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NM_000335.5(SCN5A):c.2989G>T (p.Ala997Ser) AND SCN5A-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 7, 2022
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:
RCV004532320.2

Allele description

NM_000335.5(SCN5A):c.2989G>T (p.Ala997Ser)

Genes:
LOC110121269:VISTA enhancer hs2177 [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.2989G>T (p.Ala997Ser)
Other names:
p.A997S:GCC>TCC
HGVS:
  • NC_000003.12:g.38581170C>A
  • NG_008934.1:g.73503G>T
  • NG_053884.1:g.2909C>A
  • NM_000335.5:c.2989G>TMANE SELECT
  • NM_001099404.1:c.2989G>T
  • NM_001099404.2:c.2989G>T
  • NM_001099405.2:c.2989G>T
  • NM_001160160.2:c.2989G>T
  • NM_001160161.2:c.2989G>T
  • NM_001354701.2:c.2989G>T
  • NM_198056.3:c.2989G>T
  • NP_000326.2:p.Ala997Ser
  • NP_001092874.1:p.Ala997Ser
  • NP_001092875.1:p.Ala997Ser
  • NP_001153632.1:p.Ala997Ser
  • NP_001153633.1:p.Ala997Ser
  • NP_001341630.1:p.Ala997Ser
  • NP_932173.1:p.Ala997Ser
  • NP_932173.1:p.Ala997Ser
  • LRG_289t1:c.2989G>T
  • LRG_289t3:c.2989G>T
  • LRG_289:g.73503G>T
  • LRG_289p1:p.Ala997Ser
  • NC_000003.11:g.38622661C>A
  • NM_198056.2:c.2989G>T
  • NM_198056.3:c.2989G>T
  • Q14524:p.Ala997Ser
Protein change:
A997S; ALA997SER
Links:
UniProtKB: Q14524#VAR_017676; OMIM: 600163.0019; dbSNP: rs137854609
NCBI 1000 Genomes Browser:
rs137854609
Molecular consequence:
  • NM_000335.5:c.2989G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099404.2:c.2989G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099405.2:c.2989G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160160.2:c.2989G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160161.2:c.2989G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354701.2:c.2989G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198056.3:c.2989G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
SCN5A-related disorder
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004114693PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Dec 7, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004114693.1

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

Description

The SCN5A c.2989G>T variant is predicted to result in the amino acid substitution p.Ala997Ser. This variant was reported as pathogenic in a cohort of sudden infant death syndrome cohort and in a patient with a long QT syndrome phenotype (Paludan-Müller et al. 2019. PubMed ID: 31043699; Kapplinger et al. 2009. PubMed ID: 19716085; Ackerman et al. 2001. PubMed ID: 11710892). This variant is reported in 0.00081% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/3-38622661-C-A). Taken together, this variant is interpreted as likely pathogenic.

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

Last Updated: Sep 29, 2024