7-150948984-C-T
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000238.4(KCNH2):c.2464G>A(p.Val822Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V822A) has been classified as Likely pathogenic.
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.2464G>A | p.Val822Met | missense_variant | 10/15 | ENST00000262186.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNH2 | ENST00000262186.10 | c.2464G>A | p.Val822Met | missense_variant | 10/15 | 1 | NM_000238.4 | P1 | |
KCNH2 | ENST00000330883.9 | c.1444G>A | p.Val482Met | missense_variant | 6/11 | 1 | |||
KCNH2 | ENST00000684241.1 | n.3297G>A | non_coding_transcript_exon_variant | 8/13 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Long QT syndrome 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 02, 1996 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Feb 08, 2022 | Reported in association with LQTS in multiple families (Berthet et al., 1999; Satler et al.,1996; Benhorin et al., 2002; Kapplinger et al., 2009); Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate a damaging effect as cell lines with this variant showed no voltage and showed defects in biosynthetic processing of KCNH2 (HERG) channels as the protein was retained in the endoplasmic reticulum (Zhou et al., 1998; Anderson 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: 12716119, 23303164, 12354768, 11278781, 11844290, 16432067, 10086971, 19716085, 11854117, 31557540, 8914737, 15840476, 30244407, 9694858) - |
Long QT syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jul 20, 2022 | For these reasons, this variant has been classified as Pathogenic. This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 822 of the KCNH2 protein (p.Val822Met). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of long QT syndrome and long QT syndrome (PMID: 8914737, 10086971, 10973849, 11854117, 15840476, 15851119). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 14424). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Experimental studies have shown that this missense change affects KCNH2 function (PMID: 9694858, 11278781, 23303164). - |
Cardiovascular phenotype Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 11, 2018 | The p.V822M pathogenic mutation (also known as c.2464G>A), located in coding exon 10 of the KCNH2 gene, results from a G to A substitution at nucleotide position 2464. The valine at codon 822 is replaced by methionine, an amino acid with highly similar properties. This alteration was originally described to co-segregate with long QT syndrome in multiple individuals in a large family (Satler CA et al. Am J Med Genet. 1996;65(1):27-3). Subsequently, this mutation has been reported in multiple patients with long QT (Berthet M et al. Circulation. 1999;99(11):1464-70; Lupoglazoff JM et al. Circulation. 2001;103(8):1095-101; Moss AJ et al. Circulation. 2002;105(7):794-9;Tester DJ et al. Heart Rhythm 2005;2(5):507-17; Kapplinger JD et al. Heart Rhythm. 2009;6(9):1297-303). This alteration is located in the C-terminal region of the KCNH2 gene, and functional in vitro and in vivo analyses have demonstrated deficient protein trafficking and repolarization related to a loss of function effect (Zhou Z et al. J Biol Chem. 1998;273(33):21061-6; Anderson CL et al. Circulation. 2006;113(3):365-73. Jou CJ et al. Circ Res. 2013;112(5):826-30). Based on the supporting evidence, p.V822M is interpreted as a disease-causing mutation. - |
Long QT syndrome 1 Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
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:8914737;PMID:10086971;PMID:11222472;PMID:11854117;PMID:15840476;PMID:16432067;PMID:19716085;PMID:9694858). 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