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| gene1
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stringclasses 392
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stringclasses 689
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stringclasses 654
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|---|---|---|---|---|---|---|
On the other hand, two missense mutations of the EPHA2 gene were identified in two families, SLC26A4: c.1300G>A (p.434A>T), EPHA2: c.1063G>A (@VARIANT$) and @GENE$: c.1229C>A (@VARIANT$), @GENE$: c.1532C>T (p.T511M) (Fig. 6a, b).
| 7,067,772
|
SLC26A4;20132
|
EPHA2;20929
|
p.G355R;tmVar:p|SUB|G|355|R;HGVS:p.G355R;VariantGroup:4;CorrespondingGene:1969;RS#:370923409;CA#:625329
|
p.410T>M;tmVar:p|SUB|T|410|M;HGVS:p.T410M;VariantGroup:9;CorrespondingGene:5172;RS#:111033220;CA#:261403
| 0no label
|
Discussion Here, we presented a rare large Chinese family with ER-associated SCD, in which the disease phenotypes were mainly caused by a @GENE$-@VARIANT$ mutation and modulated by the @GENE$-@VARIANT$ variant and sex (Fig 7).
| 5,426,766
|
CACNA1C;55484
|
SCN5A;22738
|
Q1916R;tmVar:p|SUB|Q|1916|R;HGVS:p.Q1916R;VariantGroup:4;CorrespondingGene:775;RS#:186867242;CA#:6389963
|
R1193Q;tmVar:p|SUB|R|1193|Q;HGVS:p.R1193Q;VariantGroup:7;CorrespondingGene:6331;RS#:41261344;CA#:17287
| 11
|
Five anencephaly cases carried rare or novel CELSR1 missense variants, three of whom carried additional rare potentially damaging PCP variants: 01F377 (CELSR1 @VARIANT$ and PRICKLE4 c.730C>G), 2F07 (CELSR1 c.8807C>T and DVL3 c.1622C>T), 618F05 (CELSR1 c.8282C>T and @GENE$ c.3979G>A). One patient (f93-80) had a novel PTK7 missense variant (c.655A>G) with a rare @GENE$ missense variant (c.1892C>T). Three patients carried missense variants both in FZD and other PCP-associated genes: 01F552 (FZD6 c.1531C>T and CELSR2 c.3800A>G), 335F07 (FZD6 c.544G>A and 2 FAT4 missense variants c.5792A>G; @VARIANT$), and 465F99 (rare FZD1 missense variant c.211C>T and a novel FAT4 missense variant c.10147G>A).
| 5,887,939
|
SCRIB;44228
|
CELSR2;1078
|
c.6362G>A;tmVar:c|SUB|G|6362|A;HGVS:c.6362G>A;VariantGroup:33;CorrespondingGene:9620;RS#:765148329;CA#:10293808
|
c.10384A>G;tmVar:c|SUB|A|10384|G;HGVS:c.10384A>G;VariantGroup:2;CorrespondingGene:4824;RS#:373263457;CA#:4677776
| 0no label
|
Amino acid conservation analysis showed that seven of the 10 variants (CELSR1 p.G1122S, CELSR1 p.R769W, @GENE$ @VARIANT$, PTK7 p.P642R, SCRIB p.G1108E, SCRIB p.G644V and @GENE$ @VARIANT$) were located at highly conserved nucleotides in human, dog, mouse, rat, and zebrafish.
| 5,966,321
|
DVL3;20928
|
SCRIB;44228
|
p.R148Q;tmVar:p|SUB|R|148|Q;HGVS:p.R148Q;VariantGroup:8;CorrespondingGene:1857;RS#:764021343;CA#:2727085
|
p.K618R;tmVar:p|SUB|K|618|R;HGVS:p.K618R;VariantGroup:2;CorrespondingGene:5754;RS#:139041676
| 0no label
|
Her mother with @VARIANT$ in @GENE$ and her father with a missense mutation c.4421C > T in @GENE$ had intermittent hematuria and proteinuria. In proband of family 29, in addition to a glycine substitution (p. (Gly1119Ala)) in COL4A3 in the heterozygous state, there was another heterozygous nonsense mutation @VARIANT$ in COL4A4 genes.
| 6,565,573
|
COL4A5;133559
|
COL4A4;20071
|
c.1339 + 3A>T;tmVar:c|SUB|A|1339+3|T;HGVS:c.1339+3A>T;VariantGroup:23;CorrespondingGene:1287
|
c.5026C > T;tmVar:c|SUB|C|5026|T;HGVS:c.5026C>T;VariantGroup:20;CorrespondingGene:1286
| 0no label
|
Patient P0432 has a @VARIANT$ (p.M1344fsX42) mutation in USH2A and a missense mutation in @GENE$ (@VARIANT$), but his father, who has neither deafness nor retinitis pigmentosa, also carries these two mutations, and his clinically affected sister does not carry the mutation in CDH23. In the USH1 patient, we found three presumably pathogenic mutations in MYO7A (c.6657T>C), @GENE$ (c.46C>G; p.L16V) and USH2A (c.9921T>G).
| 3,125,325
|
CDH23;11142
|
USH1G;56113
|
c.4030_4037delATGGCTGG;tmVar:c|DEL|4030_4037|ATGGCTGG;HGVS:c.4030_4037delATGGCTGG;VariantGroup:216;CorrespondingGene:7399
|
p.R1189W;tmVar:p|SUB|R|1189|W;HGVS:p.R1189W;VariantGroup:61;CorrespondingGene:64072;RS#:745855338;CA#:5544764
| 0no label
|
(c) Sequencing chromatograms of the heterozygous mutation c.1787A>G (p.His596Arg) in SLC20A2. (d) Sequencing chromatograms of the heterozygous mutation c.317G>C (@VARIANT$) in PDGFRB Genomic DNA was extracted from peripheral blood, and the DNA sample of the proband was subjected to screen the known causative genes for PFBC. Surprisingly, we identified two missense mutations in the proband: NM_001257180.2, exon10, @VARIANT$, p.His596Arg in @GENE$ (Figure 1c) and NM_002609.4, exon3, c.317G>C, p.Arg106Pro, rs544478083 in @GENE$ (Figure 1d).
| 8,172,206
|
SLC20A2;68531
|
PDGFRB;1960
|
p.Arg106Pro;tmVar:p|SUB|R|106|P;HGVS:p.R106P;VariantGroup:1;CorrespondingGene:5159;RS#:544478083
|
c.1787A>G;tmVar:c|SUB|A|1787|G;HGVS:c.1787A>G;VariantGroup:2;CorrespondingGene:6575
| 0no label
|
Two unrelated KS patients had heterozygous NELF mutations and mutation in a second gene: NELF/KAL1 (c.757G>A; p.Ala253Thr of NELF and @VARIANT$; p.Cys163del of @GENE$) and NELF/@GENE$ (c. 1160-13C>T of NELF and c.824G>A; @VARIANT$ of TACR3).
| 3,888,818
|
KAL1;55445
|
TACR3;824
|
c.488_490delGTT;tmVar:p|DEL|488_490|V;HGVS:p.488_490delV;VariantGroup:8;CorrespondingGene:26012
|
p.Trp275X;tmVar:p|SUB|W|275|X;HGVS:p.W275X;VariantGroup:1;CorrespondingGene:6870;RS#:144292455;CA#:144871
| 0no label
|
Variants in all known WS candidate genes (EDN3, @GENE$, MITF, PAX3, @GENE$, SNAI2, and TYRO3) were searched and a novel rare heterozygous deletion mutation (c.965delA; p.Asn322fs) was identified in the MITF gene in both patients. Moreover, heterozygous missense variants in SNAI3 (@VARIANT$; p.Arg203Cys) and TYRO3 (c.1037T>A; @VARIANT$) gene was identified in the exome data of both patients.
| 7,877,624
|
EDNRB;89
|
SOX10;5055
|
c.607C>T;tmVar:c|SUB|C|607|T;HGVS:c.607C>T;VariantGroup:1;CorrespondingGene:333929;RS#:149676512;CA#:8229366
|
p.Ile346Asn;tmVar:p|SUB|I|346|N;HGVS:p.I346N;VariantGroup:2;CorrespondingGene:7301;RS#:12148316;CA#:7494886
| 0no label
|
The @VARIANT$ (p.Cys531Tyr) SCUBE2 variant could induce BAVMs via a gain-of-function mechanism, though confirmation will require further functional studies. In patient AVM558, the de novo heterozygous missense variant @VARIANT$ (p.Arg565Gln) was identified in @GENE$ (table 1), which encodes a kinase responsible for phosphorylation of residue T312 within SMAD1, blocking SMAD1 activity in BMP/TGF-beta signalling (figure 3). Loss of MAP4K4 leads to impaired angiogenesis in vitro and in vivo. In patient AVM206, the de novo heterozygous missense variant c.2075A>G (p.Asn692Ser) was identified in CDH2 (table 1), which encodes N-cadherin, an integral mediator of cell-cell interactions. N-cadherin mediates brain angiogenesis by stabilising angiogenic capillaries, possibly by enhancing the interaction between pericytes and endothelial cells. At the molecular level, @GENE$ mediates cell-cell adhesion by regulating PI3K/Akt signalling (figure 3).
| 6,161,649
|
MAP4K4;7442
|
N-cadherin;20424
|
c.1592G>A;tmVar:c|SUB|G|1592|A;HGVS:c.1592G>A;VariantGroup:5;CorrespondingGene:1956;RS#:1212415588
|
c.1694G>A;tmVar:c|SUB|G|1694|A;HGVS:c.1694G>A;VariantGroup:5;CorrespondingGene:9448;RS#:1212415588
| 0no label
|
Deleterious variants in HS1BP3 (NM_022460.3: @VARIANT$, p.Gly32Cys) and GNA14 (NM_004297.3: @VARIANT$, p.Thr330ArgfsTer67) were identified in a father and son with segmental cranio-cervical dystonia first manifest as BSP. Deleterious variants in DNAH17,TRPV4,@GENE$,VPS13C,UNC13B,@GENE$,MYOD1, and MRPL15 were found in two or more independent pedigrees.
| 6,081,235
|
CAPN11;21392
|
SPTBN4;11879
|
c.94C>A;tmVar:c|SUB|C|94|A;HGVS:c.94C>A;VariantGroup:25;CorrespondingGene:64342
|
c.989_990del;tmVar:c|DEL|989_990|;HGVS:c.989_990del;VariantGroup:16;CorrespondingGene:9630;RS#:750424668;CA#:5094137
| 0no label
|
Four potential pathogenic variants, including @GENE$ @VARIANT$ (NM_001160160, c.G5594A), LAMA2 @VARIANT$ (NM_000426, c.G2881A), @GENE$ p.307_308del (NM_001204798, c.921_923del), and DMD p.E1028V (NM_004011, c.A3083T) were involved in the occurrence of arrhythmia and cardiomyopathy (Table 2).
| 8,739,608
|
SCN5A;22738
|
KCNH2;201
|
p.R1865H;tmVar:p|SUB|R|1865|H;HGVS:p.R1865H;VariantGroup:1;CorrespondingGene:6331;RS#:370694515;CA#:64651
|
p.A961T;tmVar:p|SUB|A|961|T;HGVS:p.A961T;VariantGroup:2;CorrespondingGene:3908;RS#:147301872;CA#:3993099
| 0no label
|
The nucleotide sequence showed a G to C transition at nucleotide 769 (c.769G>C) of the coding sequence in exon 7 of @GENE$, which results in the substitution of @VARIANT$. Additionally, the nucleotide sequence showed a monoallelic C to T transition at nucleotide 511 (c.511C>T) of the coding sequence in exon 3 of @GENE$, which results in the substitution of Arg at residue 171 to Cys. DNA sequencing of the parents' genome revealed that both mutant alleles were from their mother (Fig. 2A), who carried a heterozygous EDA mutation (c.769G>C) and a heterozygous WNT10A c.511C>T mutation, and showed absence of only the left upper lateral incisor without other clinical abnormalities. No mutations in these genes were found in the father. Sequence analyses of EDA and WNT10A genes. (A) The EDA mutation c.769G>C and WNT10A mutation @VARIANT$ were found in patient N1, who inherited the mutant allele from his mother.
| 3,842,385
|
EDA;1896
|
WNT10A;22525
|
Gly at residue 257 to Arg;tmVar:p|SUB|G|257|R;HGVS:p.G257R;VariantGroup:0;CorrespondingGene:1896;RS#:1057517882;CA#:16043329
|
c.511C>T;tmVar:c|SUB|C|511|T;HGVS:c.511C>T;VariantGroup:3;CorrespondingGene:80326;RS#:116998555;CA#:2113955
| 0no label
|
Data were fit with a Boltzmann distribution {I = Imax/(1 + exp[(V1/2 - V)/k])} for KCNQ1-WT+@GENE$ (solid line) and for KCNQ1-@VARIANT$+KCNE1 (dashed line); (E) Time constants of the tail current from CHO-K1 cells transiently transfected with @GENE$-WT+KCNE1 (solid line, n = 7) or KCNQ1-p.R583H+KCNE1 (open circles, n = 8) plotted as a function of the activation step voltage. The decay of the potassium current recorded during the test pulse to -30 mV was fit with a single exponential function (area delimited by dotted lines shown in F); (F) Stimulation protocol. Data are shown as mean +- SEM. Functional properties of the KCNH2-@VARIANT$ variant.
| 5,578,023
|
KCNE1;100760439
|
KCNQ1;100761481
|
p.R583H;tmVar:p|SUB|R|583|H;HGVS:p.R583H;VariantGroup:4;CorrespondingGene:3784;RS#:199473482;CA#:6304
|
p.C108Y;tmVar:p|SUB|C|108|Y;HGVS:p.C108Y;VariantGroup:3;CorrespondingGene:3757
| 0no label
|
We have screened 108 @GENE$ heterozygous Chinese patients for mutations in @GENE$ by sequencing. We have excluded the possibility that mutations in exon 1 of GJB2 and the deletion of GJB6 are the second mutant allele in these Chinese heterozygous probands. Two different GJB3 mutations (N166S and @VARIANT$) occurring in compound heterozygosity with the @VARIANT$ and 299delAT of GJB2 were identified in three unrelated families (235delC/N166S, 235delC/A194T and 299delAT/A194T).
| 2,737,700
|
GJB2;2975
|
GJB3;7338
|
A194T;tmVar:c|SUB|A|194|T;HGVS:c.194A>T;VariantGroup:4;CorrespondingGene:2707;RS#:117385606;CA#:118313
|
235delC;tmVar:c|DEL|235|C;HGVS:c.235delC;VariantGroup:1;CorrespondingGene:2706;RS#:80338943
| 11
|
Moller et al. reported an index case with digenic variants in MYH7 (L1038P) and @GENE$ (@VARIANT$), both encoding sarcomeric proteins that are likely to affect its structure when mutated. Petropoulou et al. reported a family severely affected by DCM and who had two digenic variations in MYH7 (@VARIANT$) and @GENE$ (Asn83His), both sarcomeric genes.
| 6,359,299
|
MYBPC3;215
|
TNNT2;68050
|
R326Q;tmVar:p|SUB|R|326|Q;HGVS:p.R326Q;VariantGroup:6;CorrespondingGene:4607;RS#:34580776;CA#:16212
|
Asp955Asn;tmVar:p|SUB|D|955|N;HGVS:p.D955N;VariantGroup:2;CorrespondingGene:4625;RS#:886039204;CA#:10587773
| 0no label
|
We observed that in 5 PCG cases heterozygous @GENE$ mutations (p.A115P, p.E229 K, and @VARIANT$) co-occurred with heterozygous TEK mutations (p.E103D, p.I148T, p.Q214P, and p.G743A) indicating a potential digenic inheritance (Fig. 1a). None of the normal controls carried both the heterozygous combinations of CYP1B1 and @GENE$ mutations. The TEK @VARIANT$ and G743A alleles were absent in 1024 controls, whereas very low frequencies of heterozygous TEK E103D (0.005) and I148T (0.016) alleles were found in the control population (Table 1).
| 5,953,556
|
CYP1B1;68035
|
TEK;397
|
p.R368H;tmVar:p|SUB|R|368|H;HGVS:p.R368H;VariantGroup:1;CorrespondingGene:1545;RS#:79204362;CA#:119016
|
Q214P;tmVar:p|SUB|Q|214|P;HGVS:p.Q214P;VariantGroup:10;CorrespondingGene:7010
| 0no label
|
We also tested the potential of the mutant TEK and CYP1B1 proteins to associate with wild-type @GENE$ and TEK, respectively. As shown in Supplementary Fig. 3a, the mutant HA-TEK proteins E103D and I148T exhibited diminished interaction with wild-type GFP-CYP1B1. On the other hand, mutant GFP-CYP1B1 @VARIANT$ and R368H showed perturbed interaction with HA-TEK. The residues @VARIANT$, I148, and Q214 lie in the N-terminal extracellular domain of TEK (Fig. 1d). This suggested that either the N-terminal @GENE$ domain was involved in the interaction with CYP1B1 or that the mutations altered the conformation of the TEK protein, which affected a secondary CYP1B1-binding site.
| 5,953,556
|
CYP1B1;68035
|
TEK;397
|
A115P;tmVar:p|SUB|A|115|P;HGVS:p.A115P;VariantGroup:0;CorrespondingGene:1545;RS#:764338357;CA#:1620052
|
E103;tmVar:p|Allele|E|103;VariantGroup:2;CorrespondingGene:7010;RS#:572527340
| 0no label
|
Specifically, the mother and her twin sister were heterozygous for the GGCX missense mutation @VARIANT$ and the ABCC6 nonsense mutation @VARIANT$, suggesting digenic inheritance of their cutaneous findings. However, the proband's younger brother and father were heterozygous carriers of the p.S300F mutation in the @GENE$ gene while they also carried the p.R1141X mutation in the ABCC6 gene; they did not display any signs of cutaneous findings or hematologic disorder. Assay of gamma-glutamyl carboxylase activity Previous studies have clearly demonstrated that the p.R1141X mutation in the @GENE$ gene in heterozygous carriers does not cause PXE.
| 2,900,916
|
GGCX;639
|
ABCC6;55559
|
p.V255M;tmVar:p|SUB|V|255|M;HGVS:p.V255M;VariantGroup:1;CorrespondingGene:2677;RS#:121909683;CA#:214957
|
p.R1141X;tmVar:p|SUB|R|1141|X;HGVS:p.R1141X;VariantGroup:6;CorrespondingGene:368;RS#:72653706;CA#:129115
| 0no label
|
Finally, BNC2 variant @VARIANT$:p.(Pro623His) (MAF = 0.002) was detected in 2 patients (patient 1 and 7) and MAML3 variant @VARIANT$:p.(Asn294Ser) (MAF = 0.0028) in patients 7 and 8 ( Table 2 ). We performed interactome analysis for the identified DSD genes using bioinformatic tools for the analysis of possible gene-protein interactions. The network comprising all genes identified is shown in Figure 1 . Overall, a connection was found for 27 of the 41 genes. MAMLD1 connects directly to MAML1/2/3. Via NOTCH1/2 8 genes are in connection with MAMLD1, namely WNT9A/9B, @GENE$, FGF10, RET, PROP1 and NRP1. Some of these genes are also central nodes for further connections; e.g. GLI3 for EVC, FGF10, GLI2, RIPK4 and @GENE$; and RET for PIK3R3 with PTPN11, which also is connected with RIPK4.
| 6,726,737
|
GLI2/3;2736;2737
|
EYA1;74943
|
c.1868C>A;tmVar:c|SUB|C|1868|A;HGVS:c.1868C>A;VariantGroup:11;CorrespondingGene:54796;RS#:114596065;CA#:204322
|
c.881A>G;tmVar:c|SUB|A|881|G;HGVS:c.881A>G;VariantGroup:16;CorrespondingGene:55534;RS#:115966590;CA#:3085269
| 0no label
|
Given their offspring was mutation carriers, we might infer that II-4 and III-1 also harbored the @GENE$-Q1916R mutation. Notably, not all CACNA1C-@VARIANT$ carriers (II-3, II-6, III-4, III-5, III-7, IV-1, IV-3, IV-4 and obligate carriers II-4 and III-1) manifested the positive phenotypes (ER pattern in ECG or nocturnal SCD). This phenotypic incomplete penetrance might be modified by @GENE$-@VARIANT$ variant and sex.
| 5,426,766
|
CACNA1C;55484
|
SCN5A;22738
|
Q1916R;tmVar:p|SUB|Q|1916|R;HGVS:p.Q1916R;VariantGroup:4;CorrespondingGene:775;RS#:186867242;CA#:6389963
|
R1193Q;tmVar:p|SUB|R|1193|Q;HGVS:p.R1193Q;VariantGroup:7;CorrespondingGene:6331;RS#:41261344;CA#:17287
| 0no label
|
Therefore, in this study, @GENE$ @VARIANT$ may be the main cause of sinoatrial node dysfunction, whereas KCNH2 p.307_308del only carried by II: 1 may potentially induce the phenotype of LQTS. However, it was hard to determine whether the coexisting interactions of @GENE$ p.307_308del and SCN5A p.R1865H increased the risk of young and early-onset LQTS, or whether KCNH2 mutation was only associated with LQTS, while SCN5A mutation was only associated with sinoatrial node dysfunction. CONCLUSIONS We firstly identified the novel digenic heterozygous mutations by WES, KCNH2 @VARIANT$ and SCN5A p.R1865H, which resulted in LQTS with repeat syncope, torsades de pointes, ventricular fibrillation, and sinoatrial node dysfunction.
| 8,739,608
|
SCN5A;22738
|
KCNH2;201
|
p.R1865H;tmVar:p|SUB|R|1865|H;HGVS:p.R1865H;VariantGroup:1;CorrespondingGene:6331;RS#:370694515;CA#:64651
|
p.307_308del;tmVar:p|DEL|307_308|;HGVS:p.307_308del;VariantGroup:16;CorrespondingGene:3757
| 0no label
|
(D) The @GENE$ mutation @VARIANT$ and WNT10A mutation c.637G>A were found in patient S2, who also inherited the mutant allele from his mother; however, his father's DNA sample could not be obtained for analysis. (E) The EDA mutation c.466C>T and @GENE$ mutation @VARIANT$ were found in patient S3, who inherited the mutant allele from his mother.
| 3,842,385
|
EDA;1896
|
WNT10A;22525
|
c.457C>T;tmVar:c|SUB|C|457|T;HGVS:c.457C>T;VariantGroup:6;CorrespondingGene:1896;RS#:397516662(Expired)
|
c.637G>A;tmVar:c|SUB|G|637|A;HGVS:c.637G>A;VariantGroup:4;CorrespondingGene:80326;RS#:147680216;CA#:211313
| 0no label
|
The nucleotide sequence showed a @VARIANT$ (c.252DelT) of the coding sequence in exon 1 of EDA; this leads to a frame shift from residue 84 and a premature termination at residue 90. Additionally, a monoallelic @VARIANT$ (c.511C>T) of the coding sequence in exon 3 of @GENE$ was detected, this leads to the substitution of Arg at residue 171 to Cys. Analyses of his parents' genome showed that the mutant @GENE$ allele was from his mother (Fig. 2C), however, we were unable to screen for WNT10A mutations because of insufficient DNA.
| 3,842,385
|
WNT10A;22525
|
EDA;1896
|
T deletion at nucleotide 252;tmVar:c|Allele|T|252;VariantGroup:9;CorrespondingGene:1896
|
C to T transition at nucleotide 511;tmVar:c|SUB|C|511|T;HGVS:c.511C>T;VariantGroup:3;CorrespondingGene:80326;RS#:116998555;CA#:2113955
| 0no label
|
Variants in all known WS candidate genes (EDN3, EDNRB, @GENE$, PAX3, SOX10, SNAI2, and TYRO3) were searched and a novel rare heterozygous deletion mutation (c.965delA; p.Asn322fs) was identified in the MITF gene in both patients. Moreover, heterozygous missense variants in @GENE$ (@VARIANT$; p.Arg203Cys) and TYRO3 (c.1037T>A; @VARIANT$) gene was identified in the exome data of both patients.
| 7,877,624
|
MITF;4892
|
SNAI3;8500
|
c.607C>T;tmVar:c|SUB|C|607|T;HGVS:c.607C>T;VariantGroup:1;CorrespondingGene:333929;RS#:149676512;CA#:8229366
|
p.Ile346Asn;tmVar:p|SUB|I|346|N;HGVS:p.I346N;VariantGroup:2;CorrespondingGene:7301;RS#:12148316;CA#:7494886
| 0no label
|
The p.Ile312Met (c.936C>G) mutation in EDA and heterozygous p.Arg171Cys (c.511C>T) mutation in @GENE$ were detected. The coding sequence in exon 9 of EDA showed a C to G transition, which results in the substitution of @VARIANT$; also, the coding sequence in exon 3 of WNT10A showed a @VARIANT$, which results in the substitution of Arg at residue 171 to Cys. Analyses of his parents' genome revealed that the mutant alleles were from his mother, who carried digenic heterozygous @GENE$ and WNT10A mutations at the same locus as that of N2 (Fig. 2B).
| 3,842,385
|
WNT10A;22525
|
EDA;1896
|
Ile at residue 312 to Met;tmVar:p|SUB|I|312|M;HGVS:p.I312M;VariantGroup:7;CorrespondingGene:1896
|
C to T transition at nucleotide 511;tmVar:c|SUB|C|511|T;HGVS:c.511C>T;VariantGroup:3;CorrespondingGene:80326;RS#:116998555;CA#:2113955
| 0no label
|
25 The RYR3 (NM_001036: c.7812C > G, @VARIANT$) and EBNA1BP2 (NM_001159936: c.1034A > T, p.Asn345Ile) variants were classified as likely benign and benign, respectively, while the TRIP6 (NM_003302: c.822G > C, p.Glu274Asp) and the @GENE$ (NM_006615: c.55G > T, @VARIANT$) variants were classified as VUS. 21 TRIP6 promotes cell migration and invasion through Wnt/beta-catenin signaling and was shown to be upregulated in colorectal tumors. 24 Therefore, @GENE$ variants that increase protein stability or expression could potentially stimulate colorectal tumorigenesis.
| 7,689,793
|
CAPN9;38208
|
TRIP6;37757
|
p.Asn2604Lys;tmVar:p|SUB|N|2604|K;HGVS:p.N2604K;VariantGroup:10;CorrespondingGene:6263;RS#:41279214;CA#:7459988
|
p.Ala19Ser;tmVar:p|SUB|A|19|S;HGVS:p.A19S;VariantGroup:17;CorrespondingGene:10753;RS#:147360179;CA#:1448452
| 0no label
|
None of the variants in genes previously associated with HI segregated with the HI phenotype with the exception of the @GENE$ [GRCh37/hg19; chr10:@VARIANT$; NM_033056: c.3101G > A; p.(Arg1034His)] and @GENE$ [GRCh37/hg19; chr17:72915838C > T; NM_173477:c.1093G > A; @VARIANT$] variants which displayed digenic inheritance (Fig. 1a).
| 6,053,831
|
PCDH15;23401
|
USH1G;56113
|
55719513C > T;tmVar:g|SUB|C|55719513|T;HGVS:g.55719513C>T;VariantGroup:5;CorrespondingGene:65217
|
p.(Asp365Asn);tmVar:p|SUB|D|365|N;HGVS:p.D365N;VariantGroup:1;CorrespondingGene:124590;RS#:538983393;CA#:8753931
| 11
|
Deleterious variants in HS1BP3 (NM_022460.3: c.94C>A, @VARIANT$) and GNA14 (NM_004297.3: @VARIANT$, p.Thr330ArgfsTer67) were identified in a father and son with segmental cranio-cervical dystonia first manifest as BSP. Deleterious variants in @GENE$,TRPV4,CAPN11,VPS13C,UNC13B,SPTBN4,@GENE$, and MRPL15 were found in two or more independent pedigrees.
| 6,081,235
|
DNAH17;72102
|
MYOD1;7857
|
p.Gly32Cys;tmVar:p|SUB|G|32|C;HGVS:p.G32C;VariantGroup:25;CorrespondingGene:64342
|
c.989_990del;tmVar:c|DEL|989_990|;HGVS:c.989_990del;VariantGroup:16;CorrespondingGene:9630;RS#:750424668;CA#:5094137
| 0no label
|
DISCUSSION We present a Chinese family with PFBC in which the previously reported heterozygous mutation c.1787A>G (@VARIANT$) in SLC20A2 and the SNP (rs544478083) c.317G>C (@VARIANT$) in PDGFRB were identified. The proband's father with the @GENE$ c.1787A>G (p.His596Arg) mutation showed obvious brain calcification but was clinically asymptomatic. The proband's mother with the @GENE$ c.317G>C (p.Arg106Pro) variant showed very slight calcification and was clinically asymptomatic.
| 8,172,206
|
SLC20A2;68531
|
PDGFRB;1960
|
p.His596Arg;tmVar:p|SUB|H|596|R;HGVS:p.H596R;VariantGroup:2;CorrespondingGene:6575
|
p.Arg106Pro;tmVar:p|SUB|R|106|P;HGVS:p.R106P;VariantGroup:1;CorrespondingGene:5159;RS#:544478083
| 0no label
|
We observed that in 5 PCG cases heterozygous CYP1B1 mutations (@VARIANT$, p.E229 K, and p.R368H) co-occurred with heterozygous TEK mutations (p.E103D, p.I148T, p.Q214P, and p.G743A) indicating a potential digenic inheritance (Fig. 1a). None of the normal controls carried both the heterozygous combinations of @GENE$ and @GENE$ mutations. The TEK @VARIANT$ and G743A alleles were absent in 1024 controls, whereas very low frequencies of heterozygous TEK E103D (0.005) and I148T (0.016) alleles were found in the control population (Table 1).
| 5,953,556
|
CYP1B1;68035
|
TEK;397
|
p.A115P;tmVar:p|SUB|A|115|P;HGVS:p.A115P;VariantGroup:0;CorrespondingGene:1545;RS#:764338357;CA#:1620052
|
Q214P;tmVar:p|SUB|Q|214|P;HGVS:p.Q214P;VariantGroup:10;CorrespondingGene:7010
| 0no label
|
In family A, a profoundly hearing impaired proband was found to be heterozygous for a novel A to G transition at nucleotide position 497 of GJB3, resulting in an asparagine into serine substitution in codon 166 (N166S) and for the 235delC of @GENE$ (Fig. 1b, d). Genotyping analysis revealed that the GJB2/@VARIANT$ was inherited from the unaffected father and the N166S of GJB3 was inherited from the normal hearing mother (Fig. 1a). In families F and K, a heterozygous missense mutation of a G-to-A transition at nucleotide 580 of GJB3 that causes A194T, was found in profoundly deaf probands, who were also heterozygous for GJB2/235delC (Fig. 1g, i) and GJB2/299-300delAT (Fig. 1l, n), respectively. In Family F, the GJB2/235delC was inherited from the unaffected father and the @VARIANT$ of @GENE$ was likely inherited from the normal hearing deceased mother (Fig. 1f).
| 2,737,700
|
GJB2;2975
|
GJB3;7338
|
235delC;tmVar:c|DEL|235|C;HGVS:c.235delC;VariantGroup:1;CorrespondingGene:2706;RS#:80338943
|
A194T;tmVar:c|SUB|A|194|T;HGVS:c.194A>T;VariantGroup:4;CorrespondingGene:2707;RS#:117385606;CA#:118313
| 0no label
|
We observed that in 5 PCG cases heterozygous CYP1B1 mutations (p.A115P, p.E229 K, and @VARIANT$) co-occurred with heterozygous TEK mutations (p.E103D, p.I148T, p.Q214P, and p.G743A) indicating a potential digenic inheritance (Fig. 1a). None of the normal controls carried both the heterozygous combinations of @GENE$ and TEK mutations. The @GENE$ Q214P and G743A alleles were absent in 1024 controls, whereas very low frequencies of heterozygous TEK @VARIANT$ (0.005) and I148T (0.016) alleles were found in the control population (Table 1).
| 5,953,556
|
CYP1B1;68035
|
TEK;397
|
p.R368H;tmVar:p|SUB|R|368|H;HGVS:p.R368H;VariantGroup:1;CorrespondingGene:1545;RS#:79204362;CA#:119016
|
E103D;tmVar:p|SUB|E|103|D;HGVS:p.E103D;VariantGroup:2;CorrespondingGene:7010;RS#:572527340;CA#:5015873
| 0no label
|
Among the 8 novel variants, 4 were classified as P (@VARIANT$ and @VARIANT$ in @GENE$, p.T803fs in DUOX2) or LP (p.D137E in @GENE$), the other were classified as VUS.
| 7,248,516
|
TSHR;315
|
DUOX2;9689
|
p.C176R;tmVar:p|SUB|C|176|R;HGVS:p.C176R;VariantGroup:32;CorrespondingGene:7038;RS#:200511116
|
p.K618*;tmVar:p|SUB|K|618|*;HGVS:p.K618*;VariantGroup:4;CorrespondingGene:7253
| 0no label
|
Recently, Gifford et al., identified three missense variants in @GENE$ (@VARIANT$), @GENE$ (Leu387Phe), and NKX2-5 (@VARIANT$) in three offspring with childhood-onset cardiomyopathy (Gifford et al., 2019).
| 7,057,083
|
MKL2;40917
|
MYH7;68044
|
Gln670His;tmVar:p|SUB|Q|670|H;HGVS:p.Q670H;VariantGroup:2;CorrespondingGene:57496
|
Ala119Ser;tmVar:p|SUB|A|119|S;HGVS:p.A119S;VariantGroup:0;CorrespondingGene:1482;RS#:137852684;CA#:120058
| 0no label
|
Five anencephaly cases carried rare or novel CELSR1 missense variants, three of whom carried additional rare potentially damaging PCP variants: 01F377 (@GENE$ c.6362G>A and PRICKLE4 c.730C>G), 2F07 (CELSR1 c.8807C>T and @GENE$ c.1622C>T), 618F05 (CELSR1 c.8282C>T and SCRIB @VARIANT$). One patient (f93-80) had a novel PTK7 missense variant (c.655A>G) with a rare CELSR2 missense variant (c.1892C>T). Three patients carried missense variants both in FZD and other PCP-associated genes: 01F552 (FZD6 c.1531C>T and CELSR2 c.3800A>G), 335F07 (FZD6 c.544G>A and 2 FAT4 missense variants c.5792A>G; c.10384A>G), and 465F99 (rare FZD1 missense variant @VARIANT$ and a novel FAT4 missense variant c.10147G>A).
| 5,887,939
|
CELSR1;7665
|
DVL3;20928
|
c.3979G>A;tmVar:c|SUB|G|3979|A;HGVS:c.3979G>A;VariantGroup:31;CorrespondingGene:23513;RS#:201563528;CA#:4918429
|
c.211C>T;tmVar:c|SUB|C|211|T;HGVS:c.211C>T;VariantGroup:8;CorrespondingGene:8321;RS#:574691354;CA#:4335060
| 0no label
|
Digenic inheritance of non-syndromic deafness caused by mutations at the gap junction proteins Cx26 and Cx31 Mutations in the genes coding for @GENE$ (Cx26) and connexin 31 (@GENE$) cause non-syndromic deafness. Here, we provide evidence that mutations at these two connexin genes can interact to cause hearing loss in digenic heterozygotes in humans. We have screened 108 GJB2 heterozygous Chinese patients for mutations in GJB3 by sequencing. We have excluded the possibility that mutations in exon 1 of GJB2 and the deletion of GJB6 are the second mutant allele in these Chinese heterozygous probands. Two different GJB3 mutations (N166S and A194T) occurring in compound heterozygosity with the 235delC and 299delAT of GJB2 were identified in three unrelated families (235delC/N166S, 235delC/A194T and @VARIANT$/@VARIANT$).
| 2,737,700
|
connexin 26;2975
|
Cx31;7338
|
299delAT;tmVar:c|DEL|299|AT;HGVS:c.299delAT;VariantGroup:12;CorrespondingGene:2706
|
A194T;tmVar:c|SUB|A|194|T;HGVS:c.194A>T;VariantGroup:4;CorrespondingGene:2707;RS#:117385606;CA#:118313
| 11
|
We identified four genetic variants (@GENE$-p.R583H, KCNH2-p.C108Y, KCNH2-p.K897T, and KCNE1-p.G38S) in an LQTS family. On the basis of in silico analysis, clinical data from our family, and the evidence from previous studies, we analyzed two mutated channels, KCNQ1-@VARIANT$ and @GENE$-@VARIANT$, using the whole-cell patch clamp technique.
| 5,578,023
|
KCNQ1;85014
|
KCNH2;201
|
p.R583H;tmVar:p|SUB|R|583|H;HGVS:p.R583H;VariantGroup:4;CorrespondingGene:3784;RS#:199473482;CA#:6304
|
p.C108Y;tmVar:p|SUB|C|108|Y;HGVS:p.C108Y;VariantGroup:3;CorrespondingGene:3757
| 0no label
|
The nucleotide sequence showed a G to C transition at nucleotide 769 (c.769G>C) of the coding sequence in exon 7 of EDA, which results in the substitution of @VARIANT$. Additionally, the nucleotide sequence showed a monoallelic C to T transition at nucleotide 511 (@VARIANT$) of the coding sequence in exon 3 of WNT10A, which results in the substitution of Arg at residue 171 to Cys. DNA sequencing of the parents' genome revealed that both mutant alleles were from their mother (Fig. 2A), who carried a heterozygous @GENE$ mutation (c.769G>C) and a heterozygous WNT10A c.511C>T mutation, and showed absence of only the left upper lateral incisor without other clinical abnormalities. No mutations in these genes were found in the father. Sequence analyses of EDA and WNT10A genes. (A) The EDA mutation c.769G>C and @GENE$ mutation c.511C>T were found in patient N1, who inherited the mutant allele from his mother.
| 3,842,385
|
EDA;1896
|
WNT10A;22525
|
Gly at residue 257 to Arg;tmVar:p|SUB|G|257|R;HGVS:p.G257R;VariantGroup:0;CorrespondingGene:1896;RS#:1057517882;CA#:16043329
|
c.511C>T;tmVar:c|SUB|C|511|T;HGVS:c.511C>T;VariantGroup:3;CorrespondingGene:80326;RS#:116998555;CA#:2113955
| 0no label
|
In family 18287 we detected a possible bilineal inheritance, with variants in both @GENE$ and @GENE$ (Figure 1). Two pregnancies were interrupted due to a prenatal finding of polycystic kidney disease at ultrasound examination at 20 and 13 gestational weeks, respectively. The mother was 33 year old; she had multicystic bilateral disease without affected family members, and showed a de novo missense variant p.(Cys331Thr) in PKD2. The father was a healthy 44 years old man with no signs of kidney cystic disease at ultrasound, and showed a variant in PKD1, p.(@VARIANT$), and a second variant in PKD2, p.(Arg872Gly). Both fetuses inherited the maternal PKD2 missense variant, in addition to the paternal p.(Ser872Gly) variant in PKD1, while only one fetus inherited the p.(@VARIANT$) PKD2 variant.
| 7,224,062
|
PKD1;250
|
PKD2;20104
|
Ser123Thr;tmVar:p|SUB|S|123|T;HGVS:p.S123T;VariantGroup:0;CorrespondingGene:5310;RS#:748717453;CA#:7833716
|
Arg872Gly;tmVar:p|SUB|R|872|G;HGVS:p.R872G;VariantGroup:9;CorrespondingGene:5311;RS#:755226061;CA#:3004303
| 0no label
|
@GENE$:@VARIANT$, predicted to alter the splice donor site of intron 3, has been classified as pathogenic. @GENE$:@VARIANT$ is a non-truncating mutation, but was previously reported as disease-causing.
| 3,949,687
|
PCDH15;23401
|
MYO7A;219
|
c.158-1G>A;tmVar:c|SUB|G|158-1|A;HGVS:c.158-1G>A;VariantGroup:18;CorrespondingGene:65217;RS#:876657418;CA#:10576348
|
p.Ala771Ser;tmVar:p|SUB|A|771|S;HGVS:p.A771S;VariantGroup:2;CorrespondingGene:4647;RS#:782384464;CA#:10576351
| 0no label
|
Recurrent Variants Identified in Our Regressive Autism Cohort In our sequenced cohort of 134 individuals with autism and regression, we identified two recurrent variants, @GENE$ c.28C > A (@VARIANT$) and @GENE$ @VARIANT$ (p.Arg248Cys).
| 7,463,850
|
GRIN2A;645
|
PLXNB2;66630
|
p.Leu10Met;tmVar:p|SUB|L|10|M;HGVS:p.L10M;VariantGroup:0;CorrespondingGene:2903
|
c.742C > T;tmVar:c|SUB|C|742|T;HGVS:c.742C>T;VariantGroup:9;CorrespondingGene:23654;RS#:779647430;CA#:10313520
| 0no label
|
Variants in all known WS candidate genes (EDN3, EDNRB, MITF, @GENE$, SOX10, SNAI2, and TYRO3) were searched and a novel rare heterozygous deletion mutation (c.965delA; @VARIANT$) was identified in the MITF gene in both patients. Moreover, heterozygous missense variants in SNAI3 (c.607C>T; p.Arg203Cys) and @GENE$ (@VARIANT$; p.Ile346Asn) gene was identified in the exome data of both patients.
| 7,877,624
|
PAX3;22494
|
TYRO3;4585
|
p.Asn322fs;tmVar:p|FS|N|322||;HGVS:p.N322fsX;VariantGroup:3;CorrespondingGene:4286
|
c.1037T>A;tmVar:c|SUB|T|1037|A;HGVS:c.1037T>A;VariantGroup:2;CorrespondingGene:7301;RS#:12148316;CA#:7494886
| 0no label
|
Similarly, SH170-377 carrying the @VARIANT$ mutation in @GENE$ also contained a previously reported homozygous @VARIANT$*36 mutant allele in Myosin XVA (MYO15A) (NM_016239) (Table 1). Although no other causative deafness mutation was detected in the initial analysis of TES data, Sanger sequencing for the low coverage area (<10x) in TES (see Table S2, Supplemental Content, which illustrates regions showing significantly low depth of coverage in TES: OTOF, STRC, and OTOA) revealed the two known pathogenic STRC mutations as a compound heterozygous configuration in SB175-334 (Table 1). To sum up, SH166-367, SH170-377, and SB175-334 which would have been considered DFNB1 without TES were found to be DFNB7/11, DFNB3, and DFNB16, respectively. Finally, a subject with the heterozygous p.R143W mutation in GJB2 (SH60-136) carried a p.D771N variant in @GENE$ (WFS1) (NM_001145853) according to TES.
| 4,998,745
|
GJB2;2975
|
Wolfram syndrome 1;4380
|
p.V193E;tmVar:p|SUB|V|193|E;HGVS:p.V193E;VariantGroup:21;CorrespondingGene:2706
|
p.Glu396Argfs;tmVar:p|FS|E|396|R|;HGVS:p.E396RfsX;VariantGroup:15;CorrespondingGene:51168;RS#:772536599;CA#:8423043
| 0no label
|
Discussion We present the first detailed clinical and pathologic data from three unrelated families with predominant distal myopathy associated with a known pathologic variant in SQSTM1 (p.Pro392Leu) and a variant in TIA1 (@VARIANT$). At the time of this report, only a single prior myopathy case with the same genetic variants has been reported, but the clinical and myopathological features were not illustrated. There are also two further cases of MRV having the same TIA1 variant but a different SQSTM1 mutation (@VARIANT$), one of whom was previously reported as having a SQSTM1-MRV. Although the causality of the coexisting @GENE$ and @GENE$ variants in myopathy has not been proven, our affected individuals from three unrelated family provide further support to the digenic nature of this myopathy.
| 5,868,303
|
SQSTM1;31202
|
TIA1;20692
|
p.Asn357Ser;tmVar:p|SUB|N|357|S;HGVS:p.N357S;VariantGroup:5;CorrespondingGene:7072;RS#:116621885;CA#:1697407
|
c.1165+1G>A;tmVar:c|SUB|G|1165+1|A;HGVS:c.1165+1G>A;VariantGroup:8;CorrespondingGene:8878;RS#:796051870(Expired)
| 0no label
|
Variants in all known WS candidate genes (EDN3, EDNRB, MITF, PAX3, @GENE$, SNAI2, and TYRO3) were searched and a novel rare heterozygous deletion mutation (c.965delA; p.Asn322fs) was identified in the @GENE$ gene in both patients. Moreover, heterozygous missense variants in SNAI3 (@VARIANT$; p.Arg203Cys) and TYRO3 (c.1037T>A; @VARIANT$) gene was identified in the exome data of both patients.
| 7,877,624
|
SOX10;5055
|
MITF;4892
|
c.607C>T;tmVar:c|SUB|C|607|T;HGVS:c.607C>T;VariantGroup:1;CorrespondingGene:333929;RS#:149676512;CA#:8229366
|
p.Ile346Asn;tmVar:p|SUB|I|346|N;HGVS:p.I346N;VariantGroup:2;CorrespondingGene:7301;RS#:12148316;CA#:7494886
| 0no label
|
The ISG20L2 and @GENE$ variants were excluded based on their frequencies in normal population cohorts. Sanger sequencing of Family 1 showed that both @VARIANT$ in S100A3 (c.229C>T, missense causing a p.R77C mutation) and a 4 bp deletion in @GENE$ (c.238-241delATTG causing a frameshift @VARIANT$) segregated completely with ILD in Family 1 based upon recessive inheritance (figure 2c and d), were in total linkage disequilibrium, and were present in a cis conformation.
| 6,637,284
|
SETDB1;32157
|
S100A13;7523
|
rs138355706;tmVar:rs138355706;VariantGroup:3;CorrespondingGene:6274;RS#:138355706
|
p.I80Gfs*13;tmVar:p|FS|I|80|G|13;HGVS:p.I80GfsX13;VariantGroup:7;CorrespondingGene:6284
| 0no label
|
On the other hand, mutant GFP-@GENE$ A115P and @VARIANT$ showed perturbed interaction with HA-@GENE$. The residues E103, I148, and @VARIANT$ lie in the N-terminal extracellular domain of TEK (Fig. 1d).
| 5,953,556
|
CYP1B1;68035
|
TEK;397
|
R368H;tmVar:p|SUB|R|368|H;HGVS:p.R368H;VariantGroup:1;CorrespondingGene:1545;RS#:79204362;CA#:119016
|
Q214;tmVar:p|Allele|Q|214;VariantGroup:10;CorrespondingGene:7010
| 0no label
|
Amino acid conservation analysis showed that seven of the 10 variants (CELSR1 p.G1122S, CELSR1 p.R769W, DVL3 p.R148Q, PTK7 p.P642R, SCRIB p.G1108E, @GENE$ p.G644V and SCRIB @VARIANT$) were located at highly conserved nucleotides in human, dog, mouse, rat, and zebrafish. The four other variants (CELSR1 p.Q2924H, @GENE$ p.R1057C and SCRIB p.R1044Q) involved less conserved nucleotides (Supplemental material, Fig. S2). Among these variants, p.R769W and p.R1057C localized to the carbonic anhydrases subunits, named the CA domain of CELSR1, @VARIANT$ was within the third PDZ domain of SCRIB, p.G1108E located very close to the fourth PDZ domain (1109-1192) of SCRIB, and p.P642R was within the fifth IGc2 domain of PTK7 (Supplemental Material, Fig. S3).
| 5,966,321
|
SCRIB;44228
|
CELSR1;7665
|
p.K618R;tmVar:p|SUB|K|618|R;HGVS:p.K618R;VariantGroup:2;CorrespondingGene:5754;RS#:139041676
|
p.R1044Q;tmVar:p|SUB|R|1044|Q;HGVS:p.R1044Q;VariantGroup:6;CorrespondingGene:23513;RS#:782787420;CA#:4918813
| 0no label
|
The @VARIANT$ nonsense variant was first detected in compound heterozygous form in a family with two affected siblings suffering from infantile ascending spastic paralysis with bulbar involvement. The ages of onset of the patients with the ALS2 variants reported in this study were later than juvenile ALS onset, which generally manifests before 25 years of age. Previous studies suggested that heterozygous variants in the @GENE$ may be causative for adult-onset sALS. MATR3 encodes three protein isoforms that have been described as nuclear-matrix and DNA/RNA binding proteins involved in transcription and stabilization of mRNA. In the present study, two novel heterozygous variants (P11S, S275N) were detected. The P11S variant affects the b isoform of the MATR3 protein (NM_001194956 and NP_001181885), contributing to splicing alteration of other isoforms. Further evidence is required to elucidate the mechanism of pathogenicity of these alterations. We discovered several variants in ALS candidate and risk genes. In a patient with LMN-dominant ALS with slow progression, we found two novel variants (@VARIANT$ and G4290R) in the @GENE$ gene.
| 6,707,335
|
ALS2;23264
|
DYNC1H1;1053
|
G1177X;tmVar:p|SUB|G|1177|X;HGVS:p.G1177X;VariantGroup:0;CorrespondingGene:57679;RS#:386134180;CA#:356568
|
T2583I;tmVar:p|SUB|T|2583|I;HGVS:p.T2583I;VariantGroup:31;CorrespondingGene:1778
| 0no label
|
In the present study, we found two variants: the E758K variant in two patients and the @VARIANT$ variant in one case, with both variants located within the coiled-coil domain (amino acid positions 331-906) of the protein, which is not in line with previous findings. Without additional functional evidence, the pathogenicity of these variants is uncertain. Three rare missense variants (R2034Q, L2118V, and @VARIANT$) of the @GENE$ gene were found. The high detection rate of missense variants of this gene is probably due to the large size of the coding region; therefore, we suggest that these SPG11 variants are unlikely to be deleterious. Variants in the SPG11 gene are most commonly associated with autosomal recessive spastic paraplegia, although homozygous variants have been recently identified in juvenile ALS, and heterozygous missense variants in sALS. Variants in UBQLN2 have been shown to be a cause of dominant X-linked ALS. A previously reported (M392V,) and a novel variant (Q84H) were found in the @GENE$ gene.
| 6,707,335
|
SPG11;41614
|
UBQLN2;81830
|
A579T;tmVar:c|SUB|A|579|T;HGVS:c.579A>T;VariantGroup:8;CorrespondingGene:3798;RS#:760135493
|
E2003D;tmVar:p|SUB|E|2003|D;HGVS:p.E2003D;VariantGroup:3;CorrespondingGene:80208;RS#:954483795
| 0no label
|
Her mother with @VARIANT$ in @GENE$ and her father with a missense mutation c.4421C > T in COL4A4 had intermittent hematuria and proteinuria. In proband of family 29, in addition to a glycine substitution (p. (@VARIANT$)) in @GENE$ in the heterozygous state, there was another heterozygous nonsense mutation c.5026C > T in COL4A4 genes.
| 6,565,573
|
COL4A5;133559
|
COL4A3;68033
|
c.1339 + 3A>T;tmVar:c|SUB|A|1339+3|T;HGVS:c.1339+3A>T;VariantGroup:23;CorrespondingGene:1287
|
Gly1119Ala;tmVar:p|SUB|G|1119|A;HGVS:p.G1119A;VariantGroup:21;CorrespondingGene:1285;RS#:764480728;CA#:2147204
| 0no label
|
In addition, the c.580G > T (@VARIANT$) and @VARIANT$ (p. Gly716Val) variants were identified by the software as harmful. In previous studies, the phenotype of the FGFR1 gene was not completely dominant, and most of the variants were inherited from a normal father or mother. However, most of the patients in our study had de novo variants; one patient inherited the variants from his father, while the other patient inherited the variants from her mother. Two female patients had a frameshift variant of the FGFR1 gene, which showed an infantile uterus and ovary. In the group with a nonreproductive phenotype, variants in the FGFR1 gene were found in one patient with cleft lip and palate, which was consistent with the report of a previous study. Another patient presented with a renal cyst and short stature. Therefore, anosmia, sexual dysplasia, irregular tooth alignment, cleft lip and palate, syndactyly, and renal abnormalities were common phenotypes of IHH patients with @GENE$ gene variants. The @GENE$ gene is located on chromosome 8q12.1 and is autosomal dominant, encoding chromosomal helicase DNA-binding protein 7.
| 8,796,337
|
FGFR1;69065
|
CHD7;19067
|
p. Gly194Cys;tmVar:p|SUB|G|194|C;HGVS:p.G194C;VariantGroup:8;CorrespondingGene:3730;RS#:1064796777
|
c.2147G > T;tmVar:c|SUB|G|2147|T;HGVS:c.2147G>T;VariantGroup:2;CorrespondingGene:2260
| 0no label
|
(D) SH175-389 harbored a monoallelic @VARIANT$ variant of GJB2 and a monoallelic @VARIANT$ variant of GJB3. DFNB1 = nonsyndromic hearing loss and deafness 1, GJB2 = gap junction protein beta 2, GJB3 = gap junction protein beta 3, GJB6 = @GENE$, @GENE$ = microphthalmia-associated transcription factor.
| 4,998,745
|
gap junction protein beta 6;4936
|
MITF;4892
|
p.V193E;tmVar:p|SUB|V|193|E;HGVS:p.V193E;VariantGroup:21;CorrespondingGene:2706
|
p.A194T;tmVar:p|SUB|A|194|T;HGVS:p.A194T;VariantGroup:18;CorrespondingGene:2707;RS#:117385606;CA#:118313
| 0no label
|
WES revealed heterozygous mutations in two genes known to affect hypothalamic and pituitary development: @VARIANT$;p.R85C in @GENE$ (MIM 607123; NM_144773.2; rs141090506) inherited from an unaffected mother and @VARIANT$;p.I436V in @GENE$ (MIM 606417; NM_018117.11; rs34602786) inherited from an unaffected father, both confirmed by Sanger sequencing (Fig. 1).
| 5,505,202
|
PROKR2;16368
|
WDR11;41229
|
c.253C>T;tmVar:c|SUB|C|253|T;HGVS:c.253C>T;VariantGroup:1;CorrespondingGene:128674;RS#:74315418;CA#:259601
|
c.1306A>G;tmVar:c|SUB|A|1306|G;HGVS:c.1306A>G;VariantGroup:3;CorrespondingGene:55717;RS#:34602786;CA#:5719694
| 11
|
Deleterious variants in HS1BP3 (NM_022460.3: @VARIANT$, p.Gly32Cys) and @GENE$ (NM_004297.3: @VARIANT$, p.Thr330ArgfsTer67) were identified in a father and son with segmental cranio-cervical dystonia first manifest as BSP. Deleterious variants in DNAH17,@GENE$,CAPN11,VPS13C,UNC13B,SPTBN4,MYOD1, and MRPL15 were found in two or more independent pedigrees.
| 6,081,235
|
GNA14;68386
|
TRPV4;11003
|
c.94C>A;tmVar:c|SUB|C|94|A;HGVS:c.94C>A;VariantGroup:25;CorrespondingGene:64342
|
c.989_990del;tmVar:c|DEL|989_990|;HGVS:c.989_990del;VariantGroup:16;CorrespondingGene:9630;RS#:750424668;CA#:5094137
| 0no label
|
Sanger sequencing of Family 1 showed that both rs138355706 in @GENE$ (c.229C>T, missense causing a p.R77C mutation) and a 4 bp deletion in @GENE$ (@VARIANT$ causing a frameshift p.I80Gfs*13) segregated completely with ILD in Family 1 based upon recessive inheritance (figure 2c and d), were in total linkage disequilibrium, and were present in a cis conformation. Allele frequency for @VARIANT$ within the population was calculated from exome sequencing of 2000 individuals and was found to be 0.1% (unpublished data from the Saudi Human Genome Project; www.saudigenomeprogram.org).
| 6,637,284
|
S100A3;2223
|
S100A13;7523
|
c.238-241delATTG;tmVar:c|DEL|238_241|ATTG;HGVS:c.238_241delATTG;VariantGroup:13;CorrespondingGene:6284
|
rs138355706;tmVar:rs138355706;VariantGroup:3;CorrespondingGene:6274;RS#:138355706
| 0no label
|
Genetic evaluation revealed heterozygous variants in the related genes @GENE$ (@VARIANT$, p.Arg896Trp) and NRXN2 (c.3176G>A, @VARIANT$), one inherited from the mother with family history of sudden infant death syndrome (SIDS) and one from the father with family history of febrile seizures. Although there are no previous reports with the digenic combination of NRXN1 and @GENE$ variants, patients with biallelic loss of NRXN1 in humans and double neurexin 1alpha/2alpha knockout mice have severe breathing abnormalities, corresponding to the respiratory phenotype of our patient.
| 6,371,743
|
NRXN1;21005
|
NRXN2;86984
|
c.2686C>T;tmVar:c|SUB|C|2686|T;HGVS:c.2686C>T;VariantGroup:1;CorrespondingGene:55777;RS#:796052777;CA#:316143
|
p.Arg1059Gln;tmVar:p|SUB|R|1059|Q;HGVS:p.R1059Q;VariantGroup:2;CorrespondingGene:9379;RS#:777033569;CA#:6078001
| 0no label
|
@GENE$ functions as a coreceptor that enhances VEGF/@GENE$ binding to stimulate VEGF signalling. In this case, both the TGF-beta and VEGF signalling pathways could be affected, potentially causing a more severe downstream effect than would occur with variants in only one of the pathways, with the mutations synergising to lead to BAVM. In patient AVM028, one novel heterozygous VUS (c.2207A>G [@VARIANT$]) in RASA1 inherited from the father and one likely pathogenic de novo novel heterozygous variant (c.311T>C [@VARIANT$]) in TIMP3 were identified (online supplementary table S2).
| 6,161,649
|
SCUBE2;36383
|
VEGFR2;55639
|
p.His736Arg;tmVar:p|SUB|H|736|R;HGVS:p.H736R;VariantGroup:6;CorrespondingGene:5921;RS#:1403332745
|
p.Leu104Pro;tmVar:p|SUB|L|104|P;HGVS:p.L104P;VariantGroup:7;CorrespondingGene:23592;RS#:1290872293
| 0no label
|
Results Cosegregating deleterious variants (GRCH37/hg19) in CACNA1A (NM_001127222.1: c.7261_7262delinsGT, p.Pro2421Val), REEP4 (NM_025232.3: @VARIANT$, p.Arg37Trp), TOR2A (NM_130459.3: @VARIANT$, p.Arg190Cys), and ATP2A3 (NM_005173.3: c.1966C>T, p.Arg656Cys) were identified in four independent multigenerational pedigrees. Deleterious variants in @GENE$ (NM_022460.3: c.94C>A, p.Gly32Cys) and GNA14 (NM_004297.3: c.989_990del, p.Thr330ArgfsTer67) were identified in a father and son with segmental cranio-cervical dystonia first manifest as BSP. Deleterious variants in DNAH17,TRPV4,CAPN11,@GENE$,UNC13B,SPTBN4,MYOD1, and MRPL15 were found in two or more independent pedigrees.
| 6,081,235
|
HS1BP3;10980
|
VPS13C;41188
|
c.109C>T;tmVar:c|SUB|C|109|T;HGVS:c.109C>T;VariantGroup:10;CorrespondingGene:80346;RS#:780399718;CA#:4663211
|
c.568C>T;tmVar:c|SUB|C|568|T;HGVS:c.568C>T;VariantGroup:12;CorrespondingGene:27433;RS#:376074923;CA#:5250615
| 0no label
|
Except for the SEMA7A gene variant [p.(@VARIANT$)], mutations identified in DUSP6, @GENE$, @GENE$, PLXNA1, and PROP1 genes were carried by HH1 family cases (HH1, HH1F, and HH1P) and involved in pathogenic digenic combinations with the DUSP6 gene variant [p.(@VARIANT$)].
| 8,446,458
|
ANOS1;55445
|
DCC;21081
|
Glu436Lys;tmVar:p|SUB|E|436|K;HGVS:p.E436K;VariantGroup:8;CorrespondingGene:54756;RS#:1411341050
|
Val114Leu;tmVar:p|SUB|V|114|L;HGVS:p.V114L;VariantGroup:5;CorrespondingGene:1848;RS#:2279574;CA#:6714072
| 0no label
|
Two different GJB3 mutations (N166S and A194T) occurring in compound heterozygosity with the 235delC and @VARIANT$ of @GENE$ were identified in three unrelated families (235delC/@VARIANT$, 235delC/A194T and 299delAT/A194T). Neither of these mutations in @GENE$ was detected in DNA from 200 unrelated Chinese controls.
| 2,737,700
|
GJB2;2975
|
Cx31;7338
|
299delAT;tmVar:c|DEL|299|AT;HGVS:c.299delAT;VariantGroup:12;CorrespondingGene:2706
|
N166S;tmVar:p|SUB|N|166|S;HGVS:p.N166S;VariantGroup:0;CorrespondingGene:2707;RS#:121908851;CA#:118311
| 0no label
|
Functional impact of the rare variants The two missense @GENE$ variants (@VARIANT$ and (p.(C498R)) and one of the PITX2 amino acid substitutions (p.(P179T)) were inferred to cause a moderate functional effect at least by one bioinformatic analysis and, experimentally, they were found to be associated with moderately disrupted transactivation. The functional impact of the second @GENE$ amino acid substitution, p.(A188T), could not be functionally evaluated due to DNA cloning difficulties. In fact, the two FOXC2 amino acid changes were found to be hypomorphic whereas the PITX2 amino acid substitution (@VARIANT$) behaved experimentally as a hypermorphic variant.
| 6,338,360
|
FOXC2;21091
|
PITX2;55454
|
p.(H395N);tmVar:p|SUB|H|395|N;HGVS:p.H395N;VariantGroup:8;CorrespondingGene:2303
|
p.(P179T);tmVar:p|SUB|P|179|T;HGVS:p.P179T;VariantGroup:3;CorrespondingGene:1545;RS#:771076928
| 0no label
|
Three rare missense variants (R2034Q, L2118V, and @VARIANT$) of the SPG11 gene were found. The high detection rate of missense variants of this gene is probably due to the large size of the coding region; therefore, we suggest that these SPG11 variants are unlikely to be deleterious. Variants in the @GENE$ gene are most commonly associated with autosomal recessive spastic paraplegia, although homozygous variants have been recently identified in juvenile ALS, and heterozygous missense variants in sALS. Variants in UBQLN2 have been shown to be a cause of dominant X-linked ALS. A previously reported (@VARIANT$,) and a novel variant (Q84H) were found in the UBQLN2 gene. The novel Q84H variant affects the N-terminal ubiquitin-like domain of the ubiquilin-2 protein, which is involved in binding to proteasome subunits. @GENE$ variants have been mostly detected in familial ALS cases that are localized within the C-terminus of the FUS protein.
| 6,707,335
|
SPG11;41614
|
FUS;2521
|
E2003D;tmVar:p|SUB|E|2003|D;HGVS:p.E2003D;VariantGroup:3;CorrespondingGene:80208;RS#:954483795
|
M392V;tmVar:p|SUB|M|392|V;HGVS:p.M392V;VariantGroup:17;CorrespondingGene:29978;RS#:104893941
| 0no label
|
The DNA sequencing chromatograms from the proband show two LRP6 and one @GENE$ heterozygous mutations. While both @GENE$ variants, p.(Ser127Thr) and p.(@VARIANT$), were inherited from her father, the WNT10A mutation, @VARIANT$ was maternally derived.
| 8,621,929
|
WNT10A;22525
|
LRP6;1747
|
Asn1075Ser;tmVar:p|SUB|N|1075|S;HGVS:p.N1075S;VariantGroup:8;CorrespondingGene:4040;RS#:202124188
|
p.(Glu167Gln);tmVar:p|SUB|E|167|Q;HGVS:p.E167Q;VariantGroup:5;CorrespondingGene:80326;RS#:148714379
| 0no label
|
The p.Ile312Met (c.936C>G) mutation in EDA and heterozygous @VARIANT$ (c.511C>T) mutation in WNT10A were detected. The coding sequence in exon 9 of EDA showed a C to G transition, which results in the substitution of @VARIANT$; also, the coding sequence in exon 3 of @GENE$ showed a C to T transition at nucleotide 511, which results in the substitution of Arg at residue 171 to Cys. Analyses of his parents' genome revealed that the mutant alleles were from his mother, who carried digenic heterozygous @GENE$ and WNT10A mutations at the same locus as that of N2 (Fig. 2B).
| 3,842,385
|
WNT10A;22525
|
EDA;1896
|
p.Arg171Cys;tmVar:p|SUB|R|171|C;HGVS:p.R171C;VariantGroup:3;CorrespondingGene:80326;RS#:116998555;CA#:2113955
|
Ile at residue 312 to Met;tmVar:p|SUB|I|312|M;HGVS:p.I312M;VariantGroup:7;CorrespondingGene:1896
| 0no label
|
Exome analysis for the proband identified three sequence variants in FTA candidate genes, two in LRP6 (g.27546T>A, @VARIANT$, p.Ser127Thr; g.124339A>G, c.3224A>G, p.Asn1075Ser) and one in @GENE$ (g.14574G>C, c.499G>C, @VARIANT$) (Figure 4A). The @GENE$ c.3224A>G mutation is a rare variant with an MAF of 0.0024 in EAS.
| 8,621,929
|
WNT10A;22525
|
LRP6;1747
|
c.379T>A;tmVar:c|SUB|T|379|A;HGVS:c.379T>A;VariantGroup:1;CorrespondingGene:4040;RS#:17848270;CA#:6455897
|
p.Glu167Gln;tmVar:p|SUB|E|167|Q;HGVS:p.E167Q;VariantGroup:5;CorrespondingGene:80326;RS#:148714379
| 0no label
|
c, d) Sequence chromatograms indicating the wild-type, homozygous affected and heterozygous carrier forms of c) the C to T transition at position c.229 changing the arginine residue to cysteine at position 77 of the @GENE$ protein (@VARIANT$; p.R77C) and d) the c.238-241delATTG (@VARIANT$) in S100A13. Mutation name is based on the full-length S100A3 (NM_002960) and @GENE$ (NM_001024210) transcripts.
| 6,637,284
|
S100A3;2223
|
S100A13;7523
|
c.229C>T;tmVar:c|SUB|C|229|T;HGVS:c.229C>T;VariantGroup:3;CorrespondingGene:6274;RS#:138355706;CA#:1116284
|
p.I80Gfs*13;tmVar:p|FS|I|80|G|13;HGVS:p.I80GfsX13;VariantGroup:7;CorrespondingGene:6284
| 0no label
|
A single SQSTM1 mutation (@VARIANT$) has been linked to MRV in one family and an unrelated patient. This patient was subsequently found to carry a coexisting @GENE$ variant (@VARIANT$, p.Asn357Ser) by Evila et al.. Evila et al.'s study reported also an additional sporadic MRV case carrying the same TIA1 variant but a different @GENE$ mutation (p.Pro392Leu), which is known to cause PDB, ALS, and FTD, but the patient's phenotype was not illustrated.
| 5,868,303
|
TIA1;20692
|
SQSTM1;31202
|
c.1165+1G>A;tmVar:c|SUB|G|1165+1|A;HGVS:c.1165+1G>A;VariantGroup:8;CorrespondingGene:8878;RS#:796051870(Expired)
|
c.1070A>G;tmVar:c|SUB|A|1070|G;HGVS:c.1070A>G;VariantGroup:5;CorrespondingGene:7072;RS#:116621885;CA#:1697407
| 0no label
|
Three patients carried missense variants both in FZD and other PCP-associated genes: 01F552 (@GENE$ @VARIANT$ and @GENE$ @VARIANT$), 335F07 (FZD6 c.544G>A and 2 FAT4 missense variants c.5792A>G; c.10384A>G), and 465F99 (rare FZD1 missense variant c.211C>T and a novel FAT4 missense variant c.10147G>A).
| 5,887,939
|
FZD6;2617
|
CELSR2;1078
|
c.1531C>T;tmVar:c|SUB|C|1531|T;HGVS:c.1531C>T;VariantGroup:29;CorrespondingGene:8323;RS#:151339003;CA#:129147
|
c.3800A>G;tmVar:c|SUB|A|3800|G;HGVS:c.3800A>G;VariantGroup:2;CorrespondingGene:1952;RS#:373263457;CA#:4677776
| 11
|
Variants in all known WS candidate genes (@GENE$, EDNRB, @GENE$, PAX3, SOX10, SNAI2, and TYRO3) were searched and a novel rare heterozygous deletion mutation (@VARIANT$; p.Asn322fs) was identified in the MITF gene in both patients. Moreover, heterozygous missense variants in SNAI3 (@VARIANT$; p.Arg203Cys) and TYRO3 (c.1037T>A; p.Ile346Asn) gene was identified in the exome data of both patients.
| 7,877,624
|
EDN3;88
|
MITF;4892
|
c.965delA;tmVar:c|DEL|965|A;HGVS:c.965delA;VariantGroup:4;CorrespondingGene:4286
|
c.607C>T;tmVar:c|SUB|C|607|T;HGVS:c.607C>T;VariantGroup:1;CorrespondingGene:333929;RS#:149676512;CA#:8229366
| 0no label
|
The nucleotide sequence showed a G to C transition at nucleotide 769 (@VARIANT$) of the coding sequence in exon 7 of EDA, which results in the substitution of Gly at residue 257 to Arg. Additionally, the nucleotide sequence showed a monoallelic C to T transition at nucleotide 511 (@VARIANT$) of the coding sequence in exon 3 of @GENE$, which results in the substitution of Arg at residue 171 to Cys. DNA sequencing of the parents' genome revealed that both mutant alleles were from their mother (Fig. 2A), who carried a heterozygous EDA mutation (c.769G>C) and a heterozygous WNT10A c.511C>T mutation, and showed absence of only the left upper lateral incisor without other clinical abnormalities. No mutations in these genes were found in the father. Sequence analyses of EDA and WNT10A genes. (A) The @GENE$ mutation c.769G>C and WNT10A mutation c.511C>T were found in patient N1, who inherited the mutant allele from his mother.
| 3,842,385
|
WNT10A;22525
|
EDA;1896
|
c.769G>C;tmVar:c|SUB|G|769|C;HGVS:c.769G>C;VariantGroup:0;CorrespondingGene:1896;RS#:1057517882;CA#:16043329
|
c.511C>T;tmVar:c|SUB|C|511|T;HGVS:c.511C>T;VariantGroup:3;CorrespondingGene:80326;RS#:116998555;CA#:2113955
| 0no label
|
(C) Sanger sequencing confirmed a homozygous in-frame deletion (@VARIANT$) in MYD88 gene and a homozygous splice-donor mutation (@VARIANT$) in CARD9 gene. (D) Western Blot of @GENE$ and @GENE$ proteins performed on PBMC, EBVB, and PHA derived T cell lines.
| 6,383,679
|
CARD9;14150
|
MYD88;1849
|
c.195_197delGGA;tmVar:p|DEL|195_197|G;HGVS:p.195_197delG;VariantGroup:2;CorrespondingGene:4615
|
c.1434+1G>C;tmVar:c|SUB|G|1434+1|C;HGVS:c.1434+1G>C;VariantGroup:0;CorrespondingGene:64170;RS#:141992399;CA#:500026
| 0no label
|
Results Cosegregating deleterious variants (GRCH37/hg19) in CACNA1A (NM_001127222.1: c.7261_7262delinsGT, p.Pro2421Val), REEP4 (NM_025232.3: c.109C>T, p.Arg37Trp), TOR2A (NM_130459.3: c.568C>T, @VARIANT$), and ATP2A3 (NM_005173.3: c.1966C>T, @VARIANT$) were identified in four independent multigenerational pedigrees. Deleterious variants in HS1BP3 (NM_022460.3: c.94C>A, p.Gly32Cys) and GNA14 (NM_004297.3: c.989_990del, p.Thr330ArgfsTer67) were identified in a father and son with segmental cranio-cervical dystonia first manifest as BSP. Deleterious variants in DNAH17,TRPV4,CAPN11,VPS13C,@GENE$,@GENE$,MYOD1, and MRPL15 were found in two or more independent pedigrees.
| 6,081,235
|
UNC13B;31376
|
SPTBN4;11879
|
p.Arg190Cys;tmVar:p|SUB|R|190|C;HGVS:p.R190C;VariantGroup:12;CorrespondingGene:27433;RS#:376074923;CA#:5250615
|
p.Arg656Cys;tmVar:p|SUB|R|656|C;HGVS:p.R656C;VariantGroup:21;CorrespondingGene:489;RS#:140404080;CA#:8297011
| 0no label
|
Two unrelated KS patients had heterozygous @GENE$ mutations and mutation in a second gene: NELF/KAL1 (c.757G>A; p.Ala253Thr of NELF and @VARIANT$; @VARIANT$ of KAL1) and NELF/TACR3 (c. 1160-13C>T of NELF and c.824G>A; p.Trp275X of @GENE$).
| 3,888,818
|
NELF;10648
|
TACR3;824
|
c.488_490delGTT;tmVar:p|DEL|488_490|V;HGVS:p.488_490delV;VariantGroup:8;CorrespondingGene:26012
|
p.Cys163del;tmVar:p|DEL|163|C;HGVS:p.163delC;VariantGroup:10;CorrespondingGene:3730
| 0no label
|
Interestingly, four of these @GENE$ mutations (p.E103D, @VARIANT$, p.Q214P, and p.G743A) co-occurred with three heterozygous mutations in another major PCG gene CYP1B1 (p.A115P, @VARIANT$, and p.R368H) in five families. The parents of these probands harbored either of the heterozygous TEK or @GENE$ alleles and were asymptomatic, indicating a potential digenic mode of inheritance.
| 5,953,556
|
TEK;397
|
CYP1B1;68035
|
p.I148T;tmVar:p|SUB|I|148|T;HGVS:p.I148T;VariantGroup:5;CorrespondingGene:7010;RS#:35969327;CA#:5015918
|
p.E229K;tmVar:p|SUB|E|229|K;HGVS:p.E229K;VariantGroup:8;CorrespondingGene:1545;RS#:57865060;CA#:145183
| 0no label
|
Consistently, internalization of EphA2 @VARIANT$ and EphA2 T511M with pendrin induced by ephrin-B2 but not ephrin-A1 was suppressed (Fig. 7b, c). On the other hand, the mutated forms of @GENE$ did not affect their ability to bind to pendrin (Fig. 7d). Discussion Proper and polarized localization of transporters in cells is essential for their function. Various previously identified pendrin mutations cause pendrin cytoplasmic localization. A subset of these mutations, such as H723R, are known to cause mis-folding of the protein, leading to accumulation in the endoplasmic reticulum. Low temperature incubation and salicylate treatment of cultured cells, which are thought to help with protein-folding processes, rescues the membrane localization of H723R. On the other hand, mis-localization of @GENE$ A372V from the plasma membrane is not restored by these treatments, suggesting these mutations may affect pendrin trafficking from the Golgi to the plasma membrane but not protein-folding. Here, we found that pendrin A372V, @VARIANT$, Q446R, and G672E did not bind to EphA2.
| 7,067,772
|
EphA2;20929
|
pendrin;20132
|
G355R;tmVar:p|SUB|G|355|R;HGVS:p.G355R;VariantGroup:4;CorrespondingGene:1969;RS#:370923409;CA#:625329
|
L445W;tmVar:p|SUB|L|445|W;HGVS:p.L445W;VariantGroup:0;CorrespondingGene:5172;RS#:111033307;CA#:253309
| 0no label
|
Only three variants were homozygous in three patients: (1) @GENE$: c.2779A>G (p.M927V) in one patient, (2) DUOX2:c.3329G>A (@VARIANT$) in one patient, and (3) @GENE$: @VARIANT$ (p.Y138X) in one patient.
| 6,098,846
|
DUOX2;9689
|
DUOXA2;57037
|
p.R1110Q;tmVar:p|SUB|R|1110|Q;HGVS:p.R1110Q;VariantGroup:22;CorrespondingGene:50506;RS#:368488511;CA#:7537915
|
c.413dupA;tmVar:c|DUP|413|A|;HGVS:c.413dupA;VariantGroup:19;CorrespondingGene:405753;RS#:1085307064
| 0no label
|
Five anencephaly cases carried rare or novel CELSR1 missense variants, three of whom carried additional rare potentially damaging PCP variants: 01F377 (CELSR1 c.6362G>A and PRICKLE4 c.730C>G), 2F07 (CELSR1 @VARIANT$ and @GENE$ c.1622C>T), 618F05 (CELSR1 c.8282C>T and @GENE$ @VARIANT$).
| 5,887,939
|
DVL3;20928
|
SCRIB;44228
|
c.8807C>T;tmVar:c|SUB|C|8807|T;HGVS:c.8807C>T;VariantGroup:24;CorrespondingGene:9620;RS#:201509338;CA#:10292625
|
c.3979G>A;tmVar:c|SUB|G|3979|A;HGVS:c.3979G>A;VariantGroup:31;CorrespondingGene:23513;RS#:201563528;CA#:4918429
| 0no label
|
We observed that in 5 PCG cases heterozygous CYP1B1 mutations (@VARIANT$, p.E229 K, and p.R368H) co-occurred with heterozygous TEK mutations (p.E103D, p.I148T, p.Q214P, and p.G743A) indicating a potential digenic inheritance (Fig. 1a). None of the normal controls carried both the heterozygous combinations of @GENE$ and TEK mutations. The @GENE$ Q214P and G743A alleles were absent in 1024 controls, whereas very low frequencies of heterozygous TEK E103D (0.005) and @VARIANT$ (0.016) alleles were found in the control population (Table 1).
| 5,953,556
|
CYP1B1;68035
|
TEK;397
|
p.A115P;tmVar:p|SUB|A|115|P;HGVS:p.A115P;VariantGroup:0;CorrespondingGene:1545;RS#:764338357;CA#:1620052
|
I148T;tmVar:p|SUB|I|148|T;HGVS:p.I148T;VariantGroup:5;CorrespondingGene:7010;RS#:35969327;CA#:5015918
| 0no label
|
(c) Sequencing chromatograms of the heterozygous mutation c.1787A>G (p.His596Arg) in SLC20A2. (d) Sequencing chromatograms of the heterozygous mutation c.317G>C (@VARIANT$) in @GENE$ Genomic DNA was extracted from peripheral blood, and the DNA sample of the proband was subjected to screen the known causative genes for PFBC. Surprisingly, we identified two missense mutations in the proband: NM_001257180.2, exon10, c.1787A>G, @VARIANT$ in @GENE$ (Figure 1c) and NM_002609.4, exon3, c.317G>C, p.Arg106Pro, rs544478083 in PDGFRB (Figure 1d).
| 8,172,206
|
PDGFRB;1960
|
SLC20A2;68531
|
p.Arg106Pro;tmVar:p|SUB|R|106|P;HGVS:p.R106P;VariantGroup:1;CorrespondingGene:5159;RS#:544478083
|
p.His596Arg;tmVar:p|SUB|H|596|R;HGVS:p.H596R;VariantGroup:2;CorrespondingGene:6575
| 0no label
|
Pathogenic effects of GBE1 @VARIANT$ and NDUFS8 I126V variants remain unknown. It is important to note that these variants changed amino acids that are highly conserved in species from human down to bacteria (data not shown). Because dominant mutations in RYR1 and CACNA1S are associated with MHS, we evaluated MH diagnostic test results from clinical history of these two subjects. Subject R302 was diagnosed as MH negative, so we ruled out a pathogenic role of the @GENE$ p.T4823 M variant in MH. Subject R462 was diagnosed as MHS, which appeared to correlate with CACNA1S @VARIANT$, previously reported in a single MHS subject. However, the frequency of this variant in the general population is about 20-fold higher than the frequencies of pathogenic CACNA1S variants associated with MHS. It is also important to note that the diagnostic test for MH has a high false-positive rate of 22%, which raises the possibility that MHS diagnosis in subject R462 may be false. Based on these results, we also ruled out a pathogenic role of the @GENE$ p. R498L variant in MH.
| 6,072,915
|
RYR1;68069
|
CACNA1S;37257
|
D413N;tmVar:p|SUB|D|413|N;HGVS:p.D413N;VariantGroup:8;CorrespondingGene:2632;RS#:752711257
|
p. R498L;tmVar:p|SUB|R|498|L;HGVS:p.R498L;VariantGroup:1;CorrespondingGene:779;RS#:150590855;CA#:78268
| 0no label
|
Variants in all known WS candidate genes (EDN3, EDNRB, MITF, PAX3, @GENE$, SNAI2, and @GENE$) were searched and a novel rare heterozygous deletion mutation (@VARIANT$; p.Asn322fs) was identified in the MITF gene in both patients. Moreover, heterozygous missense variants in SNAI3 (c.607C>T; p.Arg203Cys) and TYRO3 (@VARIANT$; p.Ile346Asn) gene was identified in the exome data of both patients.
| 7,877,624
|
SOX10;5055
|
TYRO3;4585
|
c.965delA;tmVar:c|DEL|965|A;HGVS:c.965delA;VariantGroup:4;CorrespondingGene:4286
|
c.1037T>A;tmVar:c|SUB|T|1037|A;HGVS:c.1037T>A;VariantGroup:2;CorrespondingGene:7301;RS#:12148316;CA#:7494886
| 0no label
|
Interestingly, four of these TEK mutations (p.E103D, p.I148T, p.Q214P, and @VARIANT$) co-occurred with three heterozygous mutations in another major PCG gene CYP1B1 (p.A115P, p.E229K, and p.R368H) in five families. The parents of these probands harbored either of the heterozygous TEK or CYP1B1 alleles and were asymptomatic, indicating a potential digenic mode of inheritance. Furthermore, we ascertained the interactions of TEK and CYP1B1 by co-transfection and pull-down assays in HEK293 cells. Ligand responsiveness of the wild-type and mutant TEK proteins was assessed in HUVECs using immunofluorescence analysis. We observed that recombinant TEK and @GENE$ proteins interact with each other, while the disease-associated allelic combinations of TEK (p.E103D)::CYP1B1 (p.A115P), TEK (p.Q214P)::CYP1B1 (@VARIANT$), and TEK (p.I148T)::CYP1B1 (p.R368H) exhibit perturbed interaction. The mutations also diminished the ability of TEK to respond to ligand stimulation, indicating perturbed @GENE$ signaling.
| 5,953,556
|
CYP1B1;68035
|
TEK;397
|
p.G743A;tmVar:p|SUB|G|743|A;HGVS:p.G743A;VariantGroup:12;CorrespondingGene:7010;RS#:202131936;CA#:5016449
|
p.E229K;tmVar:p|SUB|E|229|K;HGVS:p.E229K;VariantGroup:8;CorrespondingGene:1545;RS#:57865060;CA#:145183
| 0no label
|
Both homozygous and compound heterozygous variants in the @GENE$ gene have been described as causative for juvenile ALS. The G1177X nonsense variant was first detected in compound heterozygous form in a family with two affected siblings suffering from infantile ascending spastic paralysis with bulbar involvement. The ages of onset of the patients with the ALS2 variants reported in this study were later than juvenile ALS onset, which generally manifests before 25 years of age. Previous studies suggested that heterozygous variants in the ALS2 may be causative for adult-onset sALS. MATR3 encodes three protein isoforms that have been described as nuclear-matrix and DNA/RNA binding proteins involved in transcription and stabilization of mRNA. In the present study, two novel heterozygous variants (P11S, @VARIANT$) were detected. The P11S variant affects the b isoform of the @GENE$ protein (NM_001194956 and NP_001181885), contributing to splicing alteration of other isoforms. Further evidence is required to elucidate the mechanism of pathogenicity of these alterations. We discovered several variants in ALS candidate and risk genes. In a patient with LMN-dominant ALS with slow progression, we found two novel variants (T2583I and @VARIANT$) in the DYNC1H1 gene.
| 6,707,335
|
ALS2;23264
|
MATR3;7830
|
S275N;tmVar:p|SUB|S|275|N;HGVS:p.S275N;VariantGroup:9;CorrespondingGene:80208;RS#:995711809
|
G4290R;tmVar:p|SUB|G|4290|R;HGVS:p.G4290R;VariantGroup:27;CorrespondingGene:1778;RS#:748643448;CA#:7354051
| 0no label
|
One heterozygous @GENE$ splice mutation (@VARIANT$) has been described. However, the only KS individual within the family also had a heterozygous @GENE$ mutation (@VARIANT$), suggesting digenic disease.
| 3,888,818
|
NELF;10648
|
FGFR1;69065
|
c.1159-14_22del;tmVar:c|DEL|1159-14_22|;HGVS:c.1159-14_22del;VariantGroup:12;CorrespondingGene:26012
|
p.Leu342Ser;tmVar:p|SUB|L|342|S;HGVS:p.L342S;VariantGroup:2;CorrespondingGene:2260;RS#:121909638;CA#:130218
| 11
|
None of 2,504 self-declared healthy individuals in TGP has both @GENE$, @VARIANT$ (p.Asn357Ser) and @GENE$, c.1175C > T (p.Pro392Leu). No other pathogenic or suspected pathogenic variants in genes associated with muscle diseases were identified in the proband of family 2 by expanded NGS panel studies or in the proband of family 1 by WES analysis. We are aware of a prior study in which this SQSTM1 mutation may be part of a common founder haplotype including the following four loci: [Chr5: 179260153C/T, refSNP ID rs4935; Chr5: 179260213G/A, @VARIANT$; Chr5: 179264731T/C, rs10277; Ch5: 179264915G/T, rs1065154 ].
| 5,868,303
|
TIA1;20692
|
SQSTM1;31202
|
c.1070A > G;tmVar:c|SUB|A|1070|G;HGVS:c.1070A>G;VariantGroup:5;CorrespondingGene:7072;RS#:116621885;CA#:1697407
|
rs4797;tmVar:rs4797;VariantGroup:0;CorrespondingGene:8878;RS#:4797
| 0no label
|
Variant analysis and incidental findings Of the 19 variants identified in this study, four were previously reported as pathogenic disease causing variants: 1) GBE1 R524Ter; 2) PCCB G407RfrTer14; 3) NUBPL IVS8DC; 4) @GENE$ Y299Ter. Two additional variants, @VARIANT$ in @GENE$ and @VARIANT$ in CACNA1S, were also previously reported in association with Core myopathy and Malignant Hyperthermia Susceptibility (MHS), respectively.
| 6,072,915
|
OAT;231
|
RYR1;68069
|
p. T4823 M;tmVar:p|SUB|T|4823|M;HGVS:p.T4823M;VariantGroup:3;CorrespondingGene:6261;RS#:148540135;CA#:24146
|
p. R498L;tmVar:p|SUB|R|498|L;HGVS:p.R498L;VariantGroup:1;CorrespondingGene:779;RS#:150590855;CA#:78268
| 0no label
|
This analysis indicated that the @GENE$ variant c.1663G>A (rs138172448), which results in a @VARIANT$ change, and the @GENE$ gene variant c.656C>T (@VARIANT$), which results in a p.Thr219Ile change, are both predicted to be damaging.
| 6,180,278
|
CAPN3;52
|
DES;56469
|
p.Val555Ile;tmVar:p|SUB|V|555|I;HGVS:p.V555I;VariantGroup:2;CorrespondingGene:825;RS#:138172448;CA#:7511461
|
rs144901249;tmVar:rs144901249;VariantGroup:3;CorrespondingGene:1674;RS#:144901249
| 0no label
|
Variants in all known WS candidate genes (EDN3, EDNRB, @GENE$, PAX3, @GENE$, SNAI2, and TYRO3) were searched and a novel rare heterozygous deletion mutation (c.965delA; @VARIANT$) was identified in the MITF gene in both patients. Moreover, heterozygous missense variants in SNAI3 (@VARIANT$; p.Arg203Cys) and TYRO3 (c.1037T>A; p.Ile346Asn) gene was identified in the exome data of both patients.
| 7,877,624
|
MITF;4892
|
SOX10;5055
|
p.Asn322fs;tmVar:p|FS|N|322||;HGVS:p.N322fsX;VariantGroup:3;CorrespondingGene:4286
|
c.607C>T;tmVar:c|SUB|C|607|T;HGVS:c.607C>T;VariantGroup:1;CorrespondingGene:333929;RS#:149676512;CA#:8229366
| 0no label
|
The ages of onset of the patients with the @GENE$ variants reported in this study were later than juvenile ALS onset, which generally manifests before 25 years of age. Previous studies suggested that heterozygous variants in the ALS2 may be causative for adult-onset sALS. MATR3 encodes three protein isoforms that have been described as nuclear-matrix and DNA/RNA binding proteins involved in transcription and stabilization of mRNA. In the present study, two novel heterozygous variants (P11S, @VARIANT$) were detected. The P11S variant affects the b isoform of the @GENE$ protein (NM_001194956 and NP_001181885), contributing to splicing alteration of other isoforms. Further evidence is required to elucidate the mechanism of pathogenicity of these alterations. We discovered several variants in ALS candidate and risk genes. In a patient with LMN-dominant ALS with slow progression, we found two novel variants (T2583I and @VARIANT$) in the DYNC1H1 gene.
| 6,707,335
|
ALS2;23264
|
MATR3;7830
|
S275N;tmVar:p|SUB|S|275|N;HGVS:p.S275N;VariantGroup:9;CorrespondingGene:80208;RS#:995711809
|
G4290R;tmVar:p|SUB|G|4290|R;HGVS:p.G4290R;VariantGroup:27;CorrespondingGene:1778;RS#:748643448;CA#:7354051
| 0no label
|
We observed that isoproterenol could enhance the activity of LTCC in the HEK293T cells, which may be associated with the evocation of @GENE$/protein kinase A pathways by the activation of the endogenous beta2 adrenoreceptors. In summary, we investigated an extremely rare large ERS family with a high incidence of nocturnal SCD, in which we found a pathogenic mutation in @GENE$ (@VARIANT$) with loss-of-function. The penetrance was also incomplete, which was modified by a gain-of-functional SCN5A-@VARIANT$ variant and sex.
| 5,426,766
|
cAMP;110678
|
CACNA1C;55484
|
p.Q1916R;tmVar:p|SUB|Q|1916|R;HGVS:p.Q1916R;VariantGroup:4;CorrespondingGene:775;RS#:186867242;CA#:6389963
|
R1193Q;tmVar:p|SUB|R|1193|Q;HGVS:p.R1193Q;VariantGroup:7;CorrespondingGene:6331;RS#:41261344;CA#:17287
| 0no label
|
Five anencephaly cases carried rare or novel CELSR1 missense variants, three of whom carried additional rare potentially damaging PCP variants: 01F377 (CELSR1 c.6362G>A and PRICKLE4 @VARIANT$), 2F07 (CELSR1 @VARIANT$ and DVL3 c.1622C>T), 618F05 (CELSR1 c.8282C>T and SCRIB c.3979G>A). One patient (f93-80) had a novel PTK7 missense variant (c.655A>G) with a rare CELSR2 missense variant (c.1892C>T). Three patients carried missense variants both in FZD and other PCP-associated genes: 01F552 (@GENE$ c.1531C>T and CELSR2 c.3800A>G), 335F07 (FZD6 c.544G>A and 2 @GENE$ missense variants c.5792A>G; c.10384A>G), and 465F99 (rare FZD1 missense variant c.211C>T and a novel FAT4 missense variant c.10147G>A).
| 5,887,939
|
FZD6;2617
|
FAT4;14377
|
c.730C>G;tmVar:c|SUB|C|730|G;HGVS:c.730C>G;VariantGroup:12;CorrespondingGene:29964;RS#:141478229;CA#:3802865
|
c.8807C>T;tmVar:c|SUB|C|8807|T;HGVS:c.8807C>T;VariantGroup:24;CorrespondingGene:9620;RS#:201509338;CA#:10292625
| 0no label
|
These facts suggest an essential role of these amino acids on @GENE$ function that might be conserved throughout evolution. To examine whether these mutations affect the ligand-binding specificity of EphA2 to ephrin-A and ephrin-B, a pull down assay was performed with HEK293T cells due to their low level of endogenous EphA2 expression (Supplementary Fig 7a, b). While tagged versions of EphA2 G355R and EphA2 @VARIANT$ were effectively precipitated with Fc-fusion ephrin-A1 compared to EphA2 WT, Fc-fusion ephrin-B2 failed to pull down EphA2 G355R and T511M (Fig. 7a). Consistently, internalization of EphA2 G355R and EphA2 T511M with pendrin induced by @GENE$ but not ephrin-A1 was suppressed (Fig. 7b, c). On the other hand, the mutated forms of EphA2 did not affect their ability to bind to pendrin (Fig. 7d). Discussion Proper and polarized localization of transporters in cells is essential for their function. Various previously identified pendrin mutations cause pendrin cytoplasmic localization. A subset of these mutations, such as @VARIANT$, are known to cause mis-folding of the protein, leading to accumulation in the endoplasmic reticulum.
| 7,067,772
|
Eph;20936
|
ephrin-B2;3019
|
T511M;tmVar:p|SUB|T|511|M;HGVS:p.T511M;VariantGroup:5;CorrespondingGene:1969;RS#:55747232;CA#:625151
|
H723R;tmVar:p|SUB|H|723|R;HGVS:p.H723R;VariantGroup:10;CorrespondingGene:5172;RS#:121908362;CA#:253307
| 0no label
|
DISCUSSION We present a Chinese family with PFBC in which the previously reported heterozygous mutation c.1787A>G (@VARIANT$) in @GENE$ and the SNP (rs544478083) c.317G>C (@VARIANT$) in @GENE$ were identified.
| 8,172,206
|
SLC20A2;68531
|
PDGFRB;1960
|
p.His596Arg;tmVar:p|SUB|H|596|R;HGVS:p.H596R;VariantGroup:2;CorrespondingGene:6575
|
p.Arg106Pro;tmVar:p|SUB|R|106|P;HGVS:p.R106P;VariantGroup:1;CorrespondingGene:5159;RS#:544478083
| 11
|
A complete loss of this trans-activational activity was noted for the proteins with missense mutations located in the LBD (p.His310Asp and p.Asp364Tyr), the SF1 @VARIANT$, as well as both frame-shift mutations assayed (p.Arg89Glyfs*17 and p.Leu209Cysfs*87) (Figure 3). Intriguingly, a nonsense SF1 variant (p.[@VARIANT$;Tyr211*]) seemed to retain a low level of activity (Figure 3). A similar pattern was seen with the SRY/@GENE$ transfected cells; however, the magnitude of activation was in general lower than that of the SOX9/SF1 transfection (Figure 3). All the SF1 variants identified in our DSD patients showed reduced transactivation activity in vitro when co-transfected with SRY or @GENE$. This suggests that the reason these variants are pathogenic is because they result in a dramatic reduction or loss of SF1 transactivation activity in these patients.
| 5,765,430
|
SF1;138518
|
SOX9;294
|
p.47_54del;tmVar:p|DEL|47_54|;HGVS:p.47_54del;VariantGroup:30;CorrespondingGene:2516
|
Pro210Gln;tmVar:p|SUB|P|210|Q;HGVS:p.P210Q;VariantGroup:5;CorrespondingGene:2626;RS#:575307727;CA#:4630899
| 0no label
|
Recurrent Variants Identified in Our Regressive Autism Cohort In our sequenced cohort of 134 individuals with autism and regression, we identified two recurrent variants, GRIN2A @VARIANT$ (p.Leu10Met) and @GENE$ c.742C > T (@VARIANT$). The variant in @GENE$ was novel and was predicted to be damaging using both SIFT and PolyPhen.
| 7,463,850
|
PLXNB2;66630
|
GRIN2A;645
|
c.28C > A;tmVar:c|SUB|C|28|A;HGVS:c.28C>A;VariantGroup:0;CorrespondingGene:2903
|
p.Arg248Cys;tmVar:p|SUB|R|248|C;HGVS:p.R248C;VariantGroup:9;CorrespondingGene:23654;RS#:779647430;CA#:10313520
| 0no label
|
It has been reported that @GENE$ localises to the basal body and the proximal regions of the cilium, a non-motile microtubule-based organelle that projects from the cell surface. Since TTC26 is an intraflagellar transport (IFT) protein in cilia, we aimed to identify potential interactions between FLNB and TTC26. Using coimmunoprecipitation assays, we found that the myc-tagged mutant p.R50C and @VARIANT$ @GENE$ proteins pulled down the Flag-tagged mutant @VARIANT$ and p.R566L FLNB proteins, respectively (figure 2D, E).
| 7,279,190
|
FLNB;37480
|
TTC26;11786
|
p.R197C;tmVar:p|SUB|R|197|C;HGVS:p.R197C;VariantGroup:32;CorrespondingGene:79989
|
p.A2282T;tmVar:p|SUB|A|2282|T;HGVS:p.A2282T;VariantGroup:6;CorrespondingGene:2317;RS#:1339176246
| 0no label
|
Analysis of the proband's exome revealed four potential disease-causing mutations in FTA candidate genes: three heterozygous missense variants in @GENE$ (g.68531T>G, c.503T>G, p.Met168Arg; g.112084C>G, @VARIANT$, p.Ser817Cys; g.146466A>G, c.4333A>G, p.Met1445Val) and one in @GENE$ (@VARIANT$, c.637G>A, p.Gly213Ser) (Figure 2A and Figure S2A,B).
| 8,621,929
|
LRP6;1747
|
WNT10A;22525
|
c.2450C>G;tmVar:c|SUB|C|2450|G;HGVS:c.2450C>G;VariantGroup:2;CorrespondingGene:4040;RS#:2302686;CA#:6455462
|
g.14712G>A;tmVar:g|SUB|G|14712|A;HGVS:g.14712G>A;VariantGroup:7;CorrespondingGene:80326;RS#:147680216;CA#:211313
| 11
|
The proband (arrow, II.2) is heterozygous for both the @GENE$ T168fsX191 and TNFRSF13B/@GENE$ @VARIANT$ mutations. Other family members who have inherited TCF3 @VARIANT$ and TNFRSF13B/TACI C104R mutations are shown.
| 5,671,988
|
TCF3;2408
|
TACI;49320
|
C104R;tmVar:p|SUB|C|104|R;HGVS:p.C104R;VariantGroup:2;CorrespondingGene:23495;RS#:34557412;CA#:117387
|
T168fsX191;tmVar:p|FS|T|168||191;HGVS:p.T168fsX191;VariantGroup:1;CorrespondingGene:6929
| 0no label
|
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