                   
                   
               
               
                 3215/3216 
                 T29L/E78P/ 
                 + 
                 + 
                 +++ 
                 ++ 
                 ++ 
               
               
                   
                 E87D/S150T/ 
                   
                   
                   
                   
                   
               
               
                   
                 R527N/W727S 
                   
                   
                   
                   
                   
               
               
                 3217/3218 
                 W24L/S28L/ 
                 ++ 
                 ++ 
                 +++ 
                   
                 ++ 
               
               
                   
                 V50Q/Q135S/ 
                   
                   
                   
                   
                   
               
               
                   
                 S150T/G437A/ 
                   
                   
                   
                   
                   
               
               
                   
                 V522E/R527N/ 
                   
                   
                   
                   
                   
               
               
                   
                 E871L/H883R/ 
                   
                   
                   
                   
                   
               
               
                   
                 G894Q/A932S 
                   
                   
                   
                   
                   
               
               
                 3219/3220 
                 W24L/L62A/ 
                 + 
                 + 
                 +++ 
                 + 
                 + 
               
               
                   
                 E87D/E486T/ 
                   
                   
                   
                   
                   
               
               
                   
                 W727S 
                   
                   
                   
                   
                   
               
               
                 3221/3222 
                 T29L/V522E/ 
                 + 
                 + 
                 +++ 
                   
                 + 
               
               
                   
                 T670L/H711A/ 
                   
                   
                   
                   
                   
               
               
                   
                 E871L 
                   
                   
                   
                   
                   
               
               
                 3223/3224 
                 S28L/V522E/ 
                 + 
                 + 
                 ++ 
                   
                   
               
               
                   
                 R527N/T569L/ 
                   
                   
                   
                   
                   
               
               
                   
                 H711A/K830Q/ 
                   
                   
                   
                   
                   
               
               
                   
                 G894Q 
                   
                   
                   
                   
                   
               
               
                 3225/3226 
                 S28L/W727S/ 
                 + 
                 + 
                 +++ 
                 ++ 
                 +++ 
               
               
                   
                 E871L 
                   
                   
                   
                   
                   
               
               
                 3227/3228 
                 T670L/H711A/ 
                   
                   
                 +++ 
                 + 
                 ++ 
               
               
                   
                 E871L 
                   
                   
                   
                   
                   
               
               
                 3229/3230 
                 T29L/S150T/ 
                 + 
                   
                 ++ 
                   
                 + 
               
               
                   
                 G437A/W727S 
                   
                   
                   
                   
                   
               
               
                 3231/3232 
                 K267R/R527N/ 
                 ++ 
                 + 
                 +++ 
                 ++ 
                 ++ 
               
               
                   
                 W727S 
                   
                   
                   
                   
                   
               
               
                 3233/3234 
                 S150T/R527N/ 
                 + 
                 + 
                 +++ 
                 ++ 
                 ++ 
               
               
                   
                 S842G/E871L/ 
                   
                   
                   
                   
                   
               
               
                   
                 R913V 
                   
                   
                   
                   
                   
               
               
                 3235/3236 
                 T29L/S150T/ 
                 + 
                 + 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 K267R/W727S/ 
                   
                   
                   
                   
                   
               
               
                   
                 P750A/E871L/ 
                   
                   
                   
                   
                   
               
               
                   
                 H883R/A932S 
                   
                   
                   
                   
                   
               
               
                 3237/3238 
                 S28L/W727S 
                 + 
                   
                 +++ 
                 ++ 
                 ++ 
               
               
                 3239/3240 
                 T29L/E87D 
                 + 
                   
                 +++ 
                 ++ 
                 ++ 
               
               
                 3241/3242 
                 T29L/L62A/ 
                 + 
                   
                 ++ 
                 + 
                 + 
               
               
                   
                 G437A/R527N 
                   
                   
                   
                   
                   
               
               
                 3243/3244 
                 V50Q/Q135S/ 
                 + 
                 + 
                 +++ 
                 ++ 
                 ++ 
               
               
                   
                 S150T/A932S 
                   
                   
                   
                   
                   
               
               
                 3245/3246 
                 V50Q/G437A/ 
                 + 
                 + 
                 ++ 
                   
                 + 
               
               
                   
                 V522E/R527N 
                   
                   
                   
                   
                   
               
               
                 3247/3248 
                 S28L/L62A 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                 3249/3250 
                 S28L/L62A/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 K267R/A932S 
                   
                   
                   
                   
                   
               
               
                 3251/3252 
                 W24L/V50Q/ 
                 ++ 
                 ++ 
                 + 
                 + 
                 ++ 
               
               
                   
                 E486T/R527N/ 
                   
                   
                   
                   
                   
               
               
                   
                 H711A/W727S 
                   
                   
                   
                   
                   
               
               
                 3253/3254 
                 L62A/E87D/ 
                 ++ 
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 S150T/W727S 
                   
                   
                   
                   
                   
               
               
                 3255/3256 
                 S28L 
                 ++ 
                 ++ 
                 ++ 
                 +++ 
                 ++ 
               
               
                 3257/3258 
                 W24L/L62A/ 
                 +++ 
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 W727S/K830Q/ 
                   
                   
                   
                   
                   
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
               
               
                 3259/3260 
                 V522E/R527N/ 
                 ++ 
                 ++ 
                 + 
                 + 
                 ++ 
               
               
                   
                 T569L/W727S 
                   
                   
                   
                   
                   
               
               
                 3261/3262 
                 T29L/T670L/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
               
               
                 3263/3264 
                 E871L 
                 ++ 
                 +++ 
                 ++ 
                 +++ 
                 ++ 
               
               
                 3265/3266 
                 G437A/V522E/ 
                 ++ 
                 ++ 
                 + 
                   
                 + 
               
               
                   
                 R527N/T670L/ 
                   
                   
                   
                   
                   
               
               
                   
                 E871L 
                   
                   
                   
                   
                   
               
               
                 3267/3268 
                 V522E 
                 ++ 
                 ++ 
                 ++ 
                 + 
                 ++ 
               
               
                 3269/3270 
                 L62A/E87D/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 S150T 
                   
                   
                   
                   
                   
               
               
                 3271/3272 
                 W24L/S28L/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 + 
               
               
                   
                 L62A/V522E/ 
                   
                   
                   
                   
                   
               
               
                   
                 T569L/A932S 
                   
                   
                   
                   
                   
               
               
                 3273/3274 
                 W24L/E87D/ 
                 ++ 
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 Q135S/V522E/ 
                   
                   
                   
                   
                   
               
               
                   
                 T670L/H711A/ 
                   
                   
                   
                   
                   
               
               
                   
                 K830Q/S842G/ 
                   
                   
                   
                   
                   
               
               
                   
                 R913V 
                   
                   
                   
                   
                   
               
               
                 3275/3276 
                 W24L/S150T/ 
                 ++ 
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 V522E/R527N/ 
                   
                   
                   
                   
                   
               
               
                   
                 W727S/H883R/ 
                   
                   
                   
                   
                   
               
               
                   
                 G894Q 
                   
                   
                   
                   
                   
               
               
                 3277/3278 
                 T670L/K830Q/ 
                 ++ 
                 +++ 
                 ++ 
                 + 
                 ++ 
               
               
                   
                 E871L 
                   
                   
                   
                   
                   
               
               
                 3279/3280 
                 L62A/G437A/ 
                 +++ 
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 W727S 
                   
                   
                   
                   
                   
               
               
                 3281/3282 
                 S28L/V50Q/ 
                 +++ 
                 +++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 V522E/R527N/ 
                   
                   
                   
                   
                   
               
               
                   
                 H711A/W727S/ 
                   
                   
                   
                   
                   
               
               
                   
                 E871L 
                   
                   
                   
                   
                   
               
               
                 3283/3284 
                 W24L/S28L/ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
                 ++ 
               
               
                   
                 G437A/E486T/ 
                   
                   
                   
                   
                   
               
               
                   
                 R527N 
               
               
                   
               
               
                   1 All activities were determined relative to the reference polypeptide of SEQ ID NO: 2880. Levels of increased activity are defined as follows: ““+”” = 0.9 to 1.1; “++” &gt; 1.1; “+++” &gt; 2; and “++++” &gt; 3.5. 
               
            
           
         
       
     
     EXAMPLE 16 
     GAA Variants of SEQ ID NO: 3104 
     In this Example, experiments for evolution and screening of GAA variants derived from SEQ ID NO: 3104 for improved GAA activity after a series of challenges are described. Libraries of variant genes GAA encoded based off of by SEQ ID NO: 3104 were constructed, plated, grown, and screened for GAA MU-Glu activity (“Unchallenged Activity FIOPC”), as well as after plasma challenge (“Plasma Stability and Activity FIOPC”), as described in Example 11. Variants were also tested for 4-MUGlu activity after lysis of Pompe fibroblasts treated for 20 hours (“Lysate Activity from Extended Treatment of Pompe Fibroblast FIOPC”) or GAA −/−  C2C12 cells (“Lysate Activity from Extended Treatment C2C12 GAA−/− FIOPC”) or 4 hour treatments hours (“Lysate Activity from Acute Treatment of Pompe Fibroblast FIOPC”) or (“Lysate Activity from Acute Treatment C2C12 GAA−/− FIOPC”), as described in Example 11. The results of these assays are presented in Table 16-1. 
     
       
         
           
               
             
               
                 TABLE 16-1 
               
             
            
               
                   
               
               
                 Activity of GAA Variants Relative to SEQ ID NO: 3104 1   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                 Lysate 
                 Lysate 
                 Lysate 
                 Lysate 
               
               
                   
                 Amino 
                   
                   
                 Activity 
                 Activity 
                 Activity 
                 Activity 
               
               
                   
                 Acid 
                   
                   
                 from 
                 from 
                 from 
                 from 
               
               
                   
                 Differences 
                   
                 Plasma 
                 Extended 
                 Acute 
                 Extended 
                 Acute 
               
               
                   
                 (Relative 
                   
                 Stability 
                 Treatment 
                 Treatment 
                 Treatment 
                 Treatment 
               
               
                 SEQ ID 
                 to SEQ 
                 Unchallenged 
                 and 
                 of Pompe 
                 of Pompe 
                 C2C12 
                 C2C12 
               
               
                 NO: 
                 ID NO: 
                 Activity 
                 Activity 
                 Fibroblast 
                 Fibroblast 
                 GAA-/- 
                 GAA-/- 
               
               
                 (nt/aa) 
                 3104) 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
                 FIOPC 
               
               
                   
               
               
                 3285/3286 
                 L62A/L860F/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3287/3288 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 +++ 
               
               
                   
                 K830Q/L860F/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 V878S/A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3289/3290 
                 L62A/K830Q/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 L860F/V878S/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3291/3292 
                 S678T/A932S 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                 3293/3294 
                 L62A/M833I/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 L860F/A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3295/3296 
                 L62A/L860F/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 E871L/V878S 
                   
                   
                   
                   
                   
                   
               
               
                 3297/3298 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 P785Q 
                   
                   
                   
                   
                   
                   
               
               
                 3299/3300 
                 L62A/V878S/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3301/3302 
                 L62A/K830Q/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 L860F/E871L/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 R873H 
                   
                   
                   
                   
                   
                   
               
               
                 3303/3304 
                 L62A/Y248H/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 S678T/K830Q/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 V8785/A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3305/3306 
                 L62A/L860F/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 E871L 
                   
                   
                   
                   
                   
                   
               
               
                 3307/3308 
                 S678T 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                 3309/3310 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 K830Q/E871L/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 A9325 
                   
                   
                   
                   
                   
                   
               
               
                 3311/3312 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                   
                 L860F 
                   
                   
                   
                   
                   
                   
               
               
                 3313/3314 
                 L62A/A89D/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 K830Q 
                   
                   
                   
                   
                   
                   
               
               
                 3315/3316 
                 L62A/V878S 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                 3317/3318 
                 L62A/K830Q/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 +++ 
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3319/3320 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                   
                 K830Q/L860F/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3321/3322 
                 L62A/A932S 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                 3323/3324 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 L860F/V878S 
                   
                   
                   
                   
                   
                   
               
               
                 3325/3326 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 +++ 
               
               
                   
                 E871L 
                   
                   
                   
                   
                   
                   
               
               
                 3327/3328 
                 L62A 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                 3329/3330 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 +++ 
               
               
                   
                 K830Q/L860F 
                   
                   
                   
                   
                   
                   
               
               
                 3331/3332 
                 L62A/K830Q/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
                   
               
               
                 3333/3334 
                 L62A/E871L/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 +++ 
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3335/3336 
                 L62A/K830Q/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 E871L/A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3337/3338 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                   
                 K830Q/E871L 
                   
                   
                   
                   
                   
                   
               
               
                 3339/3340 
                 L860F/A932S 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                 3341/3342 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 V878S/A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3343/3344 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 K830Q 
                   
                   
                   
                   
                   
                   
               
               
                 3345/3346 
                 L62A/L860F 
                 + 
                 + 
                 + 
                 + 
                 + 
                 +++ 
               
               
                 3347/3348 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 +++ 
               
               
                   
                 V878S/A932T 
                   
                   
                   
                   
                   
                   
               
               
                 3349/3350 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 K830Q/L860F/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 V878S 
                   
                   
                   
                   
                   
                   
               
               
                 3351/3352 
                 L62A/L860F/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 V878S/A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3353/3354 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 L860F/A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3355/3356 
                 L62A/S678T 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                 3357/3358 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3359/3360 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                   
                 E871L/A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3361/3362 
                 L62A/K830Q/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                   
                 L860F/A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3363/3364 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 K830Q/V878S/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3365/3366 
                 L62A/E871L/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 +++ 
               
               
                   
                 V878S/A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3367/3368 
                 L62A/K830Q/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                   
                 L860F 
                   
                   
                   
                   
                   
                   
               
               
                 3369/3370 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                   
                 K830Q/A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3371/3372 
                 L62A/L860F/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 E871L/A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3373/3374 
                 L62A/S678T/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 +++ 
               
               
                   
                 K830Q/L860F/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 E871L/V878S/ 
                   
                   
                   
                   
                   
                   
               
               
                   
                 A932S 
                   
                   
                   
                   
                   
                   
               
               
                 3375/3376 
                 L62A/K830Q 
                 + 
                 + 
                 + 
                 + 
                 + 
                 ++ 
               
               
                 3377/3378 
                 S678T/K830Q/ 
                 + 
                 + 
                 + 
                 + 
                 + 
                 + 
               
               
                   
                 A932S 
               
               
                   
               
               
                   1 All activities were determined relative to the reference polypeptide of SEQ ID NO: 3104. Levels of increased activity are defined as follows: ““+”” = 0.9 to 1.1; “++” &gt; 1.1; “+++” &gt; 2; and “++++” &gt; 3.5. 
               
            
           
         
       
     
     EXAMPLE 17 
     Identification of Active GAA Variants with Reduced Immunogenicity 
     Putative T-cell epitopes in a WT GAA (SEQ ID NO:6) were identified using the Immune Epitope Database (IEDB; Immune Epitope Database and Analysis Resource website) tools, as known in the art and proprietary statistical analysis tools (See e.g., iedb.org and Vita et al., Nucl. Acids Res., 38(Database issue): D854-62 [2010]. Epub 2009 Nov. 11]). The WT GAA was parsed into all possible 15-mer analysis frames, with each frame overlapping the last by 14 amino acids. The 15-mer analysis frames were evaluated for immunogenic potential by scoring their 9-mer core regions for predicted binding to eight common class II HLA-DR alleles (DRBI*0101, DRBI*0301, DRB1*0401, DRB1*0701, DRB1*0801, DRB1*1101, DRB1*1301, and DRB1*1501) that collectively cover nearly 95% of the human population (See e.g., Southwood et al., J. Immunol., 160:3363-3373 [1998]), using methods recommended on the IEDB website. Potential T-cell epitope clusters contained within the enzyme (i.e., sub-regions contained within GAA which have an unusually high potential for immunogenicity) were identified using statistical analysis tools, as known in the art. 
     GAA variants that were identified in Examples 3, 4, 6, 10, and 12-16 to be active in assays described in Examples 5 and 11 were analyzed for their levels of predicted immunogenicity by evaluating their binding to the eight common Class II HLA-DR alleles. The total immunogenicity score and immunogenic hit count were calculated for each variant. The total immunogenicity score (TIS) reflects the overall predicted immunogenicity of the variant (i.e., a higher score indicates a higher level of predicted immunogenicity). The immunogenic “hit count” (IHC) indicates the number of 15-mer analysis frames with an unusually high potential for immunogenicity (i.e., a higher score indicates a higher potential for immunogenicity). Mutations resulting in a reduced total immunogenicity score and/or an immunogenic hit count compared to the reference sequence were considered to be potential “deimmunizing mutations” and are shown in Tables 17-1, 17-2, 17-3, 17-4, 17-5, 17-6, 17-7, 17-8, and 17-9. A collection of the most deimmunizing mutations were recombined to generate a number of variants that were active and predicted to be significantly less immunogenic than WT GAA. 
     
       
         
           
               
             
               
                 TABLE 17-1 
               
             
            
               
                   
               
               
                 Reduction of Total Immunogenicity Score (TIS) and Immunogenic 
               
               
                 Hit Count (IHC) for GAA Variants Relative to SEQ ID NO: 2 1   
               
            
           
           
               
               
               
               
            
               
                 SEQ ID 
                   
                 TIS Reduction 
                 IHC Reduction 
               
               
                 NO: 
                 Amino Acid Differences 
                 (Relative to SEQ ID 
                 (Relative to SEQ ID 
               
               
                 (nt/aa) 
                 (Relative to SEQ ID NO: 2) 
                 NO: 2) 
                 NO: 2) 
               
               
                   
               
               
                 7/8 
                 T150S/T486E/A750P/R883H/Q894G 
                 +++ 
                 ++++ 
               
               
                 101/102 
                 L871E 
                 +++ 
                 +++ 
               
               
                 105/106 
                 M138A 
                 + 
                   
               
               
                 109/110 
                 Q107G 
                 ++ 
                   
               
               
                 113/114 
                 Q110G 
                 ++ 
                   
               
               
                 115/116 
                 Q110L 
                 + 
                   
               
               
                 123/124 
                 R403W 
                 + 
                   
               
               
                 125/126 
                 R414P 
                 + 
                   
               
               
                 137/138 
                 S135Q 
                 + 
                   
               
               
                 145/146 
                 T148G 
                 + 
                   
               
               
                 147/148 
                 T148Y 
                 + 
                   
               
               
                 149/150 
                 T150G 
                 + 
                   
               
               
                 155/156 
                 T692Q 
                 ++ 
                 + 
               
               
                 159/160 
                 V30G 
                 +++ 
                 +++ 
               
               
                 161/162 
                 V30K 
                 ++ 
                 + 
               
               
                 163/164 
                 V30T 
                 +++ 
                 +++ 
               
               
                 183/184 
                 L275M/A281V/S402A/M431V/ 
                 ++ 
                   
               
               
                   
                 M507L/I518V/W610R/S668D 
                   
                   
               
               
                 185/186 
                 L275M/M507L/A547G/S668D/ 
                 +++ 
                 + 
               
               
                   
                 L669H/S671N 
                   
                   
               
               
                 187/188 
                 L275M/M431V/V638I 
                 ++ 
                   
               
               
                 189/190 
                 A281V/S402A/I518V/A547G/S668D 
                 ++ 
                   
               
               
                 193/194 
                 L275V/M431V/M507L/I518V/ 
                 +++ 
                 + 
               
               
                   
                 A547G/S668D/L669H/S671N 
                   
                   
               
               
                 195/196 
                 S402A/M431V/I518V/W610R 
                 + 
                   
               
               
                 197/198 
                 K106P/H191R/G280D/S402A/ 
                 ++ 
                   
               
               
                   
                 R414G/A444P/S727P 
                   
                   
               
               
                 199/200 
                 M431V/M507L/I518V/L669H/ 
                 ++ 
                 + 
               
               
                   
                 S671N 
                   
                   
               
               
                 201/202 
                 L275V/R377K/S402A/M507L/ 
                 ++ 
                 + 
               
               
                   
                 I518V/L669H/S671N/V715G 
                   
                   
               
               
                 203/204 
                 H191R/R414G/E522V/G842S/C944S 
                 + 
                   
               
               
                 207/208 
                 L275M/A281V/W610R/V638I/ 
                 ++ 
                   
               
               
                   
                 S668D/L669H 
                   
                   
               
               
                 209/210 
                 A196V/S402A/M431V/A547G/ 
                 ++ 
                   
               
               
                   
                 W610R/V638I 
                   
                   
               
               
                 211/212 
                 H191R/G280D/S402A/R414G/ 
                 ++ 
                   
               
               
                   
                 A444P/A489D/D500A/C944S 
                   
                   
               
               
                 213/214 
                 L275V/S402A/V638I/L669H/S671N 
                 + 
                 + 
               
               
                 215/216 
                 L29Q/L240I/A596P/S668D/I869L 
                 ++++ 
                 ++++ 
               
               
                 217/218 
                 K106P/G280D/S402A/R414G/ 
                 +++ 
                   
               
               
                   
                 A444P/A489D/S727P/C944S 
                   
                   
               
               
                 219/220 
                 L29Q/L240I/A596S/S668D/H700F/ 
                 ++++ 
                 +++ 
               
               
                   
                 I744V/I869T 
                   
                   
               
               
                 221/222 
                 L218S/S668D/H700F/1869T 
                 +++ 
                 + 
               
               
                 223/224 
                 M507L/A547G/W610R 
                 + 
                   
               
               
                 225/226 
                 A281V/M431V/M507L/I518V/ 
                 ++ 
                   
               
               
                   
                 A547G/W610R/V638I/S668D 
                   
                   
               
               
                 227/228 
                 H191R/G280D/R414G/A444P/ 
                 ++ 
                   
               
               
                   
                 A489D/E522V/S727P/C944S 
                   
                   
               
               
                 229/230 
                 L275V/S402A/M431V/I518V/ 
                 + 
                   
               
               
                   
                 W610R/V638I/L669H/S671N/P922L 
                   
                   
               
               
                 23/24 
                 A276Y 
                 + 
                   
               
               
                 231/232 
                 L29V/L218S/L2401/H700F/I869T 
                 ++ 
                 + 
               
               
                 233/234 
                 A547G/V638I/S668D 
                 +++ 
                 + 
               
               
                 235/236 
                 H191R/G280D/R414G/C944S 
                 + 
                   
               
               
                 237/238 
                 L275V/M431V/M507L/I518V/ 
                 + 
                 + 
               
               
                   
                 W610R/L669H/S671N 
                   
                   
               
               
                 239/240 
                 L275M/S402A/M431V/M507L/ 
                 +++ 
                   
               
               
                   
                 A547G/S671N 
                   
                   
               
               
                 241/242 
                 S402A/M431V/A547G/V638I/S671N 
                 +++ 
                   
               
               
                 243/244 
                 A281V/S402A/M507L/A547G/ 
                 + 
                   
               
               
                   
                 V638I/L669H/S671N 
                   
                   
               
               
                 245/246 
                 L275M/A281V/M507L/A547G/ 
                 ++ 
                   
               
               
                   
                 L669H/S671N 
                   
                   
               
               
                 247/248 
                 L275M/M431V/I518V/A547G/ 
                 +++ 
                 + 
               
               
                   
                 V638I/S668D 
                   
                   
               
               
                 249/250 
                 A547G/W610R/V638I/S671N 
                 ++ 
                   
               
               
                 25/26 
                 A418E/H499R 
                 + 
                   
               
               
                 251/252 
                 L275V/M431V/M507L/A547G/ 
                 ++ 
                   
               
               
                   
                 W610R/V638I/S671N 
                   
                   
               
               
                 253/254 
                 L275M/S402A/M507L/A547G/ 
                 +++ 
                   
               
               
                   
                 W610R/S671N 
                   
                   
               
               
                 255/256 
                 L275M/A281V/S402A/I518V/ 
                 ++ 
                   
               
               
                   
                 A547G/W610R/V638I/S671N 
                   
                   
               
               
                 257/258 
                 A281V/S402A/I518V/A547G/ 
                 ++ 
                   
               
               
                   
                 W610R/V638I/S668D/L669H 
                   
                   
               
               
                 259/260 
                 L275M/A281V/S402A/A547G/ 
                 ++ 
                   
               
               
                   
                 W610R/V638I/L669H/S671N 
                   
                   
               
               
                 261/262 
                 L275M/M431V/I518V/W610R/ 
                 ++ 
                 + 
               
               
                   
                 V638I/L669H/S671N 
                   
                   
               
               
                 263/264 
                 L29Q/L218S/L2401/S668D/H700F/ 
                 +++ 
                 + 
               
               
                   
                 I744V/I869L 
                   
                   
               
               
                 265/266 
                 A281V/S402A/M507L/I518V/ 
                 + 
                   
               
               
                   
                 A547G/W610R/V638I/L669H/S671N 
                   
                   
               
               
                 267/268 
                 S402A/M431V/I518V/A547G/S671N 
                 +++ 
                   
               
               
                 269/270 
                 L275V/A281V/S402A/M431V/ 
                 + 
                   
               
               
                   
                 I518V/A547G/W610R/L669H/S671N 
                   
                   
               
               
                 271/272 
                 L224F/S402A/M507L/I518V/A547G/ 
                 +++ 
                 ++ 
               
               
                   
                 V638I/S668D 
                   
                   
               
               
                 273/274 
                 N180H/S402A/M507L/A547G/ 
                 ++ 
                   
               
               
                   
                 W610R/S671N 
                   
                   
               
               
                 275/276 
                 L275M/A281V/S402A/M507L/ 
                 ++ 
                   
               
               
                   
                 I518V/A547G/V638I/L669H/S671N 
                   
                   
               
               
                 277/278 
                 K106P/T150S/T486E/Q749E/E793K/ 
                 +++ 
                 +++ 
               
               
                   
                 R883H/Q894G 
                   
                   
               
               
                 279/280 
                 L275V/A281V/M431V/I518V/ 
                 + 
                   
               
               
                   
                 A547G/V638I/L669H/S671N 
                   
                   
               
               
                 281/282 
                 L275V/S402A/A547G/W610R/ 
                 ++ 
                 + 
               
               
                   
                 V638I/L669H/S671N 
                   
                   
               
               
                 283/284 
                 L275M/S402A/A547G/V638I/ 
                 +++ 
                 + 
               
               
                   
                 L669H/S671N 
                   
                   
               
               
                 285/286 
                 K106P/T150S/T486E/N527D/A750P/ 
                 + 
                   
               
               
                   
                 E793K 
                   
                   
               
               
                 287/288 
                 S402A/M431V/I518V/A547G/ 
                 +++ 
                 + 
               
               
                   
                 W610R/S668D 
                   
                   
               
               
                 29/30 
                 A437S 
                 ++ 
                 ++ 
               
               
                 291/292 
                 L275V/M507L/I518V/A547G/V638I/ 
                 ++ 
                 + 
               
               
                   
                 L669H/S671N 
                   
                   
               
               
                 293/294 
                 N180H/S402A/M431V/M507L/ 
                 +++ 
                   
               
               
                   
                 A547G/W610R/L669H/S671N/E793G 
                   
                   
               
               
                 295/296 
                 L275V/M507L/I518V/A547G/ 
                 +++ 
                 + 
               
               
                   
                 W610R/V638I/S668D/L669H 
                   
                   
               
               
                 297/298 
                 L275V/S402A/M507L/A547G/ 
                 +++ 
                 + 
               
               
                   
                 W610R/V638I/S668D/L669H 
                   
                   
               
               
                 299/300 
                 M507L/A547G/V638I/L669H/S671N 
                 ++ 
                 + 
               
               
                 303/304 
                 T150S/R414G/T486E/Q749E/A750P/ 
                 ++ 
                   
               
               
                   
                 E793K 
                   
                   
               
               
                 305/306 
                 K106P/T150S/L218S/R414G/T486E/ 
                 +++ 
                   
               
               
                   
                 L642F/A750P/E793K/R883H 
                   
                   
               
               
                 307/308 
                 N180H/L275M/S402A/I518V/ 
                 +++ 
                 + 
               
               
                   
                 A547G/W610R/V638I/L669H/S671N 
                   
                   
               
               
                 309/310 
                 T150S/L218S/R414G/Q749E/E793K 
                 + 
                   
               
               
                 311/312 
                 L275V/M507L/A547G/W610R/ 
                 + 
                 + 
               
               
                   
                 V638I/L669H/S671N 
                   
                   
               
               
                 313/314 
                 T150S/R414G/T486E/N527D/ 
                 ++ 
                   
               
               
                   
                 A750P/Q894R 
                   
                   
               
               
                 315/316 
                 K106P/T150S/L218S/N527D/E793K/ 
                 ++ 
                 + 
               
               
                   
                 Q894G 
                   
                   
               
               
                 321/322 
                 K106P/T150S/R414G/Q749E/A750P/ 
                 ++ 
                   
               
               
                   
                 E793K/Q894R 
                   
                   
               
               
                 323/324 
                 K106P/T150S/N169S/N527D/ 
                 ++ 
                   
               
               
                   
                 Q749E/E793K/R883H 
                   
                   
               
               
                 325/326 
                 L275V/S402A/M507L/A547G/ 
                 ++ 
                 + 
               
               
                   
                 W610R/V638I/L669H/S671N 
                   
                   
               
               
                 329/330 
                 M431V/M507L/I518V/G541E/ 
                 +++ 
                 + 
               
               
                   
                 A547G/V638I/L669H/S671N 
                   
                   
               
               
                 331/332 
                 T150S/L218S/R414G/T486A/A750P/ 
                 + 
                   
               
               
                   
                 E793K 
                   
                   
               
               
                 335/336 
                 K106P/T150S/N169S/L218S/R414G/ 
                 + 
                   
               
               
                   
                 T486E/Q894R 
                   
                   
               
               
                 337/338 
                 T150S/L218S/R414G/T486E/A750P/ 
                 ++ 
                   
               
               
                   
                 E793K/R883H 
                   
                   
               
               
                 339/340 
                 K106P/T150S/N169S/L218S/R414G/ 
                 + 
                   
               
               
                   
                 Q749E/E793K 
                   
                   
               
               
                 341/342 
                 T269N/L275M/M431V/I518V/ 
                 +++ 
                 + 
               
               
                   
                 A547G/V638I/S668D/L669H 
                   
                   
               
               
                 343/344 
                 K106P/T150S/R414G/Q749E/ 
                 ++ 
                   
               
               
                   
                 E793K/Q894R 
                   
                   
               
               
                 347/348 
                 K106P/T150S/N169S/Q749E/E793K/ 
                 ++ 
                   
               
               
                   
                 R883H/Q894R 
                   
                   
               
               
                 35/36 
                 A547G 
                 + 
                   
               
               
                 353/354 
                 K106P/T150S/L218S/R414G/T486E/ 
                 + 
                   
               
               
                   
                 A750P/E793K/Q894R 
                   
                   
               
               
                 355/356 
                 K106P/T150S/N169S/L218S/R414G/ 
                 ++ 
                   
               
               
                   
                 T486E/Q749E/E793K/R883H/Q894R 
                   
                   
               
               
                 357/358 
                 K106P/T150S/N169S/L218S/T486E/ 
                 ++ 
                 + 
               
               
                   
                 R883H 
                   
                   
               
               
                 359/360 
                 K106P/T150S/N169S/L218S/R414G/ 
                 ++ 
                   
               
               
                   
                 T486E/A750P/E793K/R883H/Q894R 
                   
                   
               
               
                 361/362 
                 G36R/K106P/T150S/L218S/N527D/ 
                 + 
                   
               
               
                   
                 A750P/R883H/Q894R 
                   
                   
               
               
                 363/364 
                 K106P/T150S/N169S/L218S/T486E/ 
                 ++ 
                 + 
               
               
                   
                 Q749E/R883H 
                   
                   
               
               
                 365/366 
                 K106P/N169S/V185G/L218S/ 
                 + 
                   
               
               
                   
                 R414G/Q749E/A750P/E793K 
                   
                   
               
               
                 367/368 
                 K106P/T150S/P245S/E793K/R883H/ 
                 + 
                   
               
               
                   
                 Q894R 
                   
                   
               
               
                 369/370 
                 K106P/T150S/N169S/L218S/R414G/ 
                 ++ 
                   
               
               
                   
                 Q749E/A750P/E793K/R883H 
                   
                   
               
               
                 37/38 
                 A750P 
                 + 
                   
               
               
                 375/376 
                 T150S/L218S/R414G/Q749E/A750P/ 
                 + 
                   
               
               
                   
                 E793K/Q894R 
                   
                   
               
               
                 377/378 
                 K106P/T150S/N169S/R414G/T486E/ 
                 +++ 
                 + 
               
               
                   
                 Q749E/A750P/R883H 
                   
                   
               
               
                 379/380 
                 K106P/T150S/N169S/L218S/R414G/ 
                 ++ 
                   
               
               
                   
                 T486E/E793K/R883H 
                   
                   
               
               
                 381/382 
                 K106P/T150S/L218S/T486E/N527D/ 
                 + 
                   
               
               
                   
                 Q749E/Q894R 
                   
                   
               
               
                 383/384 
                 K106P/T150S/N169S/L218S/R414G/ 
                 + 
                   
               
               
                   
                 T486E/N527D/Q894R 
                   
                   
               
               
                 385/386 
                 T150S/L218S/R414G/T486E/Q749E/ 
                 ++ 
                   
               
               
                   
                 A750P 
                   
                   
               
               
                 387/388 
                 K106P/T150S/L218S/R414G/Q749E/ 
                 ++ 
                   
               
               
                   
                 E793K/R883H 
                   
                   
               
               
                 389/390 
                 K106P/T150S/N169S/L218S/R414G/ 
                 ++ 
                   
               
               
                   
                 T486E/N527D/A750P/Q894R 
                   
                   
               
               
                 39/40 
                 A753T 
                 + 
                   
               
               
                 391/392 
                 N169S/T486E/A750P/E793K/R883H 
                 ++ 
                   
               
               
                 393/394 
                 K106P/T150S/L218S/R414G/N527D/ 
                 +++ 
                 + 
               
               
                   
                 Q749E/A750P/R883H 
                   
                   
               
               
                 395/396 
                 K106P/T150S/L218S/R414G/Q749E/ 
                 ++ 
                   
               
               
                   
                 A750P/E793K/R883H/Q894R 
                   
                   
               
               
                 397/398 
                 K106P/T150S/N169S/L218S/R414G/ 
                 ++ 
                   
               
               
                   
                 Q749E/E793K/R883H 
                   
                   
               
               
                 399/400 
                 K106P/T150S/L218S/T486E/E793K/ 
                 + 
                   
               
               
                   
                 R883H 
                   
                   
               
               
                 401/402 
                 K106P/T150S/L218S/V331A/R414G/ 
                 ++ 
                   
               
               
                   
                 T486E/N527D/D733E/Q749E/E793K 
                   
                   
               
               
                 403/404 
                 L275M/A281V/S402A/I518V/ 
                 +++ 
                 + 
               
               
                   
                 A547G/W610R/S668D/L669H/E887D 
                   
                   
               
               
                 405/406 
                 K106P/T150S/L218S/R414G/N527D/ 
                   
                   
               
               
                   
                 Q749E/E793K/R883H/Q894G 
                 +++ 
                 ++ 
               
               
                 407/408 
                 K106P/T150S/Q749E/E793K/R883H 
                 ++ 
                   
               
               
                 409/410 
                 K106P/A112S/T150S/L218S/R414G/ 
                 ++ 
                   
               
               
                   
                 N527D/E793K/R883H 
                   
                   
               
               
                 43/44 
                 C944G 
                 + 
                   
               
               
                 47/48 
                 D274G 
                 + 
                   
               
               
                 53/54 
                 F27P 
                 + 
                 + 
               
               
                 55/56 
                 F27P/C944W 
                 + 
                 + 
               
               
                 57/58 
                 F27R 
                 + 
                 + 
               
               
                 61/62 
                 G820E 
                 + 
                   
               
               
                 63/64 
                 I375E 
                 + 
                   
               
               
                 65/66 
                 K471Q/A478S 
                 + 
                   
               
               
                 69/70 
                 K581G 
                 ++ 
                 + 
               
               
                 71/72 
                 K581T 
                 + 
                   
               
               
                 81/82 
                 L109G/G842E 
                 + 
                   
               
               
                 83/84 
                 L109P 
                 + 
                   
               
               
                 85/86 
                 L28P 
                 ++ 
                 ++ 
               
               
                 89/90 
                 L28S 
                 ++ 
                 ++ 
               
               
                 91/92 
                 L29T/A478T 
                 +++ 
                 ++ 
               
               
                 95/96 
                 L642Q 
                 + 
                   
               
               
                 97/98 
                 L642S 
                 + 
                   
               
               
                  99/100 
                 L670N 
                 +++ 
                 + 
               
               
                   
               
               
                   1 TIS reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 2, and defined as follows: 
               
               
                 “+” = 1-10; 
               
               
                 “++” &gt; 10; 
               
               
                 “+++” &gt; 20; and 
               
               
                 “++++” &gt; 50. 
               
               
                 IHC reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 2, and defined as follows: 
               
               
                 “+” = 1-3; 
               
               
                 “++” &gt; 3; 
               
               
                 “+++” &gt; 5; and 
               
               
                 “++++” &gt; 8. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 17-2 
               
             
            
               
                   
               
               
                 Reduction of Total Immunogenicity Score (TIS) and Immunogenic 
               
               
                 Hit Count to (IHC) for GAA Variants Relative SEQ ID NO: 8 1   
               
            
           
           
               
               
               
               
            
               
                   
                   
                 TIS  
                 IHC  
               
               
                 SEQ 
                   
                 Reduction 
                 Reduction 
               
               
                 ID 
                   
                 (Relative to 
                 (Relative  
               
               
                 NO: 
                 Amino Acid Differences 
                 SEQ 
                 to SEQ 
               
               
                 (nt/aa) 
                 (Relative to SEQ ID NO: 8) 
                 ID NO: 8) 
                 ID NO: 8) 
               
               
                   
               
               
                 13/14 
                 L28S/L29T/S135Q 
                 ++++ 
                 +++ 
               
               
                 413/414 
                 A418E 
                 +++ 
                 + 
               
               
                 415/416 
                 A418E/A489R 
                 +++ 
                 + 
               
               
                 431/432 
                 K106P 
                 +++ 
                 + 
               
               
                 433/434 
                 K106P/A489R/S671N 
                 +++ 
                 + 
               
               
                 445/446 
                 K106P/V638I 
                 +++ 
                 + 
               
               
                 447/448 
                 L157M 
                 +++ 
                 + 
               
               
                 469/470 
                 L218S/V638I/S671N 
                 +++ 
                   
               
               
                 509/510 
                 Q113S/A418E/A478T/A489R/ 
                 +++ 
                   
               
               
                   
                 K581T 
                   
                   
               
               
                 511/512 
                 Q113S/A418E/R455V/A478T/ 
                 +++ 
                   
               
               
                   
                 K581T 
                   
                   
               
               
                 519/520 
                 S135P/C944Y 
                 +++ 
                 + 
               
               
                 521/522 
                 S135Q 
                 +++ 
                 + 
               
               
                 523/524 
                 S135Q/A478T/A489R/K581T 
                 +++ 
                   
               
               
                 531/532 
                 S671N/Q749E 
                 +++ 
                 + 
               
               
                 441/442 
                 K106P/M138A/L218S/M431V/ 
                   
                   
               
               
                   
                 S671N/Q749E 
                 +++ 
                   
               
               
                 513/514 
                 Q113S/S135Q/A418E 
                 +++ 
                 + 
               
               
                 527/528 
                 S135Q/T148G/S150G/A418E 
                 +++ 
                 + 
               
               
                 429/430 
                 F27R 
                 +++ 
                 + 
               
               
                 425/426 
                 F27P/A418E/A478T 
                 +++ 
                 + 
               
               
                 501/502 
                 M507L/S668D 
                 +++ 
                 + 
               
               
                 495/496 
                 M138A/L218S/S668D/S671N 
                 +++ 
                 + 
               
               
                 499/500 
                 M431V/S668D/S671N 
                 ++++ 
                 ++ 
               
               
                 471/472 
                 L28S 
                 +++ 
                 ++ 
               
               
                 481/482 
                 L29T/A478T 
                 +++ 
                 +++ 
               
               
                 483/484 
                 L29T/Q113S/M138A 
                 +++ 
                 +++ 
               
               
                 485/486 
                 L29T/Q113S/P126Q/S135Q/H193Q 
                 +++ 
                 +++ 
               
               
                 487/488 
                 L29T/Q113S/S135Q 
                 +++ 
                 +++ 
               
               
                 489/490 
                 L29T/Q113S/S135Q/R455V 
                 +++ 
                 +++ 
               
               
                 491/492 
                 L29T/T148G 
                 +++ 
                 +++ 
               
               
                 473/474 
                 L285/L29T 
                 +++ 
                 +++ 
               
               
                 475/476 
                 L285/L29T/A418E 
                 ++++ 
                 +++ 
               
               
                 477/478 
                 L285/L29T/Q113S/S135Q/A418E 
                 ++++ 
                 +++ 
               
               
                 479/480 
                 L285/L29T/Q113S/S135Q/M138A 
                 ++++ 
                 +++ 
               
               
                   
               
               
                   1 TIS reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 8, and defined as follows: 
               
               
                 “+” = 1-10; 
               
               
                 “++” &gt; 10; 
               
               
                 “+++” &gt; 20; and 
               
               
                 “++++” &gt; 50. 
               
               
                 IHC reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 8, and defined as follows: 
               
               
                 “+” = 1-3; 
               
               
                 “++” &gt; 5; and 
               
               
                 “+++” &gt; 8. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 17-3 
               
             
            
               
                   
               
               
                 Reduction of Total Immunogenicity Score (TIS) and Immunogenic Hit Count 
               
               
                 (IHC) for GAA Variants Relative to SEQ ID NO: 8 1   
               
            
           
           
               
               
               
               
            
               
                   
                   
                 TIS 
                 IHC 
               
               
                 SEQ 
                   
                 Reduction 
                 Reduction 
               
               
                 ID  
                   
                 (Relative to  
                 (Relative to 
               
               
                 NO: 
                 Amino Acid Differences 
                 SEQ ID NO: 
                 SEQ ID NO: 
               
               
                 (nt/aa) 
                 (Relative to SEQ ID NO: 18) 
                 18) 
                 18) 
               
               
                   
               
               
                 19/20 
                 P39Q/R267K/A489D/E522V/S612D/Q830K/G842S 
                 + 
                   
               
               
                 371/372 
                 P39D 
                 + 
                   
               
               
                 533/534 
                 V70A/R267K/K725E/C944S 
                 + 
                   
               
               
                 535/536 
                 R267K/A489D/D500A/K725E/Q830K/C930P 
                 + 
                   
               
               
                 537/538 
                 L109P/E522V/Q830K/C944S 
                 + 
                   
               
               
                 539/540 
                 V70A/R267K/C930P/C944S 
                 + 
                   
               
               
                 543/544 
                 H734K 
                 + 
                   
               
               
                 553/554 
                 P39Q/V70A/L109P/Q830K/G842S 
                 + 
                   
               
               
                 555/556 
                 P39Q/V70A/K725E 
                 + 
                   
               
               
                 557/558 
                 P39Q/R267K/A489D/Q830K/C944S 
                 + 
                   
               
               
                 559/560 
                 C930P 
                 + 
                   
               
               
                 561/562 
                 D500A/C930P/C944S 
                 + 
                   
               
               
                 567/568 
                 P39Q/R267K 
                 + 
                   
               
               
                 575/576 
                 R267K/E522V/K725E 
                 + 
                   
               
               
                 577/578 
                 V70A/A489D/C930P 
                 + 
                   
               
               
                 585/586 
                 P39Q 
                 + 
                   
               
               
                 601/602 
                 S37F/N528S/I790V 
                 + 
                   
               
               
                 611/612 
                 S37F/A62E 
                 + 
                   
               
               
                 625/626 
                 S37F/A196T 
                 + 
                   
               
               
                 627/628 
                 S37F/A62E/D523N 
                 + 
                   
               
               
                 633/634 
                 S37F/A62E/N79S/A196T/A696S/R862Q 
                 + 
                   
               
               
                 655/656 
                 L34D 
                 + 
                   
               
               
                 657/658 
                 Y352K 
                 + 
                   
               
               
                 667/668 
                 N875D 
                 ++ 
                 ++ 
               
               
                 673/674 
                 I22R 
                 + 
                   
               
               
                 675/676 
                 L24W 
                 ++ 
                   
               
               
                 677/678 
                 L778Q 
                 + 
                   
               
               
                 685/686 
                 Y352V 
                 + 
                   
               
               
                 691/692 
                 F27K 
                 + 
                   
               
               
                 695/696 
                 S932A 
                 + 
                   
               
               
                 697/698 
                 L24R 
                 + 
                   
               
               
                 699/700 
                 L24E 
                 ++ 
                   
               
               
                 709/710 
                 F27G 
                 + 
                   
               
               
                 713/714 
                 L34M 
                 + 
                   
               
               
                 731/732 
                 A774G 
                 + 
                   
               
               
                 735/736 
                 F27W 
                 + 
                   
               
               
                 745/746 
                 R385G 
                 + 
                   
               
               
                 747/748 
                 F27G/M165I 
                 + 
                   
               
               
                 749/750 
                 V30D 
                 + 
                   
               
               
                 753/754 
                 V40W 
                 + 
                   
               
               
                 761/762 
                 E33G 
                 + 
                   
               
               
                 765/766 
                 L109D 
                 + 
                   
               
               
                 793/794 
                 Q107G 
                 ++ 
                   
               
               
                 801/802 
                 F27R 
                 + 
                   
               
               
                 803/804 
                 L934F 
                 + 
                   
               
               
                 813/814 
                 Q217D 
                 + 
                   
               
               
                 817/818 
                 L34T 
                 + 
                   
               
               
                 821/822 
                 P673N 
                 + 
               
               
                   
               
               
                   1 TIS reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 18, and defined as follows: 
               
               
                 “+” = 1-10; 
               
               
                 “++” &gt; 10; 
               
               
                 “+++” &gt; 20; and 
               
               
                 “++++” &gt; 50. 
               
               
                 IHC reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 18, and defined as follows: 
               
               
                 “+” = 1-2; 
               
               
                 “++” &gt; 2; and 
               
               
                 “+++” &gt; 5. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 17-4 
               
             
            
               
                   
               
               
                 Reduction of Total Immunogenicity Score (TIS) and Immunogenic 
               
               
                 Hit Count (IHC) for GAA Variants Relative to SEQ ID NO: 20 1   
               
            
           
           
               
               
               
               
            
               
                 SEQ ID 
                   
                 TIS Reduction 
                 IHC Reduction 
               
               
                 NO: 
                 Amino Acid Differences 
                 (Relative to SEQ  
                 (Relative to SEQ 
               
               
                 (nt/aa) 
                 (Relative to SEQ ID NO: 20) 
                 ID NO: 20) 
                 ID NO: 20) 
               
               
                   
               
               
                 829/830 
                 L24R/F27G/A89R/D500A/S842G 
                 + 
                   
               
               
                 831/832 
                 L24R/F27G/D500A/S842G 
                 + 
                   
               
               
                 833/834 
                 D500A/S932A 
                 + 
                   
               
               
                 835/836 
                 L24R/Q39H/S842G/S932A 
                 + 
                   
               
               
                 839/840 
                 D500A/S842G 
                 + 
                   
               
               
                 841/842 
                 S842G/S932A 
                 + 
                   
               
               
                 843/844 
                 A89R/A97G/Q107G 
                 ++ 
                   
               
               
                 847/848 
                 F27G/Q39H/Q49G/A97G/D500A/S842G 
                 + 
                   
               
               
                 849/850 
                 R68N/A89R/A97G/S932A 
                 + 
                   
               
               
                 851/852 
                 A89R/S842G 
                 + 
                   
               
               
                 853/854 
                 L24R/Q39D/R68S/A89R/Q107G/D500A/ 
                 ++ 
                   
               
               
                   
                 S842G 
                   
                   
               
               
                 855/856 
                 L24R/F27G/D500A/S842G/S932A 
                 + 
                   
               
               
                 857/858 
                 L24R/Q39H/Q49G/A89R/A97G/S842G/ 
                 + 
                   
               
               
                   
                 S932A 
                   
                   
               
               
                 859/860 
                 L24R/S842G/S932A 
                 + 
                   
               
               
                 861/862 
                 L24R/A89R/D500A 
                 + 
                   
               
               
                 863/864 
                 L24R/Q39H/A89R/A97D/S842G/S932A 
                 + 
                   
               
               
                 865/866 
                 L24R 
                 + 
                   
               
               
                 867/868 
                 F27G/Q49G/R68S/D500A/S842G 
                 + 
                   
               
               
                 869/870 
                 Q107G/D500A/S842G 
                 ++ 
                   
               
               
                 871/872 
                 L34T/Q39D/D500A/S932A 
                 + 
                   
               
               
                 875/876 
                 L24W/L109D/D612S 
                 +++ 
                   
               
               
                 877/878 
                 L24W/V70A/K267R/A774S 
                 + 
                   
               
               
                 879/880 
                 I22R/L24W/D612S/K725E/C944R 
                 +++ 
                   
               
               
                 881/882 
                 L24W 
                 ++ 
                   
               
               
                 883/884 
                 I22R/L24W/F27A/D489A 
                 +++ 
                   
               
               
                 887/888 
                 I22R/L24W/F27A/Q50V/Q107G/L109D/ 
                 +++ 
                   
               
               
                   
                 D489A/D612S/K725E 
                   
                   
               
               
                 889/890 
                 Q50V/D612S/C944S 
                 + 
                   
               
               
                 891/892 
                 D612S/K725E/C944S 
                 + 
                   
               
               
                 893/894 
                 L109D/D612S/A774S/C944S 
                 + 
                   
               
               
                 895/896 
                 I22R/L24W/F27A/D612S/C944R 
                 +++ 
                   
               
               
                 899/900 
                 Q50V/L109D/D489A/D612S 
                 + 
                   
               
               
                 901/902 
                 I22R/L24W/Q50V/L109D/K267R/D489A/ 
                 ++ 
                   
               
               
                   
                 A774S/C944R 
                   
                   
               
               
                 903/904 
                 I22R/L24W 
                 ++ 
                   
               
               
                 905/906 
                 L24W/Q50V/D489A/C944S 
                 ++ 
                   
               
               
                 907/908 
                 I22R/Q50V/L109D/K267R/D489A 
                 + 
                   
               
               
                 909/910 
                 L24W/D489A/C944R 
                 ++ 
                   
               
               
                 911/912 
                 L24W/K725E 
                 ++ 
                   
               
               
                 913/914 
                 L24W/L109D/C944S 
                 ++ 
                   
               
               
                 915/916 
                 D612S/P922E 
                 + 
                   
               
               
                 917/918 
                 L24W/K267R/K725E/C944S 
                 + 
                   
               
               
                 919/920 
                 Q107G/L109D 
                 ++ 
                   
               
               
                 923/924 
                 I22R/L24W/Q50V/K267R/D612S/P922E/ 
                 ++ 
                   
               
               
                   
                 C944R 
                   
                   
               
               
                 925/926 
                 I22R/L24W/F27A/D489A/D612S/A774S 
                 +++ 
                   
               
               
                 927/928 
                 L24W/F27A/Q107G/K267R/D612S/C944S 
                 +++ 
                   
               
               
                 929/930 
                 L24W/F27A/K267R/C944R 
                 ++ 
                   
               
               
                 931/932 
                 I22R/L24W/D489A 
                 ++ 
                   
               
               
                 933/934 
                 I22R/Q50V/Q107G/K267R/D489A/D612S/ 
                 ++ 
                   
               
               
                   
                 C944S 
                   
                   
               
               
                 935/936 
                 L24W/V70A/Q107G/L109D/D489A/D612S/ 
                 +++ 
                   
               
               
                   
                 K725E 
                   
                   
               
               
                 937/938 
                 I22R/L24W/Q107G/K267R/D489A/P922E 
                 +++ 
                   
               
               
                 939/940 
                 L24W/Q107G/L109D/K267R/D489A/D612S/ 
                 +++ 
                   
               
               
                   
                 K725E/A774S 
                   
                   
               
               
                 941/942 
                 L24W/F27A/C944R 
                 +++ 
                   
               
               
                 943/944 
                 D612S 
                 + 
                   
               
               
                 945/946 
                 L24W/Q50V/D612S 
                 ++ 
                   
               
               
                 947/948 
                 I22R/K267R/D489A/D612S 
                 + 
                   
               
               
                 949/950 
                 L24W/F27A/Q50V/Q107G/K267R/A774S/ 
                 +++ 
                   
               
               
                   
                 C944S 
                   
                   
               
               
                 951/952 
                 L24W/C944S 
                 ++ 
                   
               
               
                 1121/1122 
                 L818V 
                 + 
                   
               
               
                 1123/1124 
                 T148E 
                 + 
                   
               
               
                 1125/1126 
                 A741D 
                 ++ 
                   
               
               
                 1129/1130 
                 L737M 
                 + 
                   
               
               
                 1141/1142 
                 G108S 
                 ++ 
                   
               
               
                 1143/1144 
                 L259N 
                 + 
                   
               
               
                 1153/1154 
                 L238Q 
                 +++ 
                 +++ 
               
               
                 1159/1160 
                 S916A 
                 ++ 
                   
               
               
                 1167/1168 
                 M432C 
                 ++ 
                 ++ 
               
               
                 1173/1174 
                 E188Q/R377Q 
                 + 
                   
               
               
                 1175/1176 
                 K106G 
                 + 
                   
               
               
                 1177/1178 
                 K106N 
                 + 
                   
               
               
                 1179/1180 
                 L244I 
                 + 
                   
               
               
                 1181/1182 
                 A319F 
                 + 
                 + 
               
               
                 1183/1184 
                 I815M 
                 + 
                 ++ 
               
               
                 1189/1190 
                 P832E 
                 + 
                   
               
               
                 1191/1192 
                 A741T 
                 + 
                   
               
               
                 1207/1208 
                 S243R 
                 + 
                   
               
               
                 1215/1216 
                 S727T 
                 + 
                   
               
               
                 1217/1218 
                 L240I 
                 + 
                   
               
               
                 1231/1232 
                 V913A 
                 ++ 
                   
               
               
                 965/966 
                 S916R 
                 + 
                   
               
               
                 1235/1236 
                 L940G 
                 + 
                   
               
               
                 967/968 
                 P914G 
                 ++ 
                   
               
               
                 1261/1262 
                 L305Y 
                 + 
                 + 
               
               
                 971/972 
                 D923W 
                 + 
                   
               
               
                 1297/1298 
                 L305G 
                 +++ 
                 +++ 
               
               
                 981/982 
                 L742V 
                 + 
                   
               
               
                 1307/1308 
                 I815A 
                 + 
                   
               
               
                 991/992 
                 P914Q 
                 + 
                   
               
               
                 1327/1328 
                 P914E 
                 + 
                   
               
               
                 1335/1336 
                 S264C 
                 + 
                   
               
               
                 1339/1340 
                 Y248A 
                 + 
                   
               
               
                 1341/1342 
                 L305R 
                 + 
                 + 
               
               
                 1001/1002 
                 T148K 
                 + 
                   
               
               
                 1349/1350 
                 L320M 
                 + 
                   
               
               
                 1351/1352 
                 L736V 
                 + 
                   
               
               
                 1353/1354 
                 A309C 
                 ++ 
                 + 
               
               
                 1385/1386 
                 S727Q 
                 + 
                   
               
               
                 1007/1008 
                 A112H 
                 + 
                   
               
               
                 1395/1396 
                 L823A 
                 + 
                   
               
               
                 1405/1406 
                 L736W 
                 + 
                   
               
               
                 1409/1410 
                 S916I 
                 + 
                   
               
               
                 1413/1414 
                 V913E 
                 ++ 
                   
               
               
                 1427/1428 
                 L305V 
                 ++ 
                 + 
               
               
                 1435/1436 
                 Y248V 
                 + 
                   
               
               
                 1439/1440 
                 L818T 
                 ++ 
                   
               
               
                 1441/1442 
                 A741C 
                 ++ 
                   
               
               
                 1445/1446 
                 F556S 
                 ++ 
                   
               
               
                 1013/1014 
                 P914T 
                 + 
                   
               
               
                 1015/1016 
                 S916G 
                 ++ 
                   
               
               
                 1459/1460 
                 L748I 
                 + 
                   
               
               
                 1461/1462 
                 M260W 
                 + 
                   
               
               
                 1467/1468 
                 G108N 
                 ++ 
                   
               
               
                 1019/1020 
                 P914K 
                 + 
                   
               
               
                 1471/1472 
                 I816V 
                 + 
                 ++ 
               
               
                 1479/1480 
                 L748T 
                 + 
                   
               
               
                 1023/1024 
                 V913W 
                 ++ 
                   
               
               
                 1483/1484 
                 T148R/V772I 
                 + 
                   
               
               
                 1485/1486 
                 K106T 
                 + 
                   
               
               
                 1487/1488 
                 L240W/A374T 
                 ++ 
                 + 
               
               
                 1489/1490 
                 F556Y 
                 + 
                   
               
               
                 1499/1500 
                 G108V 
                 + 
                   
               
               
                 1515/1516 
                 S916V 
                 + 
                   
               
               
                 1033/1034 
                 L823F 
                 + 
                   
               
               
                 1527/1528 
                 E937Q 
                 + 
                   
               
               
                 1035/1036 
                 L305F 
                 + 
                 + 
               
               
                 1539/1540 
                 P832G 
                 + 
                   
               
               
                 1541/1542 
                 V913H 
                 ++ 
                   
               
               
                 1545/1546 
                 L252V 
                 + 
                   
               
               
                 1551/1552 
                 S243G 
                 ++ 
                 + 
               
               
                 1555/1556 
                 A741E 
                 ++ 
                   
               
               
                 1557/1558 
                 S243V 
                 + 
                   
               
               
                 1037/1038 
                 P914S 
                 + 
                   
               
               
                 1039/1040 
                 S727W 
                 + 
                   
               
               
                 1041/1042 
                 L940Q 
                 + 
                   
               
               
                 1567/1568 
                 P279E 
                 + 
                   
               
               
                 1569/1570 
                 V913Q 
                 ++ 
                   
               
               
                 1583/1584 
                 L259G 
                 + 
                   
               
               
                 1585/1586 
                 S243E 
                 +++ 
                 ++ 
               
               
                 1059/1060 
                 S402N 
                 + 
                   
               
               
                 1599/1600 
                 A253G 
                 + 
                   
               
               
                 1601/1602 
                 L736M 
                 ++ 
                   
               
               
                 1603/1604 
                 L940W 
                 + 
                   
               
               
                 1069/1070 
                 G108R 
                 + 
                   
               
               
                 1605/1606 
                 L823G 
                 + 
                   
               
               
                 1071/1072 
                 L748V 
                 + 
                   
               
               
                 1619/1620 
                 S727G 
                 + 
                   
               
               
                 1621/1622 
                 F556R 
                 ++ 
                   
               
               
                 1623/1624 
                 L261E 
                 + 
                   
               
               
                 1625/1626 
                 A309G 
                 ++ 
                   
               
               
                 1631/1632 
                 F556H 
                 ++ 
                   
               
               
                 1633/1634 
                 K106A 
                 + 
                   
               
               
                 1635/1636 
                 S402G 
                 + 
                   
               
               
                 1641/1642 
                 S262P 
                 + 
                   
               
               
                 1643/1644 
                 P914H 
                 + 
                   
               
               
                 1079/1080 
                 I333L 
                 + 
                   
               
               
                 1651/1652 
                 L329F 
                 + 
                   
               
               
                 1653/1654 
                 S246G 
                 ++ 
                 + 
               
               
                 1081/1082 
                 V312A 
                 +++ 
                 +++ 
               
               
                 1661/1662 
                 T148G 
                 + 
                   
               
               
                 1085/1086 
                 S916H 
                 ++ 
                   
               
               
                 1683/1684 
                 A741G 
                 + 
                   
               
               
                 1691/1692 
                 S246A 
                 + 
                   
               
               
                 1693/1694 
                 L940T 
                 + 
                   
               
               
                 1703/1704 
                 H387L 
                 + 
                   
               
               
                 1717/1718 
                 L244V 
                 ++ 
                 + 
               
               
                 1733/1734 
                 T148H 
                 + 
                   
               
               
                 1735/1736 
                 Y248R 
                 + 
                   
               
               
                 1101/1102 
                 P914R 
                 + 
                   
               
               
                 1757/1758 
                 A253P 
                 + 
                   
               
               
                 1105/1106 
                 N911G 
                 ++ 
                   
               
               
                 1769/1770 
                 I333V 
                 + 
                   
               
               
                 1771/1772 
                 A112P 
                 + 
                   
               
               
                 1779/1780 
                 V913L 
                 ++ 
                   
               
               
                 1785/1786 
                 L259S 
                 + 
                   
               
               
                 1787/1788 
                 L823R 
                 + 
                   
               
               
                 1789/1790 
                 L240Y 
                 + 
                   
               
               
                 1797/1798 
                 I249V/S777N 
                 + 
                   
               
               
                 1109/1110 
                 V913R 
                 + 
                   
               
               
                 1807/1808 
                 G108H 
                 + 
                   
               
               
                 1825/1826 
                 Q421P 
                 + 
                   
               
               
                 1117/1118 
                 V913G 
                 ++ 
               
               
                   
               
               
                   1 TIS reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 20, and defined as follows: 
               
               
                 “+” = 1-10; 
               
               
                 “++” &gt; 10; 
               
               
                 “+++” &gt; 20. 
               
               
                 IHC reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 20, and defined as follows: 
               
               
                 “+” = 1-3; 
               
               
                 “++” &gt; 3; 
               
               
                 “+++” &gt; 5; and 
               
               
                 “++++” &gt; 8. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 17-5 
               
             
            
               
                   
               
               
                 Reduction of Total Immunogenicity Score (TIS) and Immunogenic 
               
               
                 Hit Count (IHC) for GAA Variants Relative to SEQ ID NO: 946 1   
               
            
           
           
               
               
               
               
            
               
                 SEQ ID 
                   
                 TIS Reduction 
                 IHC Reduction 
               
               
                 NO: 
                 Amino Acid Differences 
                 (Relative to SEQ  
                 (Relative to SEQ 
               
               
                 (nt/aa) 
                 (Relative to SEQ ID NO: 946) 
                 ID NO: 946) 
                 ID NO: 946) 
               
               
                   
               
               
                 1829/1830 
                 A62W/A89R/E188W/D489A/D500A/S727W/ 
                 + 
                   
               
               
                   
                 L823F 
                   
                   
               
               
                 1831/1832 
                 S124V/D500A/S842G/R862Q 
                 + 
                   
               
               
                 1851/1852 
                 P57L/E188W/D489A/L823F/R862Q 
                 + 
                   
               
               
                 1855/1856 
                 A62W/S124V/E188W/L823F/S842G/R862Q 
                 + 
                   
               
               
                 1859/1860 
                 P57F/E614Q/S916G/S932A 
                 + 
                   
               
               
                 1869/1870 
                 P57F/A62L/V913R/S916R/S932A 
                 + 
                   
               
               
                 1871/1872 
                 A62L/N527R/S727W/S916G 
                 ++ 
                   
               
               
                 1877/1878 
                 D500A/S727W/V913R/S916R 
                 + 
                   
               
               
                 1925/1926 
                 D923W 
                 + 
                   
               
               
                 1969/1970 
                 D489A/E614Q/S916G 
                 + 
                   
               
               
                 1977/1978 
                 A62W/S727W 
                 + 
                   
               
               
                 1987/1988 
                 A62W/D489A/N527R/S916R/S932A 
                 + 
                   
               
               
                 1989/1990 
                 A62L/D489A/D500A/S932A 
                 + 
                   
               
               
                 1991/1992 
                 D500A/P914R/S916G 
                 + 
                   
               
               
                 1999/2000 
                 P57F/A62L/S916G 
                 ++ 
                   
               
               
                 2005/2006 
                 P57F/A62W/F120I/N527R/V913R/S916R 
                 + 
                   
               
               
                 2013/2014 
                 A62W/S916G 
                 ++ 
                   
               
               
                 2015/2016 
                 P57F/D489A/N527R/P914R/S916G 
                 + 
                   
               
               
                 1857/1858 
                 P57F/A62L/L305F/D500A/V913R/S916G 
                 +++ 
                 + 
               
               
                 1861/1862 
                 P57F/A62L/L305F/V913R 
                 ++ 
                 + 
               
               
                 1863/1864 
                 P57F/A62L/A437G/D500A/L761F/P914K/ 
                 + 
                 ++ 
               
               
                   
                 S916R 
                   
                   
               
               
                 1865/1866 
                 A62L/A437G/V913R/S916R 
                 +++ 
                 ++ 
               
               
                 1873/1874 
                 P57F/A62W/L305F/A437G/D500A/S727W/ 
                 +++ 
                 ++ 
               
               
                   
                 V913R/S916R 
                   
                   
               
               
                 1875/1876 
                 P57F/A437G/D500A/E614Q/S727W/P914R 
                 ++ 
                 ++ 
               
               
                 1953/1954 
                 A62W/A437G/D489A/E614Q/S727W/V913R 
                 ++ 
                 ++ 
               
               
                 1955/1956 
                 A62L/A437G/D489A/N527R/S727W/V913R/ 
                 +++ 
                 ++ 
               
               
                   
                 S932A 
                   
                   
               
               
                 1957/1958 
                 P57F/A62W/L305F/D489A/Q907K/V913R/ 
                 ++ 
                 + 
               
               
                   
                 S916G 
                   
                   
               
               
                 1959/1960 
                 P57F/A62W/L305F/S916R 
                 ++ 
                 + 
               
               
                 1961/1962 
                 P57F/A437G/D500A/N527R/S727W/S916R 
                 +++ 
                 ++ 
               
               
                 1963/1964 
                 A62L/L305F/S727W 
                 ++ 
                 + 
               
               
                 1965/1966 
                 P57F/A62L/L305F/A437G/E614Q/A683S/ 
                 +++ 
                 ++ 
               
               
                   
                 V913R/S916R/S932A 
                   
                   
               
               
                 1967/1968 
                 P57F/L305F 
                 + 
                 + 
               
               
                 1973/1974 
                 P57F/A62W/A437G/V913R/S916G 
                 +++ 
                 ++ 
               
               
                 1975/1976 
                 P57F/A62W/L305F/D489A/V913R/S916G 
                 +++ 
                 + 
               
               
                 1981/1982 
                 P57F/L305F/A437G/S916G 
                 +++ 
                 ++ 
               
               
                 1983/1984 
                 A62L/A437G/N527R/S727W 
                 ++ 
                 ++ 
               
               
                 1985/1986 
                 P57F/A62L/A437G/N527R/S727W 
                 ++ 
                 ++ 
               
               
                 1995/1996 
                 A62L/L305F/A437G/D500A/S727W/V913R 
                 +++ 
                 ++ 
               
               
                 1997/1998 
                 A437G 
                 ++ 
                 ++ 
               
               
                 2001/2002 
                 P57F/A62L/L305F/A437G/D500A/E614Q/ 
                 +++ 
                 ++ 
               
               
                   
                 S727W/S916R 
                   
                   
               
               
                 2003/2004 
                 A437G/D489A/P914R/S916R 
                 ++ 
                 ++ 
               
               
                 2007/2008 
                 A62L/A437G/N527R/S916G/S 932A 
                 +++ 
                 ++ 
               
               
                 2009/2010 
                 A437G/S727W/P914K 
                 +++ 
                 ++ 
               
               
                 2011/2012 
                 P57F/A437G/V913R/P914R 
                 ++ 
                 ++ 
               
               
                 2017/2018 
                 A437G/P914R/S916G 
                 +++ 
                 ++ 
               
               
                   
               
               
                   1 TIS reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 946, and defined as follows: 
               
               
                 “+” = 1-10; 
               
               
                 “++” &gt; 10; 
               
               
                 “+++” &gt; 20; and 
               
               
                 “++++” &gt; 50. 
               
               
                 IHC reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 946, and defined as follows: 
               
               
                 “+” = 1-3; 
               
               
                 “++” &gt; 3; 
               
               
                 “+++” &gt; 5; and 
               
               
                 “++++” &gt; 8. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 17-6 
               
             
            
               
                   
               
               
                 Reduction of Total Immunogenicity Score (TIS) and Immunogenic 
               
               
                 Hit Count (IHC) for GAA Variants Relative to SEQ ID NO: 956 1   
               
            
           
           
               
               
               
               
            
               
                 SEQ ID 
                   
                 TIS Reduction 
                 IHC Reduction 
               
               
                 NO: 
                 Amino Acid Differences 
                 (Relative to SEQ  
                 (Relative to SEQ 
               
               
                 (nt/aa) 
                 (Relative to SEQ ID NO: 1956) 
                 ID NO: 1956) 
                 ID NO: 1956) 
               
               
                   
               
               
                 2021/2022 
                 P78E/S372T/L390Q 
                 + 
                   
               
               
                 2023/2024 
                 D87E/T266N/S372T/T483S 
                 + 
                   
               
               
                 2027/2028 
                 T266N/S372T/T924N 
                 + 
                   
               
               
                 2037/2038 
                 P78E/D87E/K176T/T266N/V536T/Q615D 
                 + 
                   
               
               
                 2041/2042 
                 D87E/S372T/S777G 
                 + 
                   
               
               
                 2043/2044 
                 T266N/S372T/V536T/Q615D/T763L/S777G 
                 + 
                   
               
               
                 2053/2054 
                 P78E/T266N/T763L 
                 + 
                   
               
               
                 2055/2056 
                 P78E/D87E/T266N/S372T/A386Y/S777G 
                 + 
                   
               
               
                 2073/2074 
                 P78E/D87E/T266N/S372T/V536T 
                 + 
                   
               
               
                 2497/2498 
                 A142G 
                 + 
                   
               
               
                 2501/2502 
                 D493L 
                 + 
                   
               
               
                 2509/2510 
                 K129E 
                 + 
                   
               
               
                 2513/2514 
                 H499E 
                 + 
                   
               
               
                 2517/2518 
                 L857E 
                 + 
                   
               
               
                 2089/2090 
                 P779E 
                 + 
                   
               
               
                 2541/2542 
                 L857A 
                 + 
                   
               
               
                 2547/2548 
                 H499I 
                 + 
                   
               
               
                 2559/2560 
                 A834S 
                 + 
                   
               
               
                 2565/2566 
                 L857V 
                 + 
                   
               
               
                 2567/2568 
                 F152W 
                 + 
                   
               
               
                 2097/2098 
                 L857T 
                 + 
                   
               
               
                 2569/2570 
                 F152S 
                 + 
                   
               
               
                 2571/2572 
                 S136K 
                 + 
                   
               
               
                 2573/2574 
                 K1295 
                 + 
                   
               
               
                 2589/2590 
                 I156C 
                 + 
                   
               
               
                 2601/2602 
                 H499M 
                 + 
                   
               
               
                 2617/2618 
                 S136V 
                 + 
                   
               
               
                 2117/2118 
                 L909F 
                 + 
                   
               
               
                 2133/2134 
                 V797L 
                 + 
                   
               
               
                 2143/2144 
                 I156L 
                 + 
                   
               
               
                 2145/2146 
                 V797M 
                 + 
                   
               
               
                 2651/2652 
                 A834W 
                 + 
                   
               
               
                 2661/2662 
                 K267E 
                 + 
                   
               
               
                 2667/2668 
                 E855G 
                 + 
                   
               
               
                 2151/2152 
                 A105T 
                 ++ 
                   
               
               
                 2683/2684 
                 Q768I 
                 + 
                   
               
               
                 2685/2686 
                 V926T 
                 ++ 
                   
               
               
                 2693/2694 
                 V797F 
                 + 
                   
               
               
                 2695/2696 
                 S372D 
                 + 
                   
               
               
                 2699/2700 
                 Y765W 
                 + 
                   
               
               
                 2161/2162 
                 T826G 
                 + 
                   
               
               
                 2725/2726 
                 S856G 
                 + 
                   
               
               
                 2729/2730 
                 V797I 
                 ++ 
                   
               
               
                 2165/2166 
                 T141S 
                 + 
                   
               
               
                 2751/2752 
                 H499Q 
                 + 
                   
               
               
                 2171/2172 
                 A834H 
                 + 
                   
               
               
                 2763/2764 
                 Y125W 
                 + 
                   
               
               
                 2777/2778 
                 V926M 
                 + 
                   
               
               
                 2779/2780 
                 G139E 
                 + 
                   
               
               
                 2791/2792 
                 T924A 
                 + 
                   
               
               
                 2179/2180 
                 S136G 
                 + 
                   
               
               
                 2793/2794 
                 V797W 
                 ++ 
                   
               
               
                 2795/2796 
                 V797E 
                 ++ 
                   
               
               
                 2191/2192 
                 A496G 
                 + 
                   
               
               
                 2821/2822 
                 D401G 
                 + 
                   
               
               
                 2825/2826 
                 A834G 
                 + 
                   
               
               
                 2859/2860 
                 A105W 
                 + 
                   
               
               
                 2861/2862 
                 L857S 
                 + 
                   
               
               
                 2207/2208 
                 L693F 
                 + 
                 + 
               
               
                 2209/2210 
                 V710N 
                 ++ 
                 ++ 
               
               
                 2211/2212 
                 V710L 
                 + 
                   
               
               
                 2213/2214 
                 M663A 
                 ++ 
                 + 
               
               
                 2215/2216 
                 V710M 
                 +++ 
                 ++ 
               
               
                 2217/2218 
                 L670I 
                 + 
                   
               
               
                 2219/2220 
                 L670F 
                 + 
                   
               
               
                 2221/2222 
                 L670R 
                 + 
                 + 
               
               
                 2223/2224 
                 V710S 
                 + 
                 + 
               
               
                 2225/2226 
                 F588L 
                 ++ 
                 + 
               
               
                 2229/2230 
                 L670Q 
                 +++ 
                 + 
               
               
                 2231/2232 
                 L670T 
                 + 
                 + 
               
               
                 2233/2234 
                 K154R/F588L 
                 + 
                 + 
               
               
                 2235/2236 
                 L693Y 
                 + 
                 + 
               
               
                 2237/2238 
                 V710K 
                 + 
                 ++ 
               
               
                 2239/2240 
                 A708C 
                 +++ 
                 ++ 
               
               
                 2247/2248 
                 L670W 
                 ++ 
                 + 
               
               
                 2249/2250 
                 L670V 
                 + 
                   
               
               
                 2251/2252 
                 L693I 
                 ++ 
                 + 
               
               
                 2253/2254 
                 V589I/M663F 
                 + 
                   
               
               
                 2255/2256 
                 F588V 
                 ++ 
                 + 
               
               
                 2257/2258 
                 M663F 
                 + 
                   
               
               
                 2261/2262 
                 L670E 
                 +++ 
                 + 
               
               
                 2263/2264 
                 L670S 
                 + 
                 + 
               
               
                 2275/2276 
                 L629I 
                 ++ 
                 + 
               
               
                 2277/2278 
                 T692L 
                 + 
                 + 
               
               
                 2279/2280 
                 A711C 
                 + 
                 ++ 
               
               
                 2281/2282 
                 R577T 
                 + 
                 + 
               
               
                 2289/2290 
                 L628V 
                 + 
                   
               
               
                 2293/2294 
                 L691V 
                 + 
                   
               
               
                 2297/2298 
                 L569Y 
                 + 
                   
               
               
                 2299/2300 
                 I573Q 
                 ++ 
                 + 
               
               
                 2303/2304 
                 T692Y 
                 ++ 
                 + 
               
               
                 2305/2306 
                 L629C 
                 +++ 
                 ++ 
               
               
                 2307/2308 
                 T692I 
                 + 
                 + 
               
               
                 2311/2312 
                 S671A 
                 + 
                   
               
               
                 2315/2316 
                 L569S 
                 + 
                 + 
               
               
                 2317/2318 
                 I573M 
                 + 
                 + 
               
               
                 2321/2322 
                 T692C 
                 +++ 
                 +++ 
               
               
                 2323/2324 
                 I573H 
                 ++ 
                 + 
               
               
                 2325/2326 
                 S671T 
                 + 
                   
               
               
                 2327/2328 
                 I573D 
                 +++ 
                 + 
               
               
                 2331/2332 
                 R577D 
                 +++ 
                 ++ 
               
               
                 2333/2334 
                 L629A 
                 ++ 
                 + 
               
               
                 2335/2336 
                 T692G 
                 ++ 
                 + 
               
               
                 2339/2340 
                 R577A 
                 + 
                 + 
               
               
                 2343/2344 
                 T692F 
                 ++ 
                 ++ 
               
               
                 2345/2346 
                 R583G 
                 +++ 
                 + 
               
               
                 2351/2352 
                 A572G 
                 +++ 
                 + 
               
               
                 2353/2354 
                 A711W 
                 ++ 
                   
               
               
                 2355/2356 
                 L629G 
                 +++ 
                 ++ 
               
               
                 2357/2358 
                 I573C 
                 +++ 
                 + 
               
               
                 2359/2360 
                 L569V 
                 + 
                   
               
               
                 2361/2362 
                 L669R 
                 + 
                   
               
               
                 2363/2364 
                 L579V 
                 ++ 
                 + 
               
               
                 2365/2366 
                 A572S 
                 + 
                   
               
               
                 2371/2372 
                 V580E 
                 +++ 
                 + 
               
               
                 2373/2374 
                 A574S 
                 + 
                 + 
               
               
                 2375/2376 
                 V631I 
                 + 
                 + 
               
               
                 2377/2378 
                 A711H 
                 + 
                 ++ 
               
               
                 2381/2382 
                 V580G 
                 +++ 
                 + 
               
               
                 2383/2384 
                 V580W 
                 ++ 
                 + 
               
               
                 2385/2386 
                 R577E 
                 +++ 
                 ++ 
               
               
                 2387/2388 
                 R583C 
                 ++ 
                 + 
               
               
                 2391/2392 
                 S671G 
                 + 
                   
               
               
                 2393/2394 
                 A711G 
                 + 
                 ++ 
               
               
                 2395/2396 
                 V631L 
                 ++ 
                 + 
               
               
                 2397/2398 
                 L569T 
                 ++ 
                 + 
               
               
                 2399/2400 
                 L569H 
                 ++ 
                 + 
               
               
                 2401/2402 
                 L569Q 
                 ++ 
                 + 
               
               
                 2403/2404 
                 V631M 
                 + 
                 + 
               
               
                 2407/2408 
                 T227A 
                 + 
                 + 
               
               
                 2415/2416 
                 L871E 
                 +++ 
                 +++ 
               
               
                 2417/2418 
                 V222C 
                 ++ 
                 ++ 
               
               
                 2421/2422 
                 V878G 
                 + 
                 + 
               
               
                 2425/2426 
                 K581H 
                 + 
                 + 
               
               
                 2431/2432 
                 V878A 
                 + 
                   
               
               
                 2433/2434 
                 R873Y 
                 + 
                   
               
               
                 2437/2438 
                 K581G 
                 ++ 
                 + 
               
               
                 2439/2440 
                 V222P 
                 +++ 
                 ++ 
               
               
                 2443/2444 
                 T585Q 
                 ++ 
                 + 
               
               
                 2447/2448 
                 A229C 
                 + 
                 + 
               
               
                 2461/2462 
                 V878K 
                 + 
                   
               
               
                 2463/2464 
                 R873A 
                 + 
                   
               
               
                 2467/2468 
                 K581T 
                 + 
                   
               
               
                 2469/2470 
                 I869L 
                 + 
                   
               
               
                 2473/2474 
                 V878S 
                 + 
                 + 
               
               
                 2477/2478 
                 V878Q 
                 + 
                 + 
               
               
                 2479/2480 
                 R873F 
                 + 
                   
               
               
                 2485/2486 
                 I869S 
                 +++ 
                 ++ 
               
               
                 2487/2488 
                 V878W 
                 + 
                 + 
               
               
                 2489/2490 
                 H706F 
                 + 
                   
               
               
                 2491/2492 
                 N225D 
                 + 
                 ++ 
               
               
                 2493/2494 
                 L871K 
                 + 
                 + 
               
               
                   
               
               
                   1 TIS reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 1956, and defined as follows: 
               
               
                 “+” = 1-10; 
               
               
                 “++” &gt; 10; 
               
               
                 “+++” &gt; 20; and 
               
               
                 “++++” &gt; 50. 
               
               
                 IHC reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 1956, and defined as follows: 
               
               
                 “+” = 1-3; 
               
               
                 “++” &gt; 3; 
               
               
                 “+++” &gt; 5; and 
               
               
                 “++++” &gt; 8. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 17-7 
               
             
            
               
                   
               
               
                 Reduction of Total Immunogenicity Score (TIS) and Immunogenic 
               
               
                 Hit Count (IHC) for GAA Variants Relative to SEQ ID NO: 2496 1   
               
            
           
           
               
               
               
               
            
               
                   
                   
                 TIS Reduction 
                 IHC Reduction 
               
               
                 SEQ ID 
                   
                 (Relative  
                 (Relative  
               
               
                 NO: 
                 Amino Acid Differences 
                 to SEQ 
                 to SEQ 
               
               
                 (nt/aa) 
                 (Relative to SEQ ID NO: 2496) 
                 ID NO: 2496) 
                 ID NO: 2496) 
               
               
                   
               
               
                 2867/2868 
                 L569T/L628M/T692Y 
                 +++ 
                 +++ 
               
               
                 2869/2870 
                 L569Y/L670T/A711H 
                 ++ 
                 +++ 
               
               
                 2871/2872 
                 L569Y/L628M/L670T/T692Y/A711H/L871S 
                 +++ 
                 ++++ 
               
               
                 2873/2874 
                 V589I/L670T/Q795E/L871S 
                 +++ 
                 ++ 
               
               
                 2875/2876 
                 L628M/L670F 
                 + 
                   
               
               
                 2877/2878 
                 L569H/L628M/L670T 
                 +++ 
                 ++ 
               
               
                 2879/2880 
                 L569T/L670T/A711H/L871E 
                 ++++ 
                 ++++ 
               
               
                 2881/2882 
                 L628M/L670T/T692G/A711H/Q795E 
                 +++ 
                 ++++ 
               
               
                 2883/2884 
                 L569Y/L628M/L670T/A711H 
                 ++ 
                 +++ 
               
               
                 2885/2886 
                 L569Y/V589I/L628M/T692G/A711H/Q795E 
                 +++ 
                 +++ 
               
               
                 2887/2888 
                 L569H/T692G 
                 +++ 
                 +++ 
               
               
                 2889/2890 
                 L569Y/V589I/L670T/S678T/T692G/A711H/ 
                 +++ 
                 ++++ 
               
               
                   
                 Q795E 
                   
                   
               
               
                 2891/2892 
                 L569T/L871K 
                 ++ 
                 ++ 
               
               
                 2893/2894 
                 L569Y/V589I/L628M/L670T/T692Y/A711H 
                 +++ 
                 ++++ 
               
               
                 2895/2896 
                 V589I/L871E 
                 +++ 
                 +++ 
               
               
                 2897/2898 
                 L670T/S678T/T692Y/L871S 
                 +++ 
                 +++ 
               
               
                 2899/2900 
                 L628M/A711H/Q795E 
                 + 
                 ++ 
               
               
                 2901/2902 
                 T692G/A711H 
                 +++ 
                 +++ 
               
               
                 2903/2904 
                 V589I/L670T/T692G/Q795E/L871K 
                 +++ 
                 +++ 
               
               
                 2905/2906 
                 L569Y/V589I/A711H/L871K 
                 ++ 
                 ++ 
               
               
                 2907/2908 
                 L670T/T692G/L871K 
                 +++ 
                 +++ 
               
               
                 2909/2910 
                 L569H/T692Y 
                 +++ 
                 +++ 
               
               
                 2911/2912 
                 L569H/L628M/L670T/T692Y/A711H/L871K 
                 +++ 
                 ++++ 
               
               
                 2913/2914 
                 L670T/S678T 
                 + 
                 + 
               
               
                 2915/2916 
                 L569T/L670T/S678T/T692G/L871K 
                 +++ 
                 ++++ 
               
               
                 2917/2918 
                 V589I 
                 + 
                   
               
               
                 2919/2920 
                 L569H/V589I/L628M/L670T/S678T/T692G/ 
                 ++++ 
                 ++++ 
               
               
                   
                 A711H/Q795E/L871S 
                   
                   
               
               
                 2921/2922 
                 L569H/L670F/S678T/T692G/L871S 
                 ++++ 
                 +++ 
               
               
                 2923/2924 
                 L569T/V589I/L628M/L670F/T692G/A711H 
                 ++++ 
                 ++++ 
               
               
                 2925/2926 
                 L569H/L670T/T692G 
                 +++ 
                 +++ 
               
               
                 2927/2928 
                 L569Y/L871E 
                 +++ 
                 +++ 
               
               
                 2929/2930 
                 L569H/L628M/L670F/S678T 
                 ++ 
                 + 
               
               
                 2931/2932 
                 L569Y/L670F/S678T 
                 + 
                   
               
               
                 2933/2934 
                 L569Y/V589I/L670F 
                 ++ 
                   
               
               
                 2935/2936 
                 L569Y/V589I/L670T/L871K 
                 ++ 
                 + 
               
               
                 2937/2938 
                 L569T/L871S 
                 +++ 
                 ++ 
               
               
                 2939/2940 
                 L871K 
                 + 
                 + 
               
               
                 2941/2942 
                 L569Y/L670T 
                 + 
                 + 
               
               
                 2943/2944 
                 L569Y/T692Y/A711H 
                 ++ 
                 +++ 
               
               
                 2945/2946 
                 L871S 
                 ++ 
                 + 
               
               
                 2947/2948 
                 L569Y/A711H 
                 + 
                 ++ 
               
               
                 2949/2950 
                 L628M/L871S 
                 ++ 
                 + 
               
               
                 2951/2952 
                 L569T/V589I/L871S 
                 +++ 
                 ++ 
               
               
                 2953/2954 
                 T692G/A711H/I869L/V878S 
                 +++ 
                 +++ 
               
               
                 2955/2956 
                 A572S/F588L/S678T/T692G/I869L/V878A 
                 +++ 
                 ++ 
               
               
                 2957/2958 
                 A711H 
                 + 
                 ++ 
               
               
                 2959/2960 
                 T692G/I869S 
                 +++ 
                 +++ 
               
               
                 2961/2962 
                 A572S/T692L/I8695/V878S 
                 +++ 
                 +++ 
               
               
                 2963/2964 
                 L6291/I869L/V878S 
                 ++ 
                 + 
               
               
                 2965/2966 
                 A572S/F588L/Q795E 
                 +++ 
                 + 
               
               
                 2967/2968 
                 A711H/I869S/V878S 
                 +++ 
                 ++++ 
               
               
                 2969/2970 
                 V878S 
                 + 
                 + 
               
               
                 2971/2972 
                 S678T/T692G/A711H/I869S 
                 +++ 
                 ++++ 
               
               
                 2973/2974 
                 A572S/T692G/I869S/V878S 
                 ++++ 
                 ++++ 
               
               
                 2975/2976 
                 A572S/T692G/V878S 
                 +++ 
                 ++ 
               
               
                 2977/2978 
                 A711H/Q795E/I869S/V878S 
                 +++ 
                 ++++ 
               
               
                 2979/2980 
                 Q795E/V878S 
                 + 
                 + 
               
               
                 2981/2982 
                 T692G/A711H/Q795E/I869S 
                 +++ 
                 ++++ 
               
               
                 2983/2984 
                 S678T/T692G/Q795E/I869S 
                 +++ 
                 +++ 
               
               
                 2985/2986 
                 T692G/A711H/I869S/V878A 
                 ++++ 
                 ++++ 
               
               
                 2987/2988 
                 L569T/A711H 
                 ++ 
                 +++ 
               
               
                 2989/2990 
                 L569T/L628M/S678T/A711H 
                 ++ 
                 +++ 
               
               
                 2991/2992 
                 L569T/V589I/T692G/Q795E/L871K/V878S 
                 +++ 
                 +++ 
               
               
                 2993/2994 
                 L569T/V589I/S678T/L871K/V878S 
                 +++ 
                 ++ 
               
               
                 2995/2996 
                 L569H/A711H/I869S/V878S 
                 ++++ 
                 ++++ 
               
               
                 2997/2998 
                 S678T/Q795E/L871K/V878A 
                 + 
                 + 
               
               
                 2999/3000 
                 L569H/S678T/T692G/Q795E 
                 +++ 
                 +++ 
               
               
                 3001/3002 
                 F588L/V589I/L628M/S678T 
                 + 
                   
               
               
                 3003/3004 
                 T692Y 
                 ++ 
                 + 
               
               
                 3005/3006 
                 L569T 
                 ++ 
                 + 
               
               
                 3007/3008 
                 T692G/L871K 
                 +++ 
                 ++ 
               
               
                 3009/3010 
                 L569T/F588L/V878S 
                 +++ 
                 ++ 
               
               
                 3011/3012 
                 L569H/A711H/L871K 
                 +++ 
                 +++ 
               
               
                 3013/3014 
                 L569T/F588L/S678T/T692Y 
                 +++ 
                 +++ 
               
               
                 3015/3016 
                 L569T/F588L/A711H/I869L/L871K/V878S 
                 +++ 
                 ++++ 
               
               
                 3017/3018 
                 L569T/F588L 
                 +++ 
                 ++ 
               
               
                 3019/3020 
                 L569T/T692Y 
                 +++ 
                 +++ 
               
               
                 3021/3022 
                 L569T/S678T/I869S/V878S 
                 +++ 
                 ++++ 
               
               
                 3023/3024 
                 L628M/L629I/T692Y/L871S/V878S 
                 +++ 
                 +++ 
               
               
                 3025/3026 
                 L569T/S678T/V878S 
                 ++ 
                 ++ 
               
               
                 3027/3028 
                 L569H/A711H/Q795E/L871S/V878S 
                 +++ 
                 ++++ 
               
               
                 3029/3030 
                 A711H/L871K 
                 + 
                 ++ 
               
               
                 3031/3032 
                 T692G/A711H/Q795E/I869L/L871K/V878A 
                 +++ 
                 +++ 
               
               
                 3033/3034 
                 L569T/F588L/V589I/L628M/L629I/T692Y/ 
                 +++ 
                 ++++ 
               
               
                   
                 A711H 
                   
                   
               
               
                 3035/3036 
                 S678T/T692G/I869S 
                 +++ 
                 +++ 
               
               
                 3037/3038 
                 T692G/I869L/L871K/V878S/S916R 
                 +++ 
                 ++ 
               
               
                 3039/3040 
                 L569H/L628M 
                 ++ 
                 + 
               
               
                 3041/3042 
                 L628M/V878S 
                 + 
                 + 
               
               
                 3043/3044 
                 T692G/A711H/L871S/V878A 
                 +++ 
                 ++++ 
               
               
                 3045/3046 
                 L569T/Q795E 
                 ++ 
                 + 
               
               
                 3047/3048 
                 L569T/T692Y/A711H/I869L/L871K/V878A 
                 +++ 
                 ++++ 
               
               
                 3065/3066 
                 L810V 
                 + 
                 ++ 
               
               
                 3049/3050 
                 S246T 
                 ++ 
                 + 
               
               
                 3067/3068 
                 A60V/V589A 
                 +++ 
                 + 
               
               
                 3051/3052 
                 T585K 
                 + 
                 + 
               
               
                 3069/3070 
                 S307T 
                 + 
                   
               
               
                 3053/3054 
                 G584E 
                 + 
                 + 
               
               
                 3055/3056 
                 A812E 
                 ++ 
                 ++ 
               
               
                 3057/3058 
                 V313L 
                 + 
                 +++ 
               
               
                 3059/3060 
                 L304M 
                 + 
                   
               
               
                 3071/3072 
                 V313T 
                 ++ 
                 +++ 
               
               
                 3061/3062 
                 V313I 
                 + 
                 ++ 
               
               
                 3073/3074 
                 G584C 
                 + 
                 + 
               
               
                 3063/3064 
                 A582T 
                 + 
                 + 
               
               
                   
               
               
                   1 TIS reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 2496, and defined as follows: 
               
               
                 “+” = 1-10; 
               
               
                 “++” &gt; 10; 
               
               
                 “+++” &gt; 20; and 
               
               
                 “++++” &gt; 50. 
               
               
                 IHC reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 2496, and defined as follows: 
               
               
                 “+” = 1-3; 
               
               
                 “++” &gt; 3; 
               
               
                 “+++” &gt; 5; and 
               
               
                 “++++” &gt; 8. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 17-8 
               
             
            
               
                   
               
               
                 Reduction of Total Immunogenicity Score (TIS) and Immunogenic 
               
               
                 Hit Count (IHC) for GAA Variants Relative to SEQ ID NO: 2880 1   
               
            
           
           
               
               
               
               
            
               
                   
                   
                 TIS Reduction 
                 IHC Reduction 
               
               
                 SEQ ID 
                   
                 (Relative  
                 (Relative  
               
               
                 NO: 
                 Amino Acid Differences 
                 to SEQ 
                 to SEQ 
               
               
                 (nt/aa) 
                 (Relative to SEQ ID NO: 2880) 
                 ID NO: 2880) 
                 ID NO: 2880) 
               
               
                   
               
               
                 3075/3076 
                 R527N/L736M/A932S 
                 + 
                   
               
               
                 3107/3108 
                 A89R/L109D/A932S 
                 + 
                   
               
               
                 3109/3110 
                 L109D/S842G 
                 + 
                   
               
               
                 3123/3124 
                 L109D/A932S 
                 + 
                   
               
               
                 3127/3128 
                 R527N/W727S/L736M 
                 + 
                   
               
               
                 3141/3142 
                 L109D/L736M/A932S 
                 ++ 
                   
               
               
                 3143/3144 
                 A89R/L109D/R527N/S678T/W727S/S842G 
                 + 
                   
               
               
                 3181/3182 
                 V522E/K830Q 
                 + 
                   
               
               
                 3269/3270 
                 L62A/E87D/S150T 
                 + 
                   
               
               
                 3077/3078 
                 L109D/S678T/A812E 
                 ++ 
                 ++ 
               
               
                 3081/3082 
                 R403H/R527N/S678T/T692G/L736M/A812E/ 
                 +++ 
                 +++ 
               
               
                   
                 S842G/L860F 
                   
                   
               
               
                 3083/3084 
                 S678T/T692G/A812E 
                 +++ 
                 +++ 
               
               
                 3087/3088 
                 A89R/R527N/W727S/A812E/L860F 
                 ++ 
                 ++ 
               
               
                 3089/3090 
                 A89R/S678T/T692G/L736M/A932S 
                 +++ 
                 + 
               
               
                 3091/3092 
                 L109D/R527N/S678T/A812E 
                 ++ 
                 ++ 
               
               
                 3095/3096 
                 L109D/A812E 
                 ++ 
                 ++ 
               
               
                 3097/3098 
                 T692G/W727S/L736M/S842G/R913V 
                 +++ 
                 + 
               
               
                 3101/3102 
                 R527N/S678T/T692G/W727S/L736M/V878S 
                 +++ 
                 + 
               
               
                 3103/3104 
                 R527N/T692G/W727S/L736M/A812E 
                 +++ 
                 +++ 
               
               
                 3113/3114 
                 A89R/L109D/S678T/W727S/L736M/A812E/ 
                 ++ 
                 ++ 
               
               
                   
                 V878S 
                   
                   
               
               
                 3115/3116 
                 L109D/T692G/W727S/A812E/S842G/L860F 
                 +++ 
                 +++ 
               
               
                 3117/3118 
                 T692G/A812E 
                 +++ 
                 +++ 
               
               
                 3121/3122 
                 L109D/S678T/L736M/A812E/V878S 
                 +++ 
                 ++ 
               
               
                 3125/3126 
                 R527N/T692G/W727S/L736M/S842G/L860F/ 
                 +++ 
                 + 
               
               
                   
                 V878S 
                   
                   
               
               
                 3133/3134 
                 R527N/S678T/T692G/A812E/A932S 
                 +++ 
                 +++ 
               
               
                 3135/3136 
                 A89R/S678T/A812E/V878S 
                 + 
                 ++ 
               
               
                 3137/3138 
                 R527N/A812E 
                 ++ 
                 ++ 
               
               
                 3139/3140 
                 S678T/T692G/W727S/A812E/S842G 
                 +++ 
                 +++ 
               
               
                 3149/3150 
                 L109D/S678T/T692G/S842G/L860F/V878S/ 
                 ++ 
                 + 
               
               
                   
                 A932S 
                   
                   
               
               
                 3151/3152 
                 A89R/R527N/S678T/T692G/L736M/S842G/ 
                 +++ 
                 + 
               
               
                   
                 V878S/A932S 
                   
                   
               
               
                 3155/3156 
                 L109D/T692G/W727S/L736M/A812E 
                 +++ 
                 +++ 
               
               
                 3161/3162 
                 S678T/A812E 
                 ++ 
                 ++ 
               
               
                   
               
               
                   1 TIS reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 2880, and defined as follows: 
               
               
                 “+” = 1-10; 
               
               
                 “++” &gt; 10; 
               
               
                 “+++” &gt; 20; and 
               
               
                 “++++” &gt; 50. 
               
               
                 IHC reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 2880, and defined as follows: 
               
               
                 “+” = 1-3; 
               
               
                 “++” &gt; 3; 
               
               
                 “+++” &gt; 5; and 
               
               
                 “++++” &gt; 8. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 17-9 
               
             
            
               
                   
               
               
                 Reduction of Total Immunogenicity Score (TIS) and Immunogenic  
               
               
                 Hit Count (IHC) for GAA Variants Relative to SEQ ID NO: 3104 1   
               
            
           
           
               
               
               
            
               
                 SEQ  
                 Amino Acid Differences 
                 TIS Reduction 
               
               
                 ID NO: 
                 (Relative to SEQ  
                 (Relative to SEQ  
               
               
                 (nt/aa) 
                 ID NO: 3104) 
                 ID NO: 3104) 
               
               
                   
               
               
                 3313/3314 
                 L62A/A89D/K830Q 
                 + 
               
               
                 3317/3318 
                 L62A/K830Q/A932S 
                 + 
               
               
                 3361/3362 
                 L62A/K830Q/L860F/A932S 
                 + 
               
               
                 3367/3368 
                 L62A/K830Q/L860F 
                 + 
               
               
                 3375/3376 
                 L62A/K830Q 
                 + 
               
               
                   
               
               
                   1 TIS reduction was measured as a reduction in the number of counts compared to the reference polypeptide of SEQ ID NO: 3104, and defined as follows: “+” = 1-10. 
               
            
           
         
       
     
     While the invention has been described with reference to the specific embodiments, various changes can be made and equivalents can be substituted to adapt to a particular situation, material, composition of matter, process, process step or steps, thereby achieving benefits of the invention without departing from the scope of what is claimed. 
     For all purposes in the United States of America, each and every publication and patent document cited in this disclosure is incorporated herein by reference as if each such publication or document was specifically and individually indicated to be incorporated herein by reference. Citation of publications and patent documents is not intended as an indication that any such document is pertinent prior art, nor does it constitute an admission as to its contents or date.