rs199473505
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000238.4(KCNH2):c.982C>T(p.Arg328Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000435 in 1,614,188 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R328H) has been classified as Uncertain significance.
Frequency
Consequence
NM_000238.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNH2 | NM_000238.4 | c.982C>T | p.Arg328Cys | missense_variant | 5/15 | ENST00000262186.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNH2 | ENST00000262186.10 | c.982C>T | p.Arg328Cys | missense_variant | 5/15 | 1 | NM_000238.4 | P1 | |
KCNH2 | ENST00000532957.5 | n.1205C>T | non_coding_transcript_exon_variant | 5/9 | 2 | ||||
KCNH2 | ENST00000684241.1 | n.1815C>T | non_coding_transcript_exon_variant | 3/13 |
Frequencies
GnomAD3 genomes ? AF: 0.000611 AC: 93AN: 152264Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000570 AC: 143AN: 250832Hom.: 0 AF XY: 0.000560 AC XY: 76AN XY: 135796
GnomAD4 exome AF: 0.000417 AC: 609AN: 1461806Hom.: 3 Cov.: 32 AF XY: 0.000388 AC XY: 282AN XY: 727212
GnomAD4 genome ? AF: 0.000610 AC: 93AN: 152382Hom.: 0 Cov.: 33 AF XY: 0.000859 AC XY: 64AN XY: 74512
ClinVar
Submissions by phenotype
not provided Benign:2Other:1
Likely benign, no assertion criteria provided | provider interpretation | Stanford Center for Inherited Cardiovascular Disease, Stanford University | Nov 15, 2016 | Given the weak case data and presence in population controls, we consider this variant likely benign. One possibility is that this variant contributes to an arrhythmic phenotype, perhaps behaving as a modifier, but not be the primary driver. This is based on the fact that several of the reported cases involved either a more convincing pathogenic variant or QT-prolonging medication, several other reported cases are from cohorts that include individuals who do not have long QT, and the variant is present in individuals not selected for a long QT phenotype, with ~1% of one such cohort having the variant. This is a previously reported variant in the N-terminal region. To date, the reported cases include - drug-induced long QT, complete AV block and Torsades: 2 - patients referred for long QT genetic testing, 25-50% likely don't have long QT: 6 - patients with long QT, all major genes analyzed with no other variants: 4 - patients with long QT and another, high confidence variant: 1 - patient with prolonged QT in the setting of evidence of arrhythmogenic right ventricular cardiomyopathy and a PKP2 frameshift variant: 1 Comparing frequencies: - 4/2500 in Kapplinger series (0.16%) - 64/60,618 in ExAC (0.11%) - 38/3189 Finnish in ExAC (1.2%) -162/141,162 in gnomAD (0.11%); -115/13031 Finnish in gnomAD (0.88%) Chevalier et al (2001) reported the variant in association with what the authors described as acquired long QT syndrome. They found the variant in 1 of 16 cases. The individual with the variant was a 45yo male with no prior medical history of family history of sudden death. He was hospitalized for recent syncopal episodes. An ECG at admission showed QT prolongation and complete AV block, he was diagnosed with "Torsades de pointes" complicating an AV bock and a pacemaker was placed and the QT interval returned to normal once he was paced. Tester et al (2005) observed the variant in 2 of 541 cases. This publication is a compendium of variants identified in cases referred to Dr. Ackerman's research lab for long QT genetic testing. No individual clinical or segregation data was provided. Of note when considering this paper, it is likely that ~25% of patients in this cohort did not actually have long QT syndrome (based on the reported yield). Millat et al (2006) reported the variant in 3 of 44 unrelated individuals from their French cohort with long QT syndrome with QTc intervals ranging from 483 to 540 ms. No segregation data was provided. They analyzed 5 long QT genes. Hinterseer et al (2006) reported the variant in a 25yo woman who suffered Torsades de Pointes in the setting of transiently impaired LV function, acute respiratory distress syndrome, transient hypokalaemia and QT-prolonging drugs, with a QTc of 485-510 ms. Once her status had normalized and QT-prolonging drugs had been discontinued her QTc was 430 ms and a Dl-sotalol challenge evoked a QTc of 515 ms, which the authors felt was suggestive of a latent susceptibility to QT-prolonging drugs. Four other family members were found to have the variant, "all without clinical manifestations of LQTS". The variant was reported in 4 individuals in the Familion compendium, which includes 2500 patients referred for clinical long QT genetic testing (Kapplinger et al 2009). Those cases likely overlap with the data in Kapa et al (2009) and Giudicessi et al (2012) since these are all from Ackerman's group and use data from his cohort and from the Familion cohort. Of note in considering the cases reported by Kapplinger et al (2009) is the lack of phenotypic data on this cohort, the low yield of 36% (vs. 70% in cohorts with firm diagnoses of long QT), and the lack of clarity regarding which variants were seen with another variant (9% of the cohort had multiple variants). Stattin et al (2012) analyzed 5 long QT genes in 200 unrelated long QT patients from their Swedish cohort and identified this variant in one individual. Hedley et al (2013) report - |
not provided, no classification provided | literature only | Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust | - | This variant has been reported in the following publications (PMID:11334843;PMID:14760488;PMID:15840476;PMID:16253915;PMID:16432067;PMID:16720674;PMID:16922724;PMID:17275752;PMID:19716085;PMID:19841300). - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | KCNH2: PP2, BS1 - |
not specified Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Blueprint Genetics | Nov 10, 2015 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Mar 08, 2017 | The R328C variant in the KCNH2 gene has been previously reported in multiple unrelated individuals with LQTS and was absent in >2,600 reference alleles, when considering all published studies (Tisma-Dupanovic et al., 2013; Kapplinger et al., 2009; Tester et al., 2005; Chevalier et al., 2001). The R328C variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project; however, the 1000 Genomes Project observed this variant at low frequency in 2/198 Finnish alleles and in 2/208 Puerto Rican alleles. One previously asymptomatic individual identified to have the R328C variant developed Torsades de Pointes in the context of respiratory distress, left ventricular dysfunction, and a prolonged QT interval while being treated with multiple medications (Hinterseer et al., 2006). Several relatives who were also found to harbor this variant, including the patient's identical twin, had no clinical evidence of LQTS, leading authors to conclude this patient's arrhythmia likely resulted from multiple factors. Chevalier et al. (2001) reported R328C leads to a partial dominant-negative effect and alters KCNH2 channel function; however, subsequent functional studies found that the channel function of R328C-KCNH2 did not differ significantly from the wild type KCNH2 channel function (Grunnet et al., 2005; Anderson et al., 2006). Nevertheless, R328C is a non-conservative amino acid substitution occurring at a position that is conserved across species. Multiple missense variants in nearby residues (S320W, S320L, D323N, P334L) have been reported in Human Genome Mutation Database in association with LQTS (Stenson et al., 2014). Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or benign. - |
Long QT syndrome Benign:2
Likely benign, criteria provided, single submitter | research | CSER _CC_NCGL, University of Washington | Dec 01, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Long QT syndrome 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 06, 2020 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
KCNH2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 19, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Cardiac arrhythmia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Nov 07, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at