Submissions for variant NM_000219.6(KCNE1):c.226G>A (p.Asp76Asn)

gnomAD frequency: 0.00005  dbSNP: rs74315445

Total submissions: 21

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000222568	SCV000278993	pathogenic	not provided	2022-07-05	criteria provided, single submitter	clinical testing	Published functional studies demonstrate a damaging effect as this variant leads to a dominant-negative loss of channel function (Splawski et al., 1997; Hoppe et al., 2001; Chen et al., 2009; Du et al., 2013); 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: 9354783, 19695459, 30461122, 30609406, 32344329, 16914890, 20196769, 9354802, 10428953, 11874988, 12566567, 24400172, 24606995, 25637381, 11320260, 19340287, 24478792, 10400998, 24561134, 26410412, 26926294, 15840476, 19716085, 26187847, 27807201, 9445165, 30930557, 23631430, 23124029, 19521339, 31835641, 31941373, 31737537, 31447099, 32058015, 30847666)
Ambry Genetics	RCV000243273	SCV000319991	pathogenic	Cardiovascular phenotype	2020-12-03	criteria provided, single submitter	clinical testing	The p.D76N pathogenic mutation (also known as c.226G>A), located in coding exon 1 of the KCNE1 gene, results from a G to A substitution at nucleotide position 226. The aspartic acid at codon 76 is replaced by asparagine, an amino acid with highly similar properties. This mutation has been reported in multiple unrelated individuals with long QT syndrome (Lieve KV et al. Genet Test Mol Biomarkers 2013; 17(7):553-61; Kapplinger JD et al. Heart Rhythm 2009; 6(9):1297-303; Tester DJ et al. Heart Rhythm 2005; 2(5):507-17; Splawski I et al. Circulation 2000; 102(10):1178-85) and segregated with disease in two individuals with long QT syndrome in a family (Splawski I et al. Nat. Genet. 1997; 17(3):338-40). The alteration has been reported in compound heterozygosity with a second KCNE1 variant in siblings with Jervell and Lange-Nielsen syndrome (Schulze-Bahr E et al. Nat. Genet. 1997; 17(3):267-8). This variant has also been detected in the homozygous state in an individual with Jervell and Lange-Nielsen syndrome whose heterozygous family members had phenotypes consistent with long QT syndrome (Duggal P et al. Circulation 1998; 97(2):142-6). This variant has been reported to exhibit reduced penetrance in cohorts (Roberts JD et al. Circulation. 2020 02;141(6):429-439). In vitro assays have reported that the p.D76N alteration impairs ion channel function by altering voltage dependence and suppressing current through KCNQ1 and KCNH2-associated channels (Kurokawa J et al. Proc. Natl. Acad. Sci. U.S.A. 2003; 100(4):2122-7; Abbott GW et al. FASEB J. 2002; 16(3):390-400; Bianchi L et al. Hum. Mol. Genet. 1999; 8(8):1499-507). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. However, pathogenic and likely pathogenic KCNE1 variants typically exhibit low penetrance in the heterozygous state and may represent risk factors that manifest clinically only in the presence of additional genetic or environmental factors (Roberts JD et al. Circulation. 2020 02;141(6):429-439).
Invitae	RCV000471399	SCV000549148	pathogenic	Long QT syndrome	2024-01-09	criteria provided, single submitter	clinical testing	This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 76 of the KCNE1 protein (p.Asp76Asn). This variant is present in population databases (rs74315445, gnomAD 0.01%). This missense change has been observed in individual(s) with Jervell and Lange-Nielsen syndrome (JLNS) and long QT syndrome (PMID: 9354783, 9354802, 9445165, 19716085, 24561134, 24606995). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 13477). 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) has been performed at Invitae 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 KCNE1 protein function. Experimental studies have shown that this missense change affects KCNE1 function (PMID: 9354802, 10400998, 10428953, 11874988, 12566567, 24400172). For these reasons, this variant has been classified as Pathogenic.
Agnes Ginges Centre for Molecular Cardiology, Centenary Institute	RCV000584826	SCV000692512	uncertain significance	Arrhythmogenic right ventricular cardiomyopathy; Brugada syndrome; Sudden unexplained death	2017-03-14	criteria provided, single submitter	research	The KCNE1 Asp76Asn variant has been reported in several cases of long QT syndrome and was absent from >2000 controls, collectively (Kapplinger JD, et al., 2009; Tester DJ, et al., 2005; Duggal P, et al., 1998; Splawski I, et al., 1997). It has also been reported in 1 case of CPVT (Tester DJ, et al., 2006), 2 cases of Jervell and Lange-Neilson Syndrome (Schulze-Bahr E, et al., 1997; Duggal P, et al., 1998) and 2 cases of sudden cardiac arrest/death (Li MH, et al., 2015). The homozygous case reported in Duggal P et al. (1998) expressed a severe phenotype, compared to the compound heterozygous family in Schulze-Bahr E et al. (1997). The variant is absent from the 1000 genomes project (http://www.1000genomes.org/) and present at low frequency in the Exome Aggregation Consortium dataset (MAF= 0.000033; http://exac.broadinstitute.org/). This frequency is higher than expected given the absolute rarity of LQT5. We identified this variant in a young proband that presented with sudden cardiac death with suggested evidence of ARVC and family history of Brugada syndrome. After extensive clinical evaluation there are no individuals with a demonstrated prolonged QT, and the variant does not segregate with the phenotype of Brugada/ARVC. Computational tools MutationTaster and PolyPhen-2 predict this variant to be "disease-causing" and "probably damaging" respectively, however SIFT predicts this variant to be "tolerated". Functional studies in frog oocytes have shown that the variant results in functional consequences such as delayed cardiac repolarization and increased risk of arrhythmia's (Splawski I, et al., 1997) and negatively affects the function of potassium channels (Kurokawa J, et al., 2013; Abbott GW and Goldstein SA, 2002). In summary, based on these conflicting interpretations, we classify KCNE1 Asp76Asn as a variant of "uncertain significance".
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000606753	SCV000711385	likely pathogenic	Jervell and Lange-Nielsen syndrome	2018-07-13	criteria provided, single submitter	clinical testing	The p.Asp76Asn variant in KCNE1 (ClinVar variation ID# 13477) has been reported in the heterozygous state in at least 18 individuals with Long QT syndrome (LQTS ; Splawski 1997, Duggal 1998, Tester 2005, Tester 2006, Kapplinger 2009, Christi ansen 2014, Weeke 2014, Li 2015) as well as one affected relative (Splawski 1997 ). This variant has also been identified in 14/126618 European chromosomes by th e Genome Aggregation Database (GnomAD, http://gnomad.broadinstitute.org). This f requency is high given the prevalence of LQTS (Orphanet: ~1/2,500 individuals) a nd genetic heterogeneity of the disease but does not rule out pathogenicity as L QTS is known to have clinical variability and reduced penetrance. A pathogenic role is supported by two families with Jervell and Lange-Nielsen syndrome (JLNS) , which includes prolonged QT as one of several features. In one family, the va riant was present in the compound heterozygous state in three affected siblings (Schulze-Bar 1997). I the other family, the proband was homozygous for the p.As p76Asn variant and two heterozygous family members were reported to have LQTS (D uggal 1998). In vitro functional studies provide some evidence that the p.Asp76A sn variant may impact protein function (Splawski 1997, Kurokawa 2003, Seebohm 20 08, Haitin 2009, Chen 2009, Du 2013). However, these types of assays may not acc urately represent biological function. In vivo studies in guinea-pigs have shown that this variant affects cardiac repolarization in myocytes (Hoppe 2001). Comp utational prediction tools and conservation analysis do not provide strong suppo rt for or against an impact to the protein. In summary, this variant meets crite ria to be classified as likely pathogenic for LQTS in an autosomal dominant mann er and for JLNS in an autosomal recessive manner based upon segregation studies and functional evidence. ACMG/AMP Criteria applied: ACMG/AMP criteria applied: P M3, PS3_Moderate, PP1_Moderate.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000119080	SCV000711386	likely pathogenic	Congenital long QT syndrome	2018-07-13	criteria provided, single submitter	clinical testing	The p.Asp76Asn variant in KCNE1 (ClinVar variation ID# 13477) has been reported in the heterozygous state in at least 18 individuals with Long QT syndrome (LQTS ; Splawski 1997, Duggal 1998, Tester 2005, Tester 2006, Kapplinger 2009, Christi ansen 2014, Weeke 2014, Li 2015) as well as one affected relative (Splawski 1997 ). This variant has also been identified in 14/126618 European chromosomes by th e Genome Aggregation Database (GnomAD, http://gnomad.broadinstitute.org). This f requency is high given the prevalence of LQTS (Orphanet: ~1/2,500 individuals) a nd genetic heterogeneity of the disease but does not rule out pathogenicity as L QTS is known to have clinical variability and reduced penetrance. A pathogenic role is supported by two families with Jervell and Lange-Nielsen syndrome (JLNS) , which includes prolonged QT as one of several features. In one family, the va riant was present in the compound heterozygous state in three affected siblings (Schulze-Bar 1997). I the other family, the proband was homozygous for the p.As p76Asn variant and two heterozygous family members were reported to have LQTS (D uggal 1998). In vitro functional studies provide some evidence that the p.Asp76A sn variant may impact protein function (Splawski 1997, Kurokawa 2003, Seebohm 20 08, Haitin 2009, Chen 2009, Du 2013). However, these types of assays may not acc urately represent biological function. In vivo studies in guinea-pigs have shown that this variant affects cardiac repolarization in myocytes (Hoppe 2001). Comp utational prediction tools and conservation analysis do not provide strong suppo rt for or against an impact to the protein. In summary, this variant meets crite ria to be classified as likely pathogenic for LQTS in an autosomal dominant mann er and for JLNS in an autosomal recessive manner based upon segregation studies and functional evidence. ACMG/AMP Criteria applied: ACMG/AMP criteria applied: P M3, PS3_Moderate, PP1_Moderate.
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	RCV000014420	SCV000839962	likely pathogenic	Long QT syndrome 5	2017-10-16	criteria provided, single submitter	clinical testing	This c.226G>A (p.Asp76Asn) variant in the KCNE1 gene has been reported in multiple unrelated individuals with Long QT syndrome (LQTS; PMID: 15840476, 19716085, 24606995) and has been shown in families to segregate with the LQTS phenotype (PMID: 9354802). It has also been reported in the homozygous or compound heterozygous state in individuals with Jervell and Lange-Nielsen syndrome, with some heterozygous family members manifesting features of LQTS (PMID: 9354783, 9445165). The c.226G>A variant is rare in the general population. Functional studies have indicated that the p.Asp76Asn variant KCNE1 protein has altered activity (PMID: 10400998, 10428953, 11874988, 12566567). The c.226G>A (p.Asp76Asn) variant in the KCNE1 gene is classified as likely pathogenic.
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute	RCV000471399	SCV000987324	pathogenic	Long QT syndrome	2016-12-22	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000222568	SCV001246782	pathogenic	not provided	2017-10-01	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000222568	SCV001474376	likely pathogenic	not provided	2020-07-24	criteria provided, single submitter	clinical testing	The KCNE1 c.226G>A; p.Asp76Asn variant (rs74315445) is reported in the literature in multiple individuals affected with long QT syndrome (Christiansen 2014, Kapplinger 2009, Splawski 1997, Tester 2005). In addition, this variant was found in the homozygous or compound heterozygous state in several families with Jervell and Lange-Nielsen syndrome and was found to segregate with disease (Duggal 1998, Schulze-Bahr 1997). This variant is found in the non-Finnish European population with an overall allele frequency of 0.01% (14/129102 alleles) in the Genome Aggregation Database. The aspartate at codon 76 is highly conserved, and functional studies suggest this variant leads to altered potassium channel activity, including reduced current and faster deactivation (Kurokawa 2003, Splawski 1997). Based on available information, this variant is considered to be likely pathogenic. References: Christiansen M et al. Mutations in Danish patients with long QT syndrome and the identification of a large founder family with p.F29L in KCNH2. BMC Med Genet. 2014;15:31. Duggal P et al. Mutation of the gene for IsK associated with both Jervell and Lange-Nielsen and Romano-Ward forms of Long-QT syndrome. Circulation. 1998;97(2):142-146. Kapplinger JD al. Spectrum and prevalence of mutations from the first 2,500 consecutive unrelated patients referred for the FAMILION long QT syndrome genetic test. Heart Rhythm. 2009;6(9):1297-1303. Kurokawa J et al. Requirement of subunit expression for cAMP-mediated regulation of a heart potassium channel. Proc Natl Acad Sci U S A. 2003;100(4):2122-2127. Schulze-Bahr E et al. KCNE1 mutations cause Jervell and Lange-Nielsen syndrome. Nat Genet. 1997;17(3):267-268. Splawski I et al. Mutations in the hminK gene cause long QT syndrome and suppress IKs function. Nat Genet. 1997;17(3):338-340. Tester DJ et al. Compendium of cardiac channel mutations in 541 consecutive unrelated patients referred for long QT syndrome genetic testing. Heart Rhythm. 2005;2(5):507-517.
Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues	RCV000014420	SCV002320700	likely pathogenic	Long QT syndrome 5	2021-07-05	criteria provided, single submitter	clinical testing
AiLife Diagnostics, AiLife Diagnostics	RCV000222568	SCV002503420	pathogenic	not provided	2021-12-27	criteria provided, single submitter	clinical testing
Dept of Medical Biology, Uskudar University	RCV000471399	SCV004021977	likely pathogenic	Long QT syndrome	2024-01-08	criteria provided, single submitter	research	Criteria: PS3_Moderate, PM1, PP1, PP3
OMIM	RCV000014419	SCV000034668	pathogenic	Jervell and Lange-Nielsen syndrome 2	1998-01-20	no assertion criteria provided	literature only
OMIM	RCV000014420	SCV000034669	pathogenic	Long QT syndrome 5	1998-01-20	no assertion criteria provided	literature only
Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust	RCV000119080	SCV000153799	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:9354783;PMID:9354802;PMID:9445165;PMID:15840476;PMID:16818210;PMID:19716085;PMID:9328483;PMID:11874988). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory.
CSER _CC_NCGL, University of Washington	RCV000148512	SCV000190224	likely pathogenic	Jervell and Lange-Nielsen syndrome 1	2014-06-01	no assertion criteria provided	research
Division of Human Genetics, Children's Hospital of Philadelphia	RCV000014420	SCV000238442	likely pathogenic	Long QT syndrome 5	2015-01-08	no assertion criteria provided	research	The heterozygous variant in the KCNE1 gene (c.226G>A; p.Asp76Asn) is considered a likely pathogenic variant. This amino acid position is well conserved and the change is non-conservative while the nucleotide is only moderately conserved. The same change has been seen in 4 individuals of European origin in the ExAC database out of 121246 alleles interrogated at this position. This variant has been initially published by Schulze-Bahr et al (PMID: 9354783) in one family with Jervell and Lange-Nielsen syndrome in 3 affected siblings, it has been published in 9 individuals with Long QT by Kapplinger et al. (PMID: 19716085). Available functional studies in Xenopus laevis oocytes and in Chinese hamster ovaries indicate a reduced function for this variant relative to wild type (PMID: 11874988, 12566567).
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital	RCV000678806	SCV000804988	likely pathogenic	not specified	2017-08-01	no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000222568	SCV001921915	pathogenic	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000222568	SCV001927328	pathogenic	not provided		no assertion criteria provided	clinical testing