rs199473394
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PP3_StrongPP5_Very_Strong
The NM_000218.3(KCNQ1):c.535G>A(p.Gly179Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,612,422 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_000218.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| KCNQ1 | ENST00000155840.12 | c.535G>A | p.Gly179Ser | missense_variant | Exon 3 of 16 | 1 | NM_000218.3 | ENSP00000155840.2 | ||
| KCNQ1 | ENST00000335475.6 | c.154G>A | p.Gly52Ser | missense_variant | Exon 3 of 16 | 1 | ENSP00000334497.5 | |||
| KCNQ1 | ENST00000496887.7 | c.274G>A | p.Gly92Ser | missense_variant | Exon 4 of 16 | 5 | ENSP00000434560.2 | |||
| KCNQ1 | ENST00000646564.2 | c.478-12750G>A | intron_variant | Intron 2 of 10 | ENSP00000495806.2 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460218Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726498
GnomAD4 genome 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74346
ClinVar
Submissions by phenotype
Long QT syndrome 1 Pathogenic:4
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Long QT syndrome Pathogenic:2Benign:1Other:1
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Variant interpreted as Pathogenic and reported on 07-18-2019 by Lab or GTR ID 26957. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR ) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator John Constantino MD PhD from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. -
This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 179 of the KCNQ1 protein (p.Gly179Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with long QT syndrome (LQTS) (PMID: 10973849, 15051636, 23392653, 27041150, 27831900, 28944242). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 53063). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on KCNQ1 protein function. Experimental studies have shown that this missense change affects KCNQ1 function (PMID: 15051636, 29532034). For these reasons, this variant has been classified as Pathogenic. -
The c.535G>A (p.Gly179Ser) variant in the KCNQ1 gene has been identified in heterozygous status in at least eight individuals affected with Long QT syndrome (LQTS) (PMID:10973849, 25845942, 27831900, 28438721, 19716085, 26318259, 26669661). This variant has also been reported in bi-allelic status in several (thirteen) families affected with Long QT syndrome (PMID: 27485560, 27041150,15051636, 28944242, 28438721, 28606196, 29684900, 23392653, 29033053), and found to segregate with disease in at least three families (PMID: 28944242, 28438721, 15051636). Homozygous and compound heterozygous individuals typically display more pronounced prolongation of the QT interval compared with heterozygous relatives who are often clinically asymptomatic or with modestly prolonged QT interval, suggesting incomplete penetrance and variable expressivity for the autosomal dominant form of LQTS associated with this variant. In vitro functional studies on HEK293 cells and X. laevis oocytes have shown that this variant exerts dominant negative effect on wild type protein and reduce cell surface expression, trafficking defects and severely low channel current (PMID: 29532034, 15051636). In-silico computational prediction tools suggest that the p.Gly179Ser variant may have deleterious effect on the protein function (REVEL score: 0.931). This variant is found to be absent in the general population database (gnomAD) and interpreted as pathogenic by several submitters in the ClinVar database (ClinVar ID: 53063). Other missense substitutions affecting the same codon (p.Gly179Ala, p.Gly179Arg) have been interpreted as likely pathogenic by two ClinVar submitters (ClinVar ID: 2446426, 378906). Therefore, the c.535G>A (p.Gly179Ser) variant in the KCNQ1 gene is classified as pathogenic. -
not provided Pathogenic:3
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; In vitro functional studies demonstrate loss of function with a trafficking defect and severely reduced cell surface expression (Huang et al., 2018); This variant is associated with the following publications: (PMID: 34505893, 25637381, 15051636, 25845942, 19716085, 23392653, 25935074, 27041150, 28944242, 28438721, 28606196, 29684900, 30571187, 10973849, 27485560, 29021305, 31785541, 31447099, 32383558, 27831900, 29532034) -
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KCNQ1: PP1:Strong, PM1, PM2, PM5, PS4:Moderate, PS3:Supporting -
Congenital long QT syndrome Pathogenic:1Other:1
This variant has been reported as associated with Long QT syndrome in the following publications (PMID:10973849;PMID:15051636;PMID:19716085). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory. -
The p.Gly179Ser variant in KCNQ1 has been reported in the heterozygous state in at least 3 individuals with autosomal dominant long QT syndrome (LQTS), one of whom had a more severe phenotype and carried a presumed pathogenic variant in another LQTS gene (Splawski 2000, Kapplinger 2009, Fernandes 2015, Natarajan 2016). It has also been reported in the homozygous or compound heterozygous state in 4 individuals with severe autosomal recessive LQTS (AR-LQTS) and segregated with AR-LQTS in 3 affected relatives from 2 families (Westenskow 2004, Giudicessi 2013, Vyas 2016, Bdier 2017). Individuals with AR-LQTS typically had a more severe phenotype with an earlier age of onset than heterozygotes, but none were reported to have hearing loss. Relatives of these individuals who were heterozygous carriers of this variant were often clinically asymptomatic or had modestly prolonged QT interval; however 1 heterozygous carrier experienced sudden cardiac death (Westenskow 2004, Giudicessi 2013, Bdier 2017), suggesting reduced penetrance and variable expressivity for the autosomal dominant form of LQTS associated with this variant. In vitro functional studies and computational prediction tools support an impact on protein function (Westenskow 2004, Huang 2018). This variant has been reported by other clinical laboratories in ClinVar (Variation ID 53063) and was absent from large population studies. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant and autosomal recessive LQTS. ACMG/AMP Criteria applied: PM3_Strong, PM2, PP1_Moderate, PP3, PS3_Supporting, PS4_Supporting. -
KCNQ1-related disorder Pathogenic:1
The KCNQ1 c.535G>A variant is predicted to result in the amino acid substitution p.Gly179Ser. This variant has been reported in the heterozygous, compound heterozygous, and homozygous states in individuals and families with long QT syndrome, although heterozygous carriers have been described as asymptomatic (see, for example, Splawski et al. 2000. PubMed ID: 10973849; Westenskow et al. 2004. PubMed ID: 15051636; Al-Hassnan et al. 2017. PubMed ID: 28438721; Table S1, Westphal et al. 2020. PubMed ID: 32383558; Table S1, Schwartz et al. 2021. PubMed ID: 34505893). In vitro functional studies suggest this variant impacts protein function (Westenskow et al. 2004. PubMed ID: 15051636; Huang et al. 2018. PubMed ID: 29532034). This variant has not been reported in a large population database, indicating it is rare. This variant is interpreted as pathogenic. -
Cardiovascular phenotype Pathogenic:1
The p.G179S pathogenic mutation (also known as c.535G>A), located in coding exon 3 of the KCNQ1 gene, results from a G to A substitution at nucleotide position 535. The glycine at codon 179 is replaced by serine, an amino acid with similar properties. This alteration has been detected in the heterozygous, homozygous, and compound heterozygous state in numerous unrelated individuals with long QT syndrome (LQTS) (Splawski I, Circulation 2000 Sep; 102(10):1178-85; Kapplinger JD, Heart Rhythm 2009 Sep; 6(9):1297-303; Anderson HN, Pediatr Cardiol 2015 Oct; 36(7):1350-6; Fernandes M et al. Rev Port Cardiol, 2015 May;34:359.e1-5; Natarajan P et al. Sci Transl Med, 2016 11;8:364ra151; Al-Hassnan ZN et al. Heart Rhythm, 2017 08;14:1191-1199). The alteration has been reported to segregate with disease in multiple families, with homozygous and compound heterozygous individuals typically displaying more pronounced prolongation of the QT interval compared with heterozygous relatives (Westenskow P et al. Circulation, 2004 Apr;109:1834-41; Giudicessi JR et al. Circ Cardiovasc Genet, 2013 Apr;6:193-200; Vyas B et al. Am. J. Med. Genet. A, 2016 06;170:1510-9; Bdier AY et al. Mol Genet Genomic Med, 2017 Sep;5:592-601). Several functional studies indicate that this alteration results in a trafficking defect and reduced potassium current in heterologous expression systems (Westenskow P et al. Circulation, 2004 Apr;109:1834-41; Huang H et al. Sci Adv, 2018 03;4:eaar2631). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Cardiac arrhythmia Pathogenic:1
This missense variant replaces glycine with serine at codon 179 in the cytoplasmic linker region between transmembrane domains S2 and S3 of the KCNQ1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that this variant causes protein trafficking defect and results in significantly reduced cell surface expression and channel current (PMID: 15051636, 29532034), as well as dominant negative effect on the wild type protein (PMID: 29532034). This variant has been reported in over ten heterozygous and biallelic individuals affected with long QT syndrome (PMID: 10973849, 15051636, 23392653, 25845942, 27041150, 27831900, 28606196, 28438721, 28944242, 29684900; Color data). Biallelic individuals showed severe long QT syndrome without hearing loss (PMID: 23392653, 27041150, 28944242, 29684900). This variant has been shown to cosegregate with long QT phenotype in multiple families (PMID: 15051636, 23392653, 28438721; Color data). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at