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NM_000335.5(SCN5A):c.157C>T (p.Arg53Trp) AND Cardiovascular phenotype

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 7, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002402807.3

Allele description [Variation Report for NM_000335.5(SCN5A):c.157C>T (p.Arg53Trp)]

NM_000335.5(SCN5A):c.157C>T (p.Arg53Trp)

Gene:
SCN5A:sodium voltage-gated channel alpha subunit 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p22.2
Genomic location:
Preferred name:
NM_000335.5(SCN5A):c.157C>T (p.Arg53Trp)
HGVS:
  • NC_000003.12:g.38633151G>A
  • NG_008934.1:g.21522C>T
  • NM_000335.5:c.157C>TMANE SELECT
  • NM_001099404.2:c.157C>T
  • NM_001099405.2:c.157C>T
  • NM_001160160.2:c.157C>T
  • NM_001160161.2:c.157C>T
  • NM_001354701.2:c.157C>T
  • NM_198056.3:c.157C>T
  • NP_000326.2:p.Arg53Trp
  • NP_001092874.1:p.Arg53Trp
  • NP_001092875.1:p.Arg53Trp
  • NP_001153632.1:p.Arg53Trp
  • NP_001153633.1:p.Arg53Trp
  • NP_001341630.1:p.Arg53Trp
  • NP_932173.1:p.Arg53Trp
  • LRG_289t1:c.157C>T
  • LRG_289:g.21522C>T
  • NC_000003.11:g.38674642G>A
  • NM_198056.2:c.157C>T
Protein change:
R53W
Links:
dbSNP: rs878859550
NCBI 1000 Genomes Browser:
rs878859550
Molecular consequence:
  • NM_000335.5:c.157C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099404.2:c.157C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099405.2:c.157C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160160.2:c.157C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160161.2:c.157C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354701.2:c.157C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198056.3:c.157C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Cardiovascular phenotype
Identifiers:
MedGen: CN230736

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002704151Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Jun 7, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Variant panorama in 1,385 index patients and sensitivity of expanded next-generation sequencing panels in arrhythmogenic disorders.

Marschall C, Moscu-Gregor A, Klein HG.

Cardiovasc Diagn Ther. 2019 Oct;9(Suppl 2):S292-S298. doi: 10.21037/cdt.2019.06.06.

PubMed [citation]
PMID:
31737537
PMCID:
PMC6837920

Details of each submission

From Ambry Genetics, SCV002704151.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The p.R53W variant (also known as c.157C>T), located in coding exon 1 of the SCN5A gene, results from a C to T substitution at nucleotide position 157. The arginine at codon 53 is replaced by tryptophan, an amino acid with dissimilar properties, and is located in the cytoplasmic N-terminal region. This variant was reported as an incidental finding in a family with NOG-related proximal symphalangism and moderate hearing loss; however, cardiac phenotype was not provided (Ma C et al. BMC Med Gen. 2019;20:169). Additionally, this alteration has been detected in a Brugada syndrome genetic testing cohort; however, clinical details were limited (Marschall C et al. Cardiovasc Diagn Ther, 2019 Oct;9:S292-S298). This amino acid position is not well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024