rs770047651
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PP3PP5_Very_Strong
The NM_000238.4(KCNH2):c.1128G>A(p.Gln376=) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.0000198 in 1,415,982 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.000020 ( 1 hom. )
Consequence
KCNH2
NM_000238.4 splice_region, synonymous
NM_000238.4 splice_region, synonymous
Scores
2
Splicing: ADA: 0.9995
2
Clinical Significance
Conservation
PhyloP100: 6.13
Genes affected
KCNH2 (HGNC:6251): (potassium voltage-gated channel subfamily H member 2) This gene encodes a component of a voltage-activated potassium channel found in cardiac muscle, nerve cells, and microglia. Four copies of this protein interact with one copy of the KCNE2 protein to form a functional potassium channel. Mutations in this gene can cause long QT syndrome type 2 (LQT2). Transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, May 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
PP3
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.
PP5
Variant 7-150957291-C-T is Pathogenic according to our data. Variant chr7-150957291-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 200323.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-150957291-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| KCNH2 | NM_000238.4 | c.1128G>A | p.Gln376= | splice_region_variant, synonymous_variant | 5/15 | ENST00000262186.10 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| KCNH2 | ENST00000262186.10 | c.1128G>A | p.Gln376= | splice_region_variant, synonymous_variant | 5/15 | 1 | NM_000238.4 | P1 | |
| KCNH2 | ENST00000532957.5 | n.1351G>A | splice_region_variant, non_coding_transcript_exon_variant | 5/9 | 2 | ||||
| KCNH2 | ENST00000684241.1 | n.1961G>A | splice_region_variant, non_coding_transcript_exon_variant | 3/13 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.0000198 AC: 28AN: 1415982Hom.: 1 Cov.: 32 AF XY: 0.0000200 AC XY: 14AN XY: 700066
GnomAD4 exome
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28
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1415982
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32
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14
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700066
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GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Long QT syndrome 2 Pathogenic:2
| Likely pathogenic, criteria provided, single submitter | in vitro;research | Roden Lab, Vanderbilt University Medical Center | Oct 05, 2022 | The KCNH2 variant c.1128G>A was observed in 2 cases of LQTS and is absent from large population databases (PMID: 32893267). Splicing predictions were inconclusive for this variant. Minigene functional studies revealed aberrant splicing in the presence of this alternative allele. Collectively, this evidence supports a Likely Pathogenic classification. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | Oct 19, 2020 | Based on the classification scheme VCGS_Germline_v1.3.2, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative and loss of function are known mechanisms of disease in this gene and are associated with long QT syndrome (LQTS; MIM#2613688). Gain of function is also a known mechanism associated with short QT syndrome (MIM#16096203) (OMIM, PMID: 10753933; PMID: 21777565). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID: 20301308). (I) 0212 - Non-canonical splice site variant without proven consequence on splicing (no functional evidence available). (SP) 0219 - This variant is non-coding in an alternative transcript (UCSC, NCBI). (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0508 - In silico predictions for abnormal splicing are conflicting. (I) 0705 - No alternative changes on the same nucleotide have previous evidence for pathogenicity. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals with with LQTS. (ClinVar, PMIDs: 19716085; 25294783, 25929701). (SP) 0903 - This variant has limited evidence for segregation with disease (VCGS). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign - |
not provided Pathogenic:2
| Likely pathogenic, no assertion criteria provided | clinical testing | Stanford Center for Inherited Cardiovascular Disease, Stanford University | Aug 26, 2011 | Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. KCNH2 p.Gln376Gln Based on the information reviewed below, we classify it as likely disease causing. This specific variant has been reported in the literature in at least 4 unrelated individuals: 1 with a clinical diagnosis of LQTS (Splawski et al 2000) and 3 tested at Mayo Clinic’s Sudden Death Genomics Laboratory/Familion due to suspicion for LQTS (Tester et al 2005; Kapplinger et al 2009). This is predicted to be a splice site variant (it does not result in an amino acid change to the protein), which alters the last base of exon 5, immediately 5 prime of the canonical “GT” splice donor site. Splice site variation is an established form of disease-causing variation in the KCNH2 gene (HGMD professional version as of January 17, 2014). In silico analysis with 3 different splice algorithms predicts this variant to destroy the donor site at the exon 5/intron 5 junction, which may lead to abnormal gene splicing. In total the variant has been seen in 0/1500 published controls and 1/12,000 individuals from publicly available population datasets. There is no variation at this nucleic acid listed in the NHLBI Exome Sequencing Project dataset (http://evs.gs.washington.edu/EVS/), which currently includes variant calls on ~4300 Caucasian and ~2200 African American individuals. The phenotype of the ESP individuals is not publicly available, however the cohorts that were merged to create this dataset were all either general population samples or samples recruited for common cardiovascular disease such as hypertension. There is also no variation at this nucleotide listed in dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP) or 1000 Genomes (http://browser.1000genomes.org/index.htm) as of 6/2/2015. The variant is present in 1 European individual in the ExAC dataset, out of 5,518 Europeans total; it is not present in another 6,503 individuals of African, East Asian, South Asian, and Latino, and Other ancestry. It was not observed in published controls: 200 controls (Splawski et al 2000), 1300 controls (Kapplinger et al 2009; 47% Caucasian, 26% African American, 11% Hispanic, 10% Asian, 6% Unknown/Other). - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Apr 13, 2022 | The KCNH2 c.1128G>A; p.Gln376= variant (rs770047651) is reported in the literature in multiple individuals with diagnosis or clinical suspicion of long QT syndrome (Choi 2021, Johnson 2009, Kapa 2009, Kapplinger 2009, Moss 2002, Poterucha 2015, Splawski 2000, Steffensen 2015, Vijayakumar 2014, Walsh 2021). This variant has also been reported in one asymptomatic individual (Lacaze 2021). This variant is also reported in ClinVar (Variation ID: 200323). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This is a synonymous variant in a highly conserved nucleotide, and computational (Alamut v.2.11) and in vitro functional analyses (O’Neill 2022) predict that this variant may impact splicing by weakening the nearby canonical donor splice site. Based on available information, this variant is considered to be likely pathogenic. References: Choi SH et al. Rare Coding Variants Associated With Electrocardiographic Intervals Identify Monogenic Arrhythmia Susceptibility Genes: A Multi-Ancestry Analysis. Circ Genom Precis Med. 2021 Aug;14(4):e003300. PMID: 34319147. Johnson JN et al. Identification of a possible pathogenic link between congenital long QT syndrome and epilepsy. Neurology. 2009 Jan 20;72(3):224-31. PMID: 19038855. Kapa S et al. Genetic testing for long-QT syndrome: distinguishing pathogenic mutations from benign variants. Circulation. 2009 Nov 3;120(18):1752-60. PMID: 19841300. Kapplinger JD et 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 Sep;6(9):1297-303. PMID: 19716085. Lacaze P et al. Genetic variants associated with inherited cardiovascular disorders among 13,131 asymptomatic older adults of European descent. NPJ Genom Med. 2021 Jun 16;6(1):51. PMID: 34135346. Moss AJ et al. Increased risk of arrhythmic events in long-QT syndrome with mutations in the pore region of the human ether-a-go-go-related gene potassium channel. Circulation. 2002 Feb 19;105(7):794-9. PMID: 11854117. O’Neill M et al. Functional Assays Reclassify Suspected Splice-Altering Variants of Uncertain Significance in Mendelian Channelopathies. bioRxiv 2022.03.14.484344. Poterucha JT et al. Frequency and severity of hypoglycemia in children with beta-blocker-treated long QT syndrome. Heart Rhythm. 2015 Aug;12(8):1815-9. PMID: 25929701. Splawski I et al. Spectrum of mutations in long-QT syndrome genes. KVLQT1, HERG, SCN5A, KCNE1, and KCNE2. Circulation. 2000 Sep 5;102(10):1178-85. PMID: 10973849. Steffensen AB et al. High incidence of functional ion-channel abnormalities in a consecutive Long QT cohort with novel missense genetic variants of unknown significance. Sci Rep. 2015 Jun 12;5:10009. PMID: 26066609. Vijayakumar R et al. Electrophysiologic substrate in congenital Long QT syndrome: noninvasive mapping with electrocardiographic imaging (ECGI). Circulation. 2014 Nov 25;130(22):1936-1943. PMID: 25294783. Walsh R et al. Enhancing rare variant interpretation in inherited arrhythmias through quantitative analysis of consortium disease cohorts and population controls. Genet Med. 2021 Jan;23(1):47-58. PMID: 32893267. - |
Long QT syndrome Pathogenic:2
| Likely pathogenic, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Aug 28, 2023 | This synonymous variant causes a G to A substitution at the last nucleotide of exon 5 of the KCNH2 gene. A RNA study has shown that this variant causes an out-of-frame skipping of exon 5 (PMID: 36197721). As a result, this variant creates a frameshift and premature translation stop signal and is expected to result in an absent or non-functional protein product. This variant has been reported in at least 8 unrelated individuals affected with long QT syndrome (PMID: 10973849, 11854117, 25929701, 32893267, 36102233, ClinVar SCV000255267.11) and in several individuals suspected of having long QT syndrome (PMID: 15840476, 19716085, 23631430). This variant has also been reported in an individual affected with sudden cardiac death (PMID: 28794082). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Oct 24, 2023 | This sequence change affects codon 376 of the KCNH2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the KCNH2 protein. This variant also falls at the last nucleotide of exon 5, which is part of the consensus splice site for this exon. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with long QT syndrome (LQTS) (PMID: 10973849, 11854117, 15840476, 19716085; Invitae). ClinVar contains an entry for this variant (Variation ID: 200323). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. - |
Cardiovascular phenotype Pathogenic:1
| Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 27, 2023 | The c.1128G>A variant (also known as p.Q376Q) is located in coding exon 5 of the KCNH2 gene. This variant results from a G to A substitution at nucleotide position 1128. This nucleotide substitution does not change the glutamine at codon 376. However, this change occurs in the last base pair of coding exon 5, which makes it likely to have some effect on normal mRNA splicing. This alteration has been reported in multiple individuals with clinically diagnosed or suspected long QT syndrome (LQTS) (Splawski I et al. Circulation. 2000;102(10):1178-85; Tester DJ et al. Heart Rhythm. 2005;2(5):507-17; Kapplinger JD et al. Heart Rhythm. 2009;6(9):1297-303; Steffensen AB et al. Sci Rep. 2015; 5:10009; O'Neill MJ et al. Circ Genom Precis Med. 2022 Dec;15(6):e003782; Yee LA et al. J Am Heart Assoc. 2022 Sep;11(18):e025108). Results from a minigene assay have indicated that this alteration may result in some abnormal splicing (O'Neill MJ, et al. Circ Genom Precis Med. 2022 Dec;15(6):e003782). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis for this alteration is inconclusive. Based on the majority of available evidence to date, this variant is likely to be pathogenic. - |
Cardiac arrhythmia Pathogenic:1
| Likely pathogenic, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | May 12, 2023 | This synonymous variant causes a G to A substitution at the last nucleotide of exon 5 of the KCNH2 gene. A RNA study has shown that this variant causes an out-of-frame skipping of exon 5 (PMID: 36197721). As a result, this variant creates a frameshift and premature translation stop signal and is expected to result in an absent or non-functional protein product. This variant has been reported in at least 8 unrelated individuals affected with long QT syndrome (PMID: 10973849, 11854117, 25929701, 32893267, 36102233, ClinVar SCV000255267.11) and in several individuals suspected of having long QT syndrome (PMID: 15840476, 19716085, 23631430). This variant has also been reported in an individual affected with sudden cardiac death (PMID: 28794082). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 9
Find out detailed SpliceAI scores and Pangolin per-transcript scores at