NM_000335.5(SCN5A):c.43A>G (p.Arg15Gly) AND Cardiovascular phenotype

Germline classification:: Likely benign (1 submission)
Last evaluated:: Aug 23, 2021
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:: RCV002327435.9

Allele description [Variation Report for NM_000335.5(SCN5A):c.43A>G (p.Arg15Gly)]

NM_000335.5(SCN5A):c.43A>G (p.Arg15Gly)

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.43A>G (p.Arg15Gly)

HGVS:

NC_000003.12:g.38633265T>C
NG_008934.1:g.21408A>G
NM_000335.5:c.43A>GMANE SELECT
NM_001099404.2:c.43A>G
NM_001099405.2:c.43A>G
NM_001160160.2:c.43A>G
NM_001160161.2:c.43A>G
NM_001354701.2:c.43A>G
NM_198056.3:c.43A>G
NP_000326.2:p.Arg15Gly
NP_001092874.1:p.Arg15Gly
NP_001092875.1:p.Arg15Gly
NP_001153632.1:p.Arg15Gly
NP_001153633.1:p.Arg15Gly
NP_001341630.1:p.Arg15Gly
NP_932173.1:p.Arg15Gly
LRG_289t1:c.43A>G
LRG_289:g.21408A>G
NC_000003.11:g.38674756T>C
NC_000003.11:g.38674756T>C
NM_198056.2:c.43A>G

Protein change:

R15G

Links:

dbSNP: rs752553088

NCBI 1000 Genomes Browser:

rs752553088

Molecular consequence:

NM_000335.5:c.43A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.43A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.43A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.43A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.43A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.43A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.43A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002631254	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Aug 23, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24631775, 29247119 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002631254

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Aug 23, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Cardiac channelopathy testing in 274 ethnically diverse sudden unexplained deaths.

Wang D, Shah KR, Um SY, Eng LS, Zhou B, Lin Y, Mitchell AA, Nicaj L, Prinz M, McDonald TV, Sampson BA, Tang Y.

Forensic Sci Int. 2014 Apr;237:90-9. doi: 10.1016/j.forsciint.2014.01.014. Epub 2014 Feb 15.

PubMed [citation]

PMID:: 24631775

Applying High-Resolution Variant Classification to Cardiac Arrhythmogenic Gene Testing in a Demographically Diverse Cohort of Sudden Unexplained Deaths.

Lin Y, Williams N, Wang D, Coetzee W, Zhou B, Eng LS, Um SY, Bao R, Devinsky O, McDonald TV, Sampson BA, Tang Y.

Circ Cardiovasc Genet. 2017 Dec;10(6). doi:pii: e001839. 10.1161/CIRCGENETICS.117.001839.

PubMed [citation]

PMID:: 29247119

Details of each submission

From Ambry Genetics, SCV002631254.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 8, 2024

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