Submissions for variant NM_000218.3(KCNQ1):c.1031C>T (p.Ala344Val)

gnomAD frequency: 0.00001  dbSNP: rs199472763

Total submissions: 12

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000223824	SCV000234461	pathogenic	not provided	2022-05-17	criteria provided, single submitter	clinical testing	Not observed in large population cohorts (gnomAD); Published functional studies demonstrate a damaging effect on KCNQ1 channel function (Siebrands et al., 2006); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 15840476, 19716085, 29444113, 16931984, 12388934, 22095730, 15466642, 9386136, 17470695, 28944242, 9570196, 29033053, 31589614, 28438721, 31737537, 34505893)
Labcorp Genetics (formerly Invitae), Labcorp	RCV001384422	SCV001583910	pathogenic	Long QT syndrome	2024-01-22	criteria provided, single submitter	clinical testing	This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 344 of the KCNQ1 protein (p.Ala344Val). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with long QT syndrome (PMID: 9386136, 16922724, 17088455, 17470695, 19490272, 24217263). ClinVar contains an entry for this variant (Variation ID: 52936). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects KCNQ1 function (PMID: 16931984). For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics	RCV002381340	SCV002699821	pathogenic	Cardiovascular phenotype	2022-07-13	criteria provided, single submitter	clinical testing	The p.A344V pathogenic mutation (also known as c.1031C>T), located in coding exon 7 of the KCNQ1 gene, results from a C to T substitution at nucleotide position 1031. The alanine at codon 344 is replaced by valine, an amino acid with similar properties. This alteration has been reported in the heterozygous state in several individuals from multiple long QT syndrome (LQTS) cohorts (Donger C et al. Circulation. 1997;96(9):2778-81; Choi G et al. Circulation. 2004;110(15):2119-24; Shimizu W et al. J. Am. Coll. Cardiol. 2004;44:117-25; Tester DJ et al. Heart Rhythm. 2005;2(5):507-17; Millat G et al. Clin. Genet. 2006;70(3):214-27; Moss AJ et al. Circulation. 2007;115(19):2481-9; Kapplinger JD et al. Heart Rhythm. 2009;6(9):1297-303; Schwartz PJ et al. Eur Heart J. 2021 12;42(46):4743-4755). This variant has also been detected in the homozygous state in several individuals with severe LQTS phenotypes reminiscent of the recessive Jervell and Lange-Nielsen syndrome (JLNS) but without hearing loss (Al-Hassnan ZN et al. Heart Rhythm. 2017;epub; Bdier AT et al. Mol Gen & Gen Med. 2017:epub). Reportedly unaffected/asymptomatic heterozygous carriers of this variant have also been detected, suggesting it may result in a mild phenotype and/or exhibit reduced penetrance in the heterozygous state in some cases (Al-Hassnan ZN et al. Heart Rhythm. 2017;epub; Schwartz PJ et al. Eur Heart J. 2021 12;42(46):4743-4755). Several in vitro assays indicate this variant impacts ion channel function (Siebrands CC et al. Anesthesiology. 2006 Sep;105(3):511-20; Heijman J et al. Circ. Res. 2012 Jan;110(2):211-9; Schwartz PJ et al. Eur Heart J. 2021 12;42(46):4743-4755). Based on internal structural analysis, this variant is predicted to disturb a functionally important motif (Sun J et al. Cell. 2020 01;180(2):340-347.e9; Sun J et al. Cell. 2017 Jun;169(6):1042-1050.e9; Ambry internal data). 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.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV002470738	SCV002766702	pathogenic	Long QT syndrome 1	2020-06-11	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as Pathogenic. Following criteria are met: 0103 - Both loss- and gain-of-function are known mechanisms of disease for this gene (PMID: 19632626). (N) 0104 - Dominant Negative is a mechanism of disease for this gene. Long QT syndrome has been associated with variants resulting in both loss-of-function and dominant negative effects (PMID: 19632626). (N) 0108 - This gene is known to be associated with both recessive and dominant disease. Long QT syndrome is caused predominantly by heterozygous pathogenic variants (OMIM). (N) 0200 - Variant is predicted to result in a missense amino acid change from an alanine to a valine (exon 7). (N) 0251 - Variant is heterozygous. (N) 0302 - Variant is present in gnomAD <0.001 for a dominant condition (1 heterozygote, 0 homozygotes). (P) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (N) 0600 - Variant is located in an annotated domain or motif (S6 transmembrane helix of the ion transport domain; NCBI, PDB, Decipher, PMID: 10508236). (N) 0703 - Comparable variants have moderate previous evidence for pathogenicity. At least two different variants in the same codon resulting in a change to a threonine and a glycine have been reported as likely pathogenic (ClinVar). (P) 0801 - Strong previous evidence of pathogenicity in unrelated individuals. This variant has been has described as a mild variant and has been previously reported as pathogenic in multiple patients with long QT syndrome (ClinVar, LOVD, PMID: 10508236, PMID: 28944242). (P) 1002 - Moderate functional evidence supporting abnormal protein function. Studies show that this variant induces voltage-dependent inactivation in KCNQ1 channels and shifts the voltage dependence of KCNQ1/KCNE1 complex activation (PMID: 16931984). (P) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign
Dept of Medical Biology, Uskudar University	RCV001384422	SCV004022055	pathogenic	Long QT syndrome	2024-01-08	criteria provided, single submitter	research	Criteria: PS4_Strong, PS3_Moderate, PM1, PM2, PP3
Molecular Genetics Laboratory - Cardiogenetics, CHU de Nantes	RCV002470738	SCV004024168	pathogenic	Long QT syndrome 1	2023-08-01	criteria provided, single submitter	clinical testing
New York Genome Center	RCV002470738	SCV004176139	pathogenic	Long QT syndrome 1	2023-08-11	criteria provided, single submitter	clinical testing	The c.1031C>T variant in KCNQ1 has previously been reported in individuals with long QT syndrome (PMID: 9386136, 28944242, 31737537, 34505893) and it has been deposited in ClinVar [ClinVar ID: 52936] as Pathogenic by multiple submitters with affected status provided. The c.1031C>T variant is observed in 1 allele (~0.00017% minor allele frequency with 0 homozygote) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8, All of Us), suggesting it is not a common benign variant in the populations represented in those databases. The c.1031C>T variant in KCNQ1 is located in exon 7 of this 16-exon gene and is predicted to replace an evolutionarily conserved alanine amino acid with valine at position 344 (p.(Ala344Val) in the ion transport domain of the encoded protein [UniProt ID: P51787]. Functional studies demonstrated loss of potassium channel function (PMID: 34505893). Different missense variants affecting the same aminoacid residue (p.Ala344) and neighbouring residues within the S segment have been reported in individuals with long QT syndrome in the literature [PMID: 28349240]. Based on available evidence this c.1031C>T p.(Ala344Val) variant identified in KCNQ1 is classified as Pathogenic.
Color Diagnostics, LLC DBA Color Health	RCV003591636	SCV004358402	pathogenic	Cardiac arrhythmia	2023-10-03	criteria provided, single submitter	clinical testing	This missense variant replaces alanine with valine at codon 344 of the KCNQ1 protein. This variant is found within a highly conserved region in transmembrane domain S6 (a.a. 328-348). Rare non-truncating variants in this region have been shown to be significantly overrepresented in individuals with long QT syndrome (PMID: 32893267). Functional studies have shown that this variant affects gating properties and increases channel sensitivity to anesthetics (PMID: 16931984, 32015334 ). This variant has been reported in heterozygous state in over ten unrelated individuals affected with long QT syndrome (PMID: 9386136, 15840476, 19716085, 20851114, 24217263, 26669661, 27920829, 32298319, 32893267, 34505893, 34884666) and in homozygous state in at least three individuals affected with severe long QT syndrome without hearing loss (PMID: 28438721, 28944242). This variant has been report to be a de novo occurrence in a child with severe long QT syndrome in compound heterozygous state with p.Ala300Thr variant in the same gene (PMID: 34884666). This variant has also been observed in over twenty unaffected heterozygous individuals (PMID: 9386136, 28438721, 28944242, 34505893). 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.
All of Us Research Program, National Institutes of Health	RCV001384422	SCV004829732	pathogenic	Long QT syndrome	2023-08-16	criteria provided, single submitter	clinical testing	This variant has been reported in multiple individuals with long QT syndrome (PMID: 9386136, 15466642, 15840476, 19716085, 9570196, 17470695, 32893267, 36102233). This variant is absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). This variant is located in a well-established functional domain of the protein where other pathogenic or likely pathogenic variants have been described (PMID: 19716085). It is predicted to be deleterious by in silico analysis. Functional studies suggest that this variant results in a deleterious effect on the protein (PMID: 16931984).
Mayo Clinic Laboratories, Mayo Clinic	RCV000223824	SCV005413965	pathogenic	not provided	2024-07-31	criteria provided, single submitter	clinical testing	PP3, PM2, PS3, PS4
Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust	RCV000057534	SCV000089053	not provided	Congenital long QT syndrome		no assertion provided	literature only	This variant has been reported as associated with Long QT syndrome in the following publications (PMID:9386136;PMID:15466642;PMID:15840476;PMID:19716085;PMID:9570196;PMID:17470695). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory.
Stanford Center for Inherited Cardiovascular Disease, Stanford University	RCV000223824	SCV000280136	pathogenic	not provided	2015-07-16	no assertion criteria provided	clinical testing	Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. KCNQ1 p.Ala344Val This variant has been published in multiple cases of long QT syndrome. Donger et al (1997) reported the variant in 6 members of one family with long QT syndrome. It’s not clear how many of those family members actually had clinically diagnosed long QT. The average QTc among those family members was 471 ms (+/-32) and 2 of the 6 carriers were symptomatic (syncope). Tester et al (2005) reported the variant in three cases of long QT syndrome referred to Mayo Clinic’s Sudden Death Genomics Laboratory for genetic testing. In a study on genotype-phenotype correlations, Moss et al (2007) reported 17 individuals with this variant, though it is not clear if they all had a clinical diagnosis of long QT syndrome. Another missense variant at the same codon has been reported in someone with long QT syndrome: p.Ala344Glu (Tester et al 2005). Tester et al (2005) did not see the variant in more than 750 control individuals of varied ancestry. Donger et al (1997) did not observe the variant in 100 control subjects, for a total of 1050 control individuals. As of Oct 2013: It is not present in the NHLBI Exome Sequencing Project dataset of approximately 6500 individuals of Caucasian and African American ancestry. Based on these data it is very likely that this variant causes long QT syndrome and that the risk of cardiac events is increased because of the location of this variant. It affects a highly conserved amino acid residue in an important functional domain of the protein: the S6 transmembrane domain. Of note, variants like this one that are located in the transmembrane region of the channel are correlated with a higher risk of cardiac events (hazard ratio 2.06), independent of traditional clinical risk factors such as age, gender, and QTc length (Moss et al 2007).