rs121912510
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000238.4(KCNH2):c.2453C>T(p.Ser818Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S818P) has been classified as Uncertain significance.
Frequency
Consequence
NM_000238.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNH2 | NM_000238.4 | c.2453C>T | p.Ser818Leu | missense_variant | 10/15 | ENST00000262186.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNH2 | ENST00000262186.10 | c.2453C>T | p.Ser818Leu | missense_variant | 10/15 | 1 | NM_000238.4 | P1 | |
KCNH2 | ENST00000330883.9 | c.1433C>T | p.Ser478Leu | missense_variant | 6/11 | 1 | |||
KCNH2 | ENST00000684241.1 | n.3286C>T | non_coding_transcript_exon_variant | 8/13 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251432Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135894
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727238
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Long QT syndrome 2 Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 15, 2000 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues | Sep 10, 2019 | - - |
Long QT syndrome Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Aug 17, 2023 | This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 818 of the KCNH2 protein (p.Ser818Leu). This variant is present in population databases (rs121912510, gnomAD 0.003%). This missense change has been observed in individual(s) with long QT syndrome (PMID: 10086971, 17088455, 18441445, 23158531, 26669661). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 14432). 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 KCNH2 function (PMID: 10996323, 16432067, 23303164). For these reasons, this variant has been classified as Pathogenic. - |
Cardiovascular phenotype Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 27, 2020 | The p.S818L pathogenic mutation (also known as c.2453C>T), located in coding exon 10 of the KCNH2 gene, results from a C to T substitution at nucleotide position 2453. The serine at codon 818 is replaced by leucine, an amino acid with dissimilar properties. This variant was described in a confirmed de novo case with torsades de pointes and syncope, as well as in her asymptomatic young daughter with prolonged QTc (Berthet M et al. Circulation, 1999 Mar;99:1464-70). This variant has also been reported in additional long QT syndrome cohorts (Nagaoka I et al. Circ. J., 2008 May;72:694-9; Crotti L et al. J. Am. Coll. Cardiol., 2012 Dec;60:2515-24; Stattin EL et al. BMC Cardiovasc Disord, 2012 Oct;12:95). Functional studies have demonstrated trafficking deficiency with significant reduction in potassium channel function (Anderson CL et al. Circulation, 2006 Jan;113:365-73; Perry MD et al. J. Physiol. (Lond.), 2016 07;594:4031-49). This allele was reported in one heterozygous individual in population-based 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
Pathogenic, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Oct 10, 2023 | This missense variant replaces serine with leucine at codon 818 in the KCNH2 protein. This variant is found within the highly conserved cyclic nucleotide binding domain (aa 742-842). 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 causes trafficking defects resulting in reduced membrane expression and impaired channel function (PMID: 10996323, 16432067, 23303164, 26958806, 31557540). This variant has been reported in over twenty individuals affected with long QT syndrome (PMID: 10086971, 18441445, 21440677, 23158531, 26669661, 27920829, 32893267, 35253369, 36102233) and has been observed to be a de novo occurrence in at least one of the probands (PMID: 10086971). This variant has also been reported in an individual affected with sudden cardiac death and idiopathic left ventricular hypertrophy (PMID: 32011662). Two relatives of this proband also carried this variant, who were both affected with long QT syndrome. This variant has been identified in 1/251432 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. - |
Congenital long QT syndrome Other:1
not provided, no classification provided | literature only | Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust | - | This variant has been reported as associated with Long QT syndrome in the following publications (PMID:10086971;PMID:10996323;PMID:11222472;PMID:16432067;PMID:16831322;PMID:18441445). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at