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NM_181798.1(KCNQ1):c.1563C>T (p.Val521=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(6);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 1, 2020
Accession:
VCV000138008.6
Variation ID:
138008
Description:
single nucleotide variant
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NM_181798.1(KCNQ1):c.1563C>T (p.Val521=)

Allele ID
141711
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p15.4
Genomic location
11: 2847916 (GRCh38) GRCh38 UCSC
11: 2869146 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.9:g.2869146C>T
NC_000011.10:g.2847916C>T
NM_000218.2:c.1944C>T NP_000209.2:p.Val648= synonymous
... more HGVS
Protein change
-
Other names
p.V648V:GTC>GTT
Canonical SPDI
NC_000011.10:2847915:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00021
The Genome Aggregation Database (gnomAD) 0.00010
1000 Genomes Project 0.00080
The Genome Aggregation Database (gnomAD), exomes 0.00017
Trans-Omics for Precision Medicine (TOPMed) 0.00034
Links
dbSNP: rs201698592
ClinGen: CA006611
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Mar 19, 2013 RCV000126442.2
Benign 1 criteria provided, single submitter Dec 1, 2020 RCV000631840.4
Benign 1 criteria provided, single submitter Apr 27, 2017 RCV001103215.1
Benign 1 criteria provided, single submitter Apr 27, 2017 RCV001103216.1
Benign 1 criteria provided, single submitter Apr 27, 2017 RCV001105132.1
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001105133.1
Benign 1 criteria provided, single submitter Nov 21, 2018 RCV001184987.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KCNQ1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh38
GRCh37
1161 1427
KCNQ1-AS1 - - - GRCh38
GRCh38
- 167

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Mar 19, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000169949.11
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Jervell and Lange-Nielsen syndrome 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001259942.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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, … (more)
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Long QT syndrome 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001259943.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (2)
Comment:
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, … (more)
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Short QT syndrome 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001262054.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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, … (more)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Atrial fibrillation, familial, 3
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001262055.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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, … (more)
Benign
(Nov 21, 2018)
criteria provided, single submitter
Method: clinical testing
Arrhythmia
Allele origin: germline
Color Health, Inc
Accession: SCV001351099.1
Submitted: (May 19, 2020)
Evidence details
Benign
(Dec 01, 2020)
criteria provided, single submitter
Method: clinical testing
Long QT syndrome
Allele origin: germline
Invitae
Accession: SCV000752937.4
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Postmortem molecular analysis of KCNQ1, KCNH2, KCNE1 and KCNE2 genes in sudden unexplained nocturnal death syndrome in the Chinese Han population. Liu C Forensic science international 2013 PMID: 23890619
Genetic polymorphisms in KCNQ1, HERG, KCNE1 and KCNE2 genes in the Chinese, Malay and Indian populations of Singapore. Koo SH British journal of clinical pharmacology 2006 PMID: 16487223

Text-mined citations for rs201698592...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 14, 2021