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NM_198056.2(SCN5A):c.1604G>A (p.Arg535Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Apr 2, 2018)
Last evaluated:
Nov 22, 2017
Accession:
VCV000067672.1
Variation ID:
67672
Description:
single nucleotide variant
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NM_198056.2(SCN5A):c.1604G>A (p.Arg535Gln)

Allele ID
78567
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p22.2
Genomic location
3: 38603998 (GRCh38) GRCh38 UCSC
3: 38645489 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_289:g.50675G>A
NC_000003.11:g.38645489C>T
NC_000003.12:g.38603998C>T
... more HGVS
Protein change
R535Q
Other names
-
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00002
Exome Aggregation Consortium (ExAC) 0.00002
Links
ClinGen: CA015071
UniProtKB: Q14524#VAR_074713
dbSNP: rs199473121
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Nov 22, 2017 RCV000638649.1
Pathogenic 1 criteria provided, single submitter Aug 3, 2016 RCV000677695.1
not provided 1 no assertion provided - RCV000058435.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SCN5A Some evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1475 1633

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Nov 22, 2017)
criteria provided, single submitter
Method: clinical testing
Brugada syndrome
Allele origin: germline
Invitae
Accession: SCV000760187.1
Submitted: (Apr 02, 2018)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces arginine with glutamine at codon 535 of the SCN5A protein (p.Arg535Gln). The arginine residue is highly conserved and there is a ... (more)
Pathogenic
(Aug 03, 2016)
criteria provided, single submitter
Method: clinical testing
Long QT syndrome 3
Allele origin: unknown
Equipe Genetique des Anomalies du Developpement,Université de Bourgogne
Study: Clinvar_gadteam_Clinical_exome_analysis_3
Accession: SCV000803843.1
Submitted: (Feb 06, 2018)
Evidence details
not provided
(-)
no assertion provided
Method: literature only
Congenital long QT syndrome
Allele origin: germline
Cardiovascular Biomedical Research Unit,Royal Brompton & Harefield NHS Foundation Trust
Accession: SCV000089955.3
Submitted: (Sep 22, 2016)
Evidence details
Publications
PubMed (2)
Comment:
This variant has been reported as associated with Long QT syndrome in the following publications (PMID:19716085). This is a literature report, and does not necessarily ... (more)

Citations for this variant

Title Author Journal Year Link
The disease-specific phenotype in cardiomyocytes derived from induced pluripotent stem cells of two long QT syndrome type 3 patients. Fatima A PloS one 2013 PMID: 24349418
Paralogous annotation of disease-causing variants in long QT syndrome genes. Ware JS Human mutation 2012 PMID: 22581653
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

Record last updated Oct 27, 2019