Submissions for variant NM_000218.3(KCNQ1):c.944A>G (p.Tyr315Cys)

dbSNP: rs74462309

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000182138	SCV000234441	pathogenic	not provided	2022-05-11	criteria provided, single submitter	clinical testing	Published functional studies demonstrate a damaging effect as this variant results in reduced potassium channel current in vitro (Bianchi et al., 2000); 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; This variant is associated with the following publications: (PMID: 15466642, 24269949, 19490272, 14678125, 9693036, 9927399, 17470695, 15840476, 19261104, 23575362, 23130128, 12877697, 12702160, 24606995, 18774102, 23098067, 19716085, 24217263, 28749187, 27920829, 28438721, 10868744, 14760488, 20541041, 10220144, 31447099, 34135346, 11087258)
Ambry Genetics	RCV000619103	SCV000737748	pathogenic	Cardiovascular phenotype	2023-02-01	criteria provided, single submitter	clinical testing	The p.Y315C pathogenic mutation (also known as c.944A>G), located in coding exon 7 of the KCNQ1 gene, results from an A to G substitution at nucleotide position 944. The tyrosine at codon 315 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration impacts the highly conserved ion selectivity filter (TIGYGD) located between transmembrane helices S5 and S6. This alteration has been detected in multiple unrelated individuals reported to have confirmed or suspected long QT syndrome, with variable expressivity in some cases (LQTS) (Splawski I et al. Genomics. 1998;51(1):86-97; Chen S et al. Clin Genet. 2003;63(4):273-82; Moss AJ et al. Circulation. 2007; Kapplinger JD et al. Heart Rhythm. 2009;6(9):1297-303; 115(19):2481-9; Itoh H et al. Heart Rhythm. 2010;7(10):1411-8; Bartos DC et al. Heart Rhythm. 2014;11(3):459-68). One study reported this alteration to result in a dominant negative effect on wild-type IKs current when expressed with wild-type channel in vitro (Bianchi L et al. Am J Physiol Heart Circ Physiol. 2000;279(6):H3003-11). Internal structural analysis indicates that this variant disrupts the ion channel pore and is expected to eliminate the K+ selectivity of the K+ channel (Tao X et al. Science. 2009;326(5960):1668-74; Whorton MR and MacKinnon R. Cell. 2011;147(1):199-208; Ambry internal data). In addition, another alteration affecting this codon (p.Y315S, c.944A>C) has also been reported in association with LQTS (Jongbloed RJ et al. Hum Mutat. 1999;13(4):301-10). 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.
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	RCV000709732	SCV000839970	likely pathogenic	Long QT syndrome 1	2017-11-03	criteria provided, single submitter	clinical testing	The c.944A>G (p.Tyr315Cys) variant in the KCNQ1 gene has been observed in multiple individuals with long QT syndrome (PMID: 9693036, 10868744, 12702160, 15840476, 14760488, 15466642). In addition, experimental studies have shown that this missense change leads to altered KCNQ1 protein function (PMID: 11087258). The c.944A>G (p.Tyr315Cys) variant in the KCNQ1 gene is classified as likely pathogenic.
Invitae	RCV000678812	SCV001588720	pathogenic	Long QT syndrome	2023-10-29	criteria provided, single submitter	clinical testing	This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 315 of the KCNQ1 protein (p.Tyr315Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with long QT syndrome (PMID: 9693036, 12702160, 18774102, 21451124, 24217263, 24606995). ClinVar contains an entry for this variant (Variation ID: 53140). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt KCNQ1 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects KCNQ1 function (PMID: 11087258, 21451124). For these reasons, this variant has been classified as Pathogenic.
CeGaT Center for Human Genetics Tuebingen	RCV000182138	SCV002544488	pathogenic	not provided	2022-05-01	criteria provided, single submitter	clinical testing	KCNQ1: PM1, PM2, PM5, PS4:Moderate, PP3, PS3:Supporting
Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust	RCV000057816	SCV000089336	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:9693036;PMID:10868744;PMID:12702160;PMID:12877697;PMID:14678125;PMID:14760488;PMID:15466642;PMID:15840476;PMID:19716085;PMID:9927399;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	RCV000182138	SCV000280167	pathogenic	not provided	2016-03-02	no assertion criteria provided	provider interpretation	p.Tyr315Cys (c.944A>G, p.Y315C) in the KCNQ1 gene The variant was re-reviewed March 2nd, 2016. There was both new case data and new allele frequency data, both of which further support pathogenicity and shift our classification from likely pathogenic to pathogenic. The variant has been seen in at least 13 unrelated cases of long QT syndrome (not including this patient). We seen this variant in one other family with long QT in our center. Splawski et al (1998) reported this variant in a patient with long QT syndrome, presumably from their American cohort (ancestry not noted). Priori et al (1999) reported the variant in a patient from their Italian cohort with long QT syndrome. Chen et al (2003) observed the variant in two siblings with long QT syndrome (cohort studied at Cleveland clinic, recruited from clinics in North America, South America, Europe; ancestry not provided). Choi et al (2004) reported the variant in an "LQT1 index case" (no other phenotypic data provided) who had a cousin with exertional syncope and a near-drowning event (cohort studied in Dr. Ackerman's lab at Mayo; ancestry not provided). This case likely overlaps with Nemec et al (2003) and Tester et al (2005), also from Dr. Ackerman's group. The variant was observed in 4 patients included in the Familion compendium publication with no phenotype or ancestry data (Kapplinger et al 2009). This publication reports on variants observed in patients referred for long QT syndrome genetic testing using the Familion test at PGxHealth (now Transgenomics). Napolitano et al (2000) reported the variant in a woman with QT-prolongation and arrest in the setting of a QT-prolonging medication (cisapride) (ancestry not noted but patient likely from Italy). Patients with this variant are included in two papers on genotype-phenotype correlations (Zareba et al 2003, Moss et al 2007). The subjects were drawn from the various long QT registries and many of the authors overlap with the other publications reviewed here, so at least some of the cases are likely redundant with those summarized above. Stattin et al (2012) studied 200 unrelated index cases of LQTS referred for care in Sweden between 3/2006 and 10/2009. KCNQ1, KCNH2, KCNE1, KCNE2, and SCN5A were analyzed. The variant of interest was found in a single proband; no segregation data is reported. Hedley et al (2013) studied 44 South African congenital LQTS patients, screening them for variants in the coding regions of KCNQ1, KCNH2, KCNE1, KCNE2, and SCN5A. The variant of interest was found in one patient (no segregation data reported). Christiansen et al (2014) assessed 70 unrelated Danish LQTS probands by variant screening of KCNQ1, KCNH2, KCNE1, KCNE2, and SCN5A. The variant of interest was found in a single proband; no segregation data is reported. In silico analysis with PolyPhen-2 predicts the variant to be probably damaging. Grantham score is 5.29. The tyrosine at codon 315 is completely conserved across species, as are neighboring amino acids. Other variants have been reported in association with disease at this codon (p.Tyr315Ser, p.Tyr315Phe) and nearby codons (p.Ile313Met, p.Gly314Asp, p.Gly314Ala, p.Gly314Ser, p.Gly314Cys, p.Gly314Arg, p.Gly314Val, p.GLy316Glu, p.GLy316Arg). Functional studies have shown a decrease in potassium current (Bianchi et al 2000). The variant is in the pore region of the channel. Variants in this region are much more likely to be pathogenic than benign. There is also some evidence that they confer a higher risk of events (Moss et al 2007), though other studies have not found such a difference (Zareba et al 2003). Barsheshet et al (2012) found that carriers of missense variants in the cytoplasmic loops had the highest risk of events as well as the greatest response to beta-blockade. The patient's variant is not in the cytoplasmic loop. Moss et al (2007) reported a higher risk with dominant negative variants and classify this variant as dominant negative. In total the variant has not been seen in ~65,000 published controls and individuals from publicly available population datasets. The variant was not observed in the following laboratory and published control samples: Splawski et al (1998) did not observe the variant in 200 controls (ancestry not reported), Kapplinger et al (2009) did not observe the variant in 1300 control individuals of varying ancestries. The variant is not listed in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/), which currently includes variant calls on ~64,000 individuals of European, African, Latino and Asian descent (as of 3/1/16). However, another variation at codon 315 is listed (p.Tyr315Tyr; 11:2604688T/C), having been observed in 1 (east Asian) out of 121060 total alleles.
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital	RCV000678812	SCV000804998	likely pathogenic	Long QT syndrome	2017-01-18	no assertion criteria provided	clinical testing
deCODE genetics, Amgen	RCV000709732	SCV004022220	likely pathogenic	Long QT syndrome 1	2023-07-21	no assertion criteria provided	research	The variant NM_000218.3:c.944A>G (chr11:2583457) in KCNQ1 was detected in 17 heterozygotes out of 58K WGS Icelanders (MAF= 0,015%). Following imputation in a set of 166K Icelanders (48 imputed heterozygotes) we observed an association with an elongation of the qt interval on ECG using measurements from 80068 individuals (Effect (SD)= 2.21, P= 5.38e-26) and heart failure using 20765 cases and 367806 controls (OR= 3.17, P= 1.31e-02). This variant has been reported in ClinVar previously as pathogenic/likely pathogenic. Based on ACMG criteria (PS4, PM1, PP3, PP5) this variant classifies as likely pathogenic.