ClinVar Genomic variation as it relates to human health
NM_000218.3(KCNQ1):c.477+5G>A
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000218.3(KCNQ1):c.477+5G>A
Variation ID: 53047 Accession: VCV000053047.67
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 11p15.5 11: 2528023 (GRCh38) [ NCBI UCSC ] 11: 2549253 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Dec 6, 2016 Feb 20, 2024 Jan 25, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000218.3:c.477+5G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
intron variant NM_001406836.1:c.477+5G>A intron variant NM_001406837.1:c.207+5G>A intron variant NM_001406838.1:c.477+5G>A intron variant NM_181798.2:c.96+5G>A intron variant NC_000011.10:g.2528023G>A NC_000011.9:g.2549253G>A NG_008935.1:g.88033G>A LRG_287:g.88033G>A LRG_287t1:c.477+5G>A - Protein change
- Other names
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- Canonical SPDI
- NC_000011.10:2528022:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- sequence_variant_affecting_splicing Sequence Ontology [SO:1000071]
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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KCNQ1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh38 GRCh37 |
1648 | 2506 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (1) |
criteria provided, single submitter
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Jan 25, 2024 | RCV000046061.19 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Mar 24, 2022 | RCV000182254.17 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 3, 2017 | RCV000506366.15 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Aug 1, 2023 | RCV000851189.11 | |
Pathogenic (1) |
criteria provided, single submitter
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Feb 15, 2018 | RCV000826192.12 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 10, 2022 | RCV002288548.8 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 31, 2022 | RCV002336179.8 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Aug 21, 2023 | RCV001841645.11 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Feb 15, 2018)
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criteria provided, single submitter
Method: clinical testing
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Congenital long QT syndrome
(Autosomal dominant inheritance)
Affected status: not provided
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000967742.1
First in ClinVar: Aug 26, 2019 Last updated: Aug 26, 2019 |
Comment:
The c.477+5G>A variant in KCNQ1 has been reported in the heterozygous state in > 5 individuals with Long QT syndrome (LQTS), and in the compound … (more)
The c.477+5G>A variant in KCNQ1 has been reported in the heterozygous state in > 5 individuals with Long QT syndrome (LQTS), and in the compound heterozygous sta te in one individual with Jervell and Lange-Nielsen syndrome (JLNS; Ackerman 199 9, Chouabe 2000, Hofman 2011, Crehalet 2012, Obeyesekere 2012). It segregated wi th prolonged QT-intervals in at least 3 relatives from 2 different families, inc luding that of the individual with JNLS (Ackerman 1999, Chouabe 2000). At least two relatives who were heterozygous carriers of this variant were clinically asy mptomatic for LQTS, suggesting reduced penetrance (Chouabe 2000). The c.477+5G>A variant has also been reported by other clinical laboratories in ClinVar (Varia tion ID: 53047). In addition, it has been identified in 1/30782 South Asian chr omosomes and 2/111700 European chromosomes by the Genome Aggregation Database (g nomAD, http://gnomad.broadinstitute.org/; dbSNP rs397508111). This variant is lo cated in the 5' splice region. Functional studies using patient cDNA have shown that the c.477+5G>A variant impacts splicing (Chouabe 2000, Crehalet 2012), lead ing to an aberrant mRNA transcript that is predicted to encode the first 159 ami no acids of the protein, followed by 4 aberrant residues and a premature termina tion codon. This would likely result in an absent protein. Loss-of-function vari ants in KCNQ1 are associated with LQTS (also known as Romano-Ward syndrome) in t he heterozygous state and with JLNS in the compound heterozygous or homozygous s tate. In summary, this variant meets criteria to be classified as pathogenic for LQTS in an autosomal dominant manner based upon presence in multiple affected i ndividuals, segregation studies, predicted impact to the protein, and functional studies. ACMG/AMP Criteria applied (Richards 2015): PVS1, PM2, PS4_Moderate, PP 1_Supporting. (less)
Number of individuals with the variant: 3
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Pathogenic
(May 23, 2019)
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criteria provided, single submitter
Method: research
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Long QT syndrome 1
Affected status: unknown
Allele origin:
maternal
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HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology
Study: AGHI_WGS
Accession: SCV000993435.1 First in ClinVar: Sep 22, 2019 Last updated: Sep 22, 2019 |
Observation 1:
Number of individuals with the variant: 1
Observation 2:
Number of individuals with the variant: 1
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Pathogenic
(Aug 10, 2022)
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criteria provided, single submitter
Method: clinical testing
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Long QT syndrome 1
Affected status: yes
Allele origin:
germline
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MGZ Medical Genetics Center
Accession: SCV002581660.1
First in ClinVar: Oct 15, 2022 Last updated: Oct 15, 2022 |
Number of individuals with the variant: 2
Sex: male
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Pathogenic
(Oct 05, 2022)
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criteria provided, single submitter
Method: research, in vitro
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Long QT syndrome 1
Affected status: unknown, not applicable
Allele origin:
unknown,
not applicable
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Roden Lab, Vanderbilt University Medical Center
Accession: SCV002588740.1
First in ClinVar: Nov 05, 2022 Last updated: Nov 05, 2022 |
Comment:
The KCNQ1 c.477+5G>A variant was observed in 7 cases of LQTS and was observed rarely in population databases (PMID: 32893267). The variant is highly predicted … (more)
The KCNQ1 c.477+5G>A variant was observed in 7 cases of LQTS and was observed rarely in population databases (PMID: 32893267). The variant is highly predicted to alter mRNA splicing. A minigene assay provided experimental support for this prediction. Collectively, this evidence allows the classification of this variant as Pathogenic. (less)
Observation 1: Observation 2:
Method: Minigene Assay
Result:
A HEK293T minigene assay showed multiple pseudoexon inclusions and exon skipping in the variant but not WT plasmid.
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Pathogenic
(Jan 31, 2022)
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criteria provided, single submitter
Method: clinical testing
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Cardiovascular phenotype
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002634712.1
First in ClinVar: Nov 29, 2022 Last updated: Nov 29, 2022 |
Comment:
The c.477+5G>A intronic pathogenic mutation results from a G to A substitution 5 nucleotides after coding exon 2 in the KCNQ1 gene. This mutation (also … (more)
The c.477+5G>A intronic pathogenic mutation results from a G to A substitution 5 nucleotides after coding exon 2 in the KCNQ1 gene. This mutation (also known as IVS2+5G>A, IVS1+5G>A and c.639+5G>A) has been reported in multiple individuals with long QT syndrome (LQTS) and in numerous LQTS cohorts, and has segregated with prolonged QT interval in several small families (Ackerman MJ et al. Mayo Clin. Proc. 1999;74:1088-94; Chouabe C et al. Cardiovasc. Res. 2000;45:971-80; Millat G et al. Clin. Genet. 2006;70:214-27; Kapplinger JD et al. Heart Rhythm. 2009;6:1297-303; Hofman N et al. Neth Heart J. 2011;19:10-16; Crehalet H et al. Cardiogenetics. 2012;2:e6; Obeyesekere MN et al. J. Cardiovasc. Electrophysiol. 2012;23:637-42; Cuneo BF et al. Circ Arrhythm Electrophysiol. 2013;6:946-51; Al-Hassnan ZN et al. Heart Rhythm. 2017;14:1191-1199). In addition, this mutation has been detected in the homozygous state in two families, and in trans with other KCNQ1 alterations (p.Y171*, p.R243H, and p.K581*) in additional unrelated individuals with autosomal recessive Jervell and Lange-Nielson syndrome (JLNS) (Chouabe C et al. Cardiovasc. Res. 2000;45:971-80; Giudicessi JR et al. Circ Cardiovasc Genet. 2013;6:193-200; Amirian A et al. J Mol Genet med. 2018;12:(3); Qiu Y et al. Neural Plast. 2020 May;2020:3569359). An in vitro minigene assay indicated that this mutation leads to the utilization of a cryptic donor site 80 nt downstream in intron 2, resulting in a frameshift and premature truncation (Crehalet H et al. Cardiogenetics. 2012;2:e6). Alterations affecting the same splice site (c.477+5G>C and c.477+1G>A) have also been associated with LQTS (Kapplinger JD et al. Heart Rhythm. 2009;6:1297-303). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. (less)
Number of individuals with the variant: 1
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Pathogenic
(Mar 24, 2022)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000234557.13
First in ClinVar: Jul 05, 2015 Last updated: Mar 04, 2023 |
Comment:
Not observed at significant frequency in large population cohorts (gnomAD); Non-canonical splice site variant demonstrated to result in loss-of-function (Crehalet et al., 2012); Reported in … (more)
Not observed at significant frequency in large population cohorts (gnomAD); Non-canonical splice site variant demonstrated to result in loss-of-function (Crehalet et al., 2012); Reported in ClinVar as pathogenic or likely pathogenic (ClinVar Variant ID# 53047; ClinVar); This variant is associated with the following publications: (PMID: 7446532, 25525159, 10973849, 18441444, 16922724, 10560595, 19716085, 21350584, 23124029, 15840476, 10728423, 22429796, 28438721, 23995044, 32048431, 31737537, 31447099, 34135346, 23392653, 32508908) (less)
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Pathogenic
(Aug 01, 2023)
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criteria provided, single submitter
Method: clinical testing
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Long QT syndrome 1
Affected status: yes
Allele origin:
germline
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Molecular Genetics Laboratory - Cardiogenetics, CHU de Nantes
Accession: SCV004024178.1
First in ClinVar: Aug 13, 2023 Last updated: Aug 13, 2023 |
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Pathogenic
(Jan 14, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV003826504.2
First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024 |
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Pathogenic
(Mar 06, 2023)
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criteria provided, single submitter
Method: clinical testing
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Cardiac arrhythmia
Affected status: unknown
Allele origin:
germline
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Color Diagnostics, LLC DBA Color Health
Accession: SCV001340893.3
First in ClinVar: Jun 22, 2020 Last updated: Feb 14, 2024 |
Comment:
This variant causes a G to A nucleotide substitution at the +5 position of intron 2 splice donor site of the KCNQ1 gene. Splice site … (more)
This variant causes a G to A nucleotide substitution at the +5 position of intron 2 splice donor site of the KCNQ1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. A mini-gene assay has shown that this variant activates an alternate splice donor site at c.477+80, which results in a frameshift and premature protein truncation (Crehalet et al., 2012, doi.org/10.4081/cardiogenetics.2012.e6). This variant has been reported in over ten individuals affected with long QT syndrome or prolonged QT interval (PMID: 10560595, 10728423, 10973849, 16922724, 22429796, 28438721; Crehalet et al., 2012, doi.org/10.4081/cardiogenetics.2012.e; Hofman 2013, dissertation, Univ. of Amsterdam, ISBN 9789461822116). This variant has also been identified in five biallelic individuals affected with autosomal recessive Jervell and Lange-Nielsen syndrome (PMID: 10728423, 23392653, 32508908; Amirian 2018, doi:10.4172/1747-0862.1000359), indicating that this variant contributes to disease. This variant has been identified in 3/250976 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. (less)
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Pathogenic
(Jan 03, 2017)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000604065.1
First in ClinVar: Sep 30, 2017 Last updated: Sep 30, 2017 |
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Pathogenic
(Aug 21, 2023)
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criteria provided, single submitter
Method: clinical testing
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Cardiac arrhythmia
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV004038740.1
First in ClinVar: Oct 07, 2023 Last updated: Oct 07, 2023 |
Comment:
Variant summary: KCNQ1 c.477+5G>A alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly … (more)
Variant summary: KCNQ1 c.477+5G>A alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict the variant abolishes the 5 canonical splicing donor site. Two predict the variant weakens the 5' canonical splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing in Hela cells by a minigene splicing assay (Crehalet_2012). The variant allele was found at a frequency of 1.2e-05 in 250976 control chromosomes. c.477+5G>A has been reported in the literature in multiple individuals affected with features of autosomal dominant Arrhythmia including prolonged QT/QTc interval or Long-QT Syndrome (examples, Crehalet_2012, Yee_2022, Al-Hassnan_2017). This variant has also been observed at a compound heterozygous state along with second pathogenic variants in at-least two individuals diagnosed with autosomal recessive Jervell and Lange-Nielsen syndrome (examples, Chouabe_2000, Qiu_2020), which the patients present both congenital sensorineural deafness and prolonged QT intervals. These data indicate that the variant is very likely to be associated with both diseases. The following publications have been ascertained in the context of this evaluation (PMID: 28438721, 10728423, 32508908, 36102233, Crehalet_2012 without PMID). 11 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(Jan 25, 2024)
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criteria provided, single submitter
Method: clinical testing
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Long QT syndrome
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000074074.11
First in ClinVar: Jul 03, 2013 Last updated: Feb 20, 2024 |
Comment:
This sequence change falls in intron 2 of the KCNQ1 gene. It does not directly change the encoded amino acid sequence of the KCNQ1 protein. … (more)
This sequence change falls in intron 2 of the KCNQ1 gene. It does not directly change the encoded amino acid sequence of the KCNQ1 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs397508111, gnomAD 0.003%). This variant has been observed in individuals with Jervell and Lange-Nielsen syndrome (JLNS) and/or long QT syndrome (PMID: 10560595, 10973849, 16922724, 22429796, 23392653). This variant is also known as c.639+5G>A, IVSI+5G>A, IVS2+5G>A, and M159sp. ClinVar contains an entry for this variant (Variation ID: 53047). 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. (less)
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Germline Functional Evidence
Functional
Help
The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence |
Method
Help
A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter. |
Result
Help
A brief description of the result of this method for this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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sequence_variant_affecting_splicing
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Roden Lab, Vanderbilt University Medical Center
Accession: SCV002588740.1
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Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Functional Assays Reclassify Suspected Splice-Altering Variants of Uncertain Significance in Mendelian Channelopathies. | O'Neill MJ | Circulation. Genomic and precision medicine | 2022 | PMID: 36197721 |
Sex Differences and Utility of Treadmill Testing in Long-QT Syndrome. | Yee LA | Journal of the American Heart Association | 2022 | PMID: 36102233 |
Jervell and Lange-Nielsen Syndrome due to a Novel Compound Heterozygous KCNQ1 Mutation in a Chinese Family. | Qiu Y | Neural plasticity | 2020 | PMID: 32508908 |
Clinical profile and mutation spectrum of long QT syndrome in Saudi Arabia: The impact of consanguinity. | Al-Hassnan ZN | Heart rhythm | 2017 | PMID: 28438721 |
Arrhythmia phenotype during fetal life suggests long-QT syndrome genotype: risk stratification of perinatal long-QT syndrome. | Cuneo BF | Circulation. Arrhythmia and electrophysiology | 2013 | PMID: 23995044 |
Prevalence and potential genetic determinants of sensorineural deafness in KCNQ1 homozygosity and compound heterozygosity. | Giudicessi JR | Circulation. Cardiovascular genetics | 2013 | PMID: 23392653 |
Fetal heart rate predictors of long QT syndrome. | Mitchell JL | Circulation | 2012 | PMID: 23124029 |
Mutations in cytoplasmic loops of the KCNQ1 channel and the risk of life-threatening events: implications for mutation-specific response to β-blocker therapy in type 1 long-QT syndrome. | Barsheshet A | Circulation | 2012 | PMID: 22456477 |
End-recovery QTc: a useful metric for assessing genetic variants of unknown significance in long-QT syndrome. | Obeyesekere MN | Journal of cardiovascular electrophysiology | 2012 | PMID: 22429796 |
Recurrent and Founder Mutations in the Netherlands: the Long-QT Syndrome. | Hofman N | Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation | 2011 | PMID: 21350584 |
Spectrum and prevalence of mutations from the first 2,500 consecutive unrelated patients referred for the FAMILION long QT syndrome genetic test. | Kapplinger JD | Heart rhythm | 2009 | PMID: 19716085 |
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. | Buratti E | Nucleic acids research | 2007 | PMID: 17576681 |
Spectrum of pathogenic mutations and associated polymorphisms in a cohort of 44 unrelated patients with long QT syndrome. | Millat G | Clinical genetics | 2006 | PMID: 16922724 |
Compendium of cardiac channel mutations in 541 consecutive unrelated patients referred for long QT syndrome genetic testing. | Tester DJ | Heart rhythm | 2005 | PMID: 15840476 |
Spectrum of mutations in long-QT syndrome genes. KVLQT1, HERG, SCN5A, KCNE1, and KCNE2. | Splawski I | Circulation | 2000 | PMID: 10973849 |
Novel mutations in KvLQT1 that affect Iks activation through interactions with Isk. | Chouabe C | Cardiovascular research | 2000 | PMID: 10728423 |
Swimming, a gene-specific arrhythmogenic trigger for inherited long QT syndrome. | Ackerman MJ | Mayo Clinic proceedings | 1999 | PMID: 10560595 |
Statistical features of human exons and their flanking regions. | Zhang MQ | Human molecular genetics | 1998 | PMID: 9536098 |
4-Keto-gamma-carotene(beta, psi-caroten-4-one), the major pigment of an Arthrobacter sp. | Fiasson JL | Canadian journal of biochemistry | 1976 | PMID: 1000359 |
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Text-mined citations for rs397508111 ...
HelpRecord last updated Mar 23, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.