Spreadsheet: 11fd814d-0da8-4e80-82a3-9cd0a844fa58
Sheet: Table S2 Utah Family CNVs

Chromosome | Start (hg19) | End (hg19) | [NAME]? | Reference | Gain/Loss | [NAME] (bp) | Gene | Custom iSelect Array Probes | Comments
chr1 | 4737693 | 4746636 | N |  | Loss | 8943 | AJAP1 | 20
chr1 | 10624023 | 10627542 | N |  | Loss | 3519 | PEX14 | 14
chr1 | 145714421 | 146101228 | N |  | Gain | 386807 | more than 10 genes | 20
chr1 | 169704308 | 169732211 | N |  | Loss | 27903 | C1orf112 | 20
chr1 | 179456385 | 179472635 | N |  | Loss | 16250 | C1orf125/DKFZp434N1720 | 20
chr1 | 204193679 | 204209979 | N |  | Loss | 16300 | PLEKHA6 | 20
chr1 | 215858193 | 215861879 | Y | 4 | Loss | 3686 | USH2A | 19
chr1 | 225508461 | 225511454 | N |  | Loss | 2993 | [NAME] | 14
chr1 | 228848896 | 228853665 | N |  | Loss | 4769 | 5' of RHOU | 11
chr1 | 237993724 | 237995299 | N |  | Loss | 1575 | RYR2 | 15
chr1 | 243860912 | 243861049 | N |  | Loss | 137 | AKT3 | 10
chr2 | 12685369 | 12693172 | N |  | Loss | 7803 | AK001558 | 16
chr2 | 32982548 | 33050816 | Y | 2,5 | Gain | 68268 | TTC27, AK095182 | 15
chr2 | 37904904 | 37909117 | N |  | Gain | 4213 | 5' of [NAME] | 19
chr2 | 45997209 | 45997519 | N |  | Loss | 310 | PRKCE | 11
chr2 | 51272055 | 51336043 | Y | 2,4 | Loss | 63988 | 5' of NRXN1 (10 kb) | 83 | includes overlapping literature CNVs
chr2 | 52420563 | 52584090 | N |  | Loss | 163527 | 5' of NRXN1 (1 Mb) | 20
chr2 | 58346718 | 58349248 | Y | 2 | Loss | 2530 | VRK2 | 12
chr2 | 62195814 | 62230970 | N |  | Loss | 35156 | COMMD1, CR603473 | 20
chr2 | 75014711 | 75044204 | N |  | Loss | 29493 | 5' of HK2 | 20
chr2 | 79330766 | 79342811 | N |  | Gain | 12045 | 5' of REG1B, 5' of REG1A | 17
chr2 | 120130796 | 120145728 | N |  | Loss | 14932 | 5' of C2orf76, 5' of TMEM37 | 20
chr2 | 236424336 | 236465062 | N |  | Loss | 40726 | AGAP1 | 20
chr3 | 6724453 | 7046515 | N |  | Gain | 322062 | AF279782, GRM7 | 20
chr3 | 12387768 | 12393125 | N |  | Loss | 5357 | PPARG | 20
chr3 | 21731567 | 21734331 | N |  | Gain | 2764 | ZNF385D | 14
chr3 | 57051604 | 57053353 | N |  | Gain | 1749 | ARHGEF3 | 13
chr3 | 60774451 | 60777932 | Y | 3 | Gain | 3481 | FHIT | 16
chr3 | 63962828 | 63964474 | N |  | Loss | 1646 | ATXN7 | 13
chr3 | 74566042 | 74584605 | N |  | Loss | 18563 | CNTN3 | 20
chr3 | 171090367 | 171092891 | N |  | Gain | 2524 | TNIK | 16
chr3 | 172596081 | 172617355 | N |  | Gain | 21274 | SPATA16 | 20
chr4 | 58811798 | 58816810 | N |  | Loss | 5012 | 3' of BC034799 (480 kb) | 14
chr4 | 80865807 | 80887173 | N |  | Loss | 21366 | ANTXR2/DKFZp667K1925 | 17
chr4 | 101551216 | 101616281 | N |  | Loss | 65065 | 5' of EMCN (200 kb) | 20
chr4 | 134924034 | 135188390 | N |  | Loss | 264356 | PABPC4L | 20
chr4 | 185734577 | 185740215 | N |  | Loss | 5638 | ACSL1 | 18
chr4 | 189084983 | 189117429 | N |  | Loss | 32446 | 3' of TRIML1 | 20
chr5 | 20436884 | 20449034 | N |  | Loss | 12150 | CDH18 | 20
chr5 | 58469036 | 58470270 | N |  | Loss | 1234 | PDE4D | 12
chr5 | 99634772 | 99682698 | N |  | Loss | 47926 | 5' of FAM174A (190 kb) | 20
chr5 | 132621489 | 132630849 | Y | 2,4 | Gain | 9360 | FSTL4 | 20
chr5 | 142599442 | 142602063 | N |  | Loss | 2621 | ARHGAP26/KIAA0621 | 14
chr5 | 151582812 | 151583410 | N |  | Loss | 598 | AK001582 | 12
chr6 | 7425246 | 7464367 | N |  | Gain | 39121 | 3' of RIOK1 | 20
chr6 | 10856101 | 10872458 | N |  | Loss | 16357 | 3' of TMEM14B and GCM2, 5' of MAK and SYCP2L | 20
chr6 | 42126761 | 42128299 | N |  | Loss | 1538 | GUCA1A | 16
chr6 | 44113916 | 44180221 | N |  | Loss | 66305 | CAPN11, TMEM63B | 20
chr6 | 47864831 | 49244526 | N |  | Loss | 1379695 | C6orf138 | 25
chr6 | 53856580 | 53864523 | N |  | Loss | 7943 | AK056584 | 19
chr6 | 62443739 | 62462295 | N |  | Loss | 18556 | KHDRBS2 | 17
chr6 | 119419595 | 119427038 | Y | 2 | Loss | 7443 | FAM184A | 18
chr6 | 123893763 | 123897553 | N |  | Loss | 3790 | TRDN | 14
chr6 | 139985775 | 140128887 | N |  | Gain | 143112 | BC039503 | 20
chr6 | 147588752 | 147664671 | Y | 2 | Gain | 75919 | STXBP5 | 20
chr6 | 161189018 | 161218651 | N |  | Loss | 29633 | 3' of PLG | 20
chr7 | 6838712 | 6864071 | N |  | Loss | 25359 | C7orf28B | 15
chr7 | 11782637 | 11783917 | Y | 4 | Loss | 1280 | THSD7A | 12
chr7 | 13962113 | 13962620 | Y | 2 | Loss | 507 | ETV1 | 11
chr7 | 71597328 | 71603027 | N |  | Gain | 5699 | CALN1 | 14
chr7 | 105285949 | 105321353 | N |  | Loss | 35404 | ATXN7L1 | 20
chr7 | 124546250 | 124580202 | Y | 4 | Loss | 33952 | POT1, hypothetical proteins | 20
chr8 | 3160739 | 3160885 | N |  | Loss | 146 | CSMD1/KIAA1890 | 10
chr8 | 3169351 | 3169808 | N |  | Loss | 457 | CSMD1/KIAA1890 | 11
chr8 | 3479586 | 3480400 | N |  | Loss | 814 | CSMD1 | 12
chr8 | 4907673 | 4911422 | N |  | Loss | 3749 | 5' of CSMD1 60 kb) | 20
chr8 | 31977229 | 31989597 | N |  | Loss | 12368 | NRG1 | 20
chr8 | 52261992 | 52265315 | N |  | Loss | 3323 | PXDNL | 15
chr8 | 84323466 | 84337983 | N |  | Loss | 14517 | 3' of BC038578 | 20
chr8 | 85281895 | 85304198 | N |  | Loss | 22303 | RALYL | 20
chr8 | 86471729 | 86553130 | N |  | Gain | 81401 | 3' of REXO1L1 | 20
chr8 | 100402969 | 100406592 | N |  | Loss | 3623 | VPS13B | 10
chr9 | 7036350 | 7051859 | N |  | Loss | 15509 | JMJD2C | 20
chr9 | 28027694 | 28039222 | N |  | Gain | 11528 | LINGO2 | 20
chr9 | 28190069 | 28347679 | N |  | Loss | 157610 | LINGO2 | 20
chr9 | 75206337 | 75207666 | N |  | Gain | 1329 | TMC1 | 11
chr9 | 116468123 | 116631674 | N |  | Gain | 163551 | 5' of [NAME] (5 kb) | 12
chr9 | 139083019 | 139113146 | N |  | Gain | 30127 | LHX3, QSOX2 | 20
chr10 | 27361202 | 27381349 | N |  | Loss | 20147 | ANKRD26 | 20
chr10 | 33217225 | 33222978 | N |  | Loss | 5753 | ITGB1 | 11
chr10 | 38914665 | 42953131 | N |  | Loss | 4038466 | AK131313, BC039000 | 20
chr10 | 52133698 | 52232708 | Y | 3 | Gain | 99010 | SGMS1/SMS1 | 20
chr10 | 60793303 | 60857532 | Y | 3 | Gain | 64229 | 5' of PHYHIPL (80 kb) | 20
chr10 | 68350062 | 68375800 | N |  | Loss | 25738 | CTNNA3 | 20
chr10 | 81032555 | 81037800 | N |  | Loss | 5245 | ZMIZ1 | 14
chr10 | 83893626 | 84175018 | N |  | Loss | 281392 | NRG3 | 13
chr10 | 86939018 | 86970632 | N |  | Loss | 31614 | AK097624 | 20
chr10 | 89720106 | 89723874 | N |  | Loss | 3768 | PTEN | 12
chr10 | 91210650 | 91217984 | N |  | Loss | 7334 | SLC16A12 | 19
chr10 | 92274764 | 92289762 | Y | 2 | Loss | 14998 | 3' of BC037970 | 15
chr11 | 7488341 | 7489819 | N |  | Gain | 1478 | SYT9, AK128569 | 16
chr11 | 12002139 | 12007077 | N |  | Gain | 4938 | [NAME] | 20
chr11 | 12374189 | 12374712 | N |  | Loss | 523 | MICALCL | 11
chr11 | 16569019 | 16576640 | N |  | Loss | 7621 | SOX6/DKFZp434N1217 | 12
chr11 | 31000774 | 31000929 | N |  | Gain | 155 | DCDC5/KIAA1493 | 10
chr11 | 60228735 | 60229382 | N |  | Loss | 647 | MS4A1 | 11
chr11 | 98148399 | 98212796 | N |  | Gain | 64397 | 5' of CNTN5 (700 kb) | 20
chr11 | 100817655 | 100820663 | N |  | Loss | 3008 | FLJ32810 | 14
chr11 | 131405729 | 131406206 | N |  | Gain | 477 | NTM, AK128059 | 11
chr12 | 60173356 | 60173878 | Y | 4 | Gain | 522 | SLC16A7/MCT2 | 13
chr12 | 73062598 | 73088289 | Y | 2 | Loss | 25691 | 3' of TRHDE | 20
chr12 | 75547922 | 75572356 | N |  | Loss | 24434 | [NAME] | 20
chr12 | 80880491 | 80895554 | N |  | Loss | 15063 | PTPRQ | 20
chr12 | 80988331 | 81019079 | N |  | Loss | 30748 | PTPRQ | 20
chr12 | 81618586 | 81626675 | N |  | Loss | 8089 | ACSS3 | 17
chr12 | 97870273 | 97875696 | N |  | Loss | 5423 | NCRMS/AK056164 | 20
chr12 | 102097012 | 102106306 | N |  | Loss | 9294 | CHPT1 | 13
chr12 | 127308503 | 127315005 | Y, small overlap | 4 | Loss | 6502 | between BC069215 and BC037858 | 19
chr13 | 40087689 | 40088007 | N |  | Loss | 318 | LHFP | 12
chr13 | 49284461 | 49343043 | N |  | Gain | 58582 | 3' of CYSLTR2 | 20
chr13 | 50163809 | 50179454 | N |  | Loss | 15645 | 5' of RCBTB1 | 17
chr13 | 93448487 | 93461603 | N |  | Loss | 13116 | [NAME] | 17
chr13 | 94357235 | 94369759 | N |  | Loss | 12524 | [NAME] | 20
chr14 | 23862374 | 23888040 | N |  | Loss | 25666 | MYH6, [NAME], MIR208B | 20
chr14 | 28506099 | 28520243 | N |  | Loss | 14144 | between BC148262 and CR597916 | 20
chr14 | 32904231 | 32909169 | N |  | Gain | 4938 | AKAP6 | 20
chr14 | 33859159 | 33860185 | N |  | Gain | 1026 | [NAME] | 11
chr14 | 37928753 | 37948391 | N |  | Loss | 19638 | MIPOL1 | 15
chr14 | 68068610 | 68071772 | N |  | Loss | 3162 | 5' of PIGH | 15
chr15 | 33605301 | 33617521 | N |  | Gain | 12220 | RYR3 | 20
chr15 | 47518807 | 47527672 | N |  | Loss | 8865 | SEMA6D | 16
chr15 | 58851369 | 58853307 | N |  | Gain | 1938 | LIPC | 14
chr15 | 60074956 | 60103803 | Y | 5 | Loss | 28847 | 5' of BNIP2 (90 kb) | 20
chr15 | 66521832 | 66524433 | N |  | Loss | 2601 | MEGF11 | 17
chr15 | 87830530 | 87870489 | N |  | Loss | 39959 | between AGBL1, and TMEM83, NTRK3 | 20
chr16 | 16245729 | 16256767 | N |  | Loss | 11038 | ABCC6, MRP6 | 34 | includes overlapping literature CNVs
chr16 | 21363810 | 21602618 | N |  | Loss | 238808 | More than 10 genes | 25
chr16 | 82446255 | 82711504 | Y | 5 | Gain | 265249 | CDH13 | 24
chr16 | 83909041 | 83926368 | N |  | Loss | 17327 | 5' of MLYCD, 3' of HSBP1 | 20
chr17 | 4007594 | 4324408 | Y | 4 | Gain | 316814 | ZZEF1, KIAA0399, CYB5D2, ANKFY1, UBE2G1, SPNS3 | 20
chr17 | 21556170 | 25363654 | N |  | Loss | 3807484 | BC070367, FAM27L, BC039120, CR592140, CR592128 | 20 | much of this region spans the centromere and is heterochromatic
chr17 | 39211908 | 39221312 | N |  | Loss | 9404 | KRTAP2-4 | 15
chr17 | 64258845 | 64259329 | N |  | Loss | 484 | 5' of APOH and 5' of PRKCA | 11
chr18 | 30037470 | 30037675 | N |  | Loss | 205 | FAM59A | 10
chr20 | 4234781 | 4238447 | N |  | Gain | 3666 | 5' of ADRA1D | 16
chr20 | 6013320 | 6017259 | N |  | Loss | 3939 | CRLS1/DKFZp762C112 | 14
chr20 | 15755244 | 15765167 | N |  | Loss | 9923 | MACROD2 | 20
chr20 | 47337049 | 47341312 | N |  | Gain | 4263 | PREX1 | 14
chr20 | 49132410 | 49132637 | N |  | Loss | 227 | PTPN1 | 10
chr20 | 56248075 | 56252910 | N |  | Loss | 4835 | PMEPA1 | 20
chr21 | 17311697 | 17435462 | N |  | Loss | 123765 | 5' of C21orf34, 3' of USP25 | 20
chr21 | 42855515 | 42855647 | Y | 1 | Gain | 132 | TMPRSS2 | 10
chr22 | 30731066 | 30731540 | N |  | Gain | 474 | SF3A1 | 10
chr22 | 33459104 | 33470309 | N |  | Loss | 11205 | 5' of SYN3 | 20
chr22 | 39515118 | 39525791 | N |  | Loss | 10673 | 3' of APOBEC3H, 3' of CBX7 | 20
chr22 | 44251958 | 44257056 | N |  | Loss | 5098 | SULT4A1/SULTX3 | 19
chr22 | 44641315 | 44641594 | N |  | Gain | 279 | KIAA1644 | 10
chr22 | 51055900 | 51234443 | Y | 4 | Gain | 178543 | ARSA, SHANK3, BC050343, ACR, MGC70863, RABL2B | 10
chrX | 3206732 | 3216695 | N |  | Loss | 9963 | 3' of MXRA5, ARSF | 19
chrX | 57285994 | 57291268 | N |  | Gain | 5274 | 5' of FAAH2 | 11
chrX | 133460586 | 133466162 | N |  | Loss | 5576 | 5' of [NAME] | 11
chrX | 142769032 | 142781735 | N |  | Loss | 12703 | 5' of SLITRK4, 3' of SPANXN2 | 15
chrX | 151041009 | 151042244 | N |  | Loss | 1235 | 5' of MAGEA4 | 12
References: |  |  |  |  |  |  |  | Total = 2,642 [NAME]
1. [NAME], 2006
2. AGP, 2007
3. Sebat et al., 2007
4. [NAME] et al., 2008
5. Christian et al., 2008