NM_000335.5(SCN5A):c.86C>T (p.Ala29Val) AND Brugada syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 25, 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:: RCV001043149.4

Allele description [Variation Report for NM_000335.5(SCN5A):c.86C>T (p.Ala29Val)]

NM_000335.5(SCN5A):c.86C>T (p.Ala29Val)

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.86C>T (p.Ala29Val)

Other names:

p.A29V:GCA>GTA

HGVS:

NC_000003.12:g.38633222G>A
NG_008934.1:g.21451C>T
NM_000335.5:c.86C>TMANE SELECT
NM_001099404.2:c.86C>T
NM_001099405.2:c.86C>T
NM_001160160.2:c.86C>T
NM_001160161.2:c.86C>T
NM_001354701.2:c.86C>T
NM_198056.3:c.86C>T
NP_000326.2:p.Ala29Val
NP_001092874.1:p.Ala29Val
NP_001092875.1:p.Ala29Val
NP_001153632.1:p.Ala29Val
NP_001153633.1:p.Ala29Val
NP_001341630.1:p.Ala29Val
NP_932173.1:p.Ala29Val
NP_932173.1:p.Ala29Val
LRG_289t1:c.86C>T
LRG_289:g.21451C>T
LRG_289p1:p.Ala29Val
NC_000003.11:g.38674713G>A
NM_198056.2:c.86C>T

Protein change:

A29V

Links:

dbSNP: rs562675882

NCBI 1000 Genomes Browser:

rs562675882

Molecular consequence:

NM_000335.5:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Brugada syndrome
Synonyms:: Sudden unexpected nocturnal death syndrome; Sudden unexplained nocturnal death syndrome; Sudden Unexplained Death Syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015263; MedGen: C1142166; OMIM: PS601144

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001206866	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 25, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 23098067, 28611029, 33221895, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001206866

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 25, 2022)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Founder mutations characterise the mutation panorama in 200 Swedish index cases referred for Long QT syndrome genetic testing.

Stattin EL, Boström IM, Winbo A, Cederquist K, Jonasson J, Jonsson BA, Diamant UB, Jensen SM, Rydberg A, Norberg A.

BMC Cardiovasc Disord. 2012 Oct 25;12:95. doi: 10.1186/1471-2261-12-95.

PubMed [citation]

PMID:: 23098067
PMCID:: PMC3520728

Whole Exome Sequencing Identifies Truncating Variants in Nuclear Envelope Genes in Patients With Cardiovascular Disease.

Haskell GT, Jensen BC, Samsa LA, Marchuk D, Huang W, Skrzynia C, Tilley C, Seifert BA, Rivera-Muñoz EA, Koller B, Wilhelmsen KC, Liu J, Alhosaini H, Weck KE, Evans JP, Berg JS.

Circ Cardiovasc Genet. 2017 Jun;10(3). doi: 10.1161/CIRCGENETICS.116.001443.

PubMed [citation]

PMID:: 28611029
PMCID:: PMC5497793

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001206866.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 29 of the SCN5A protein (p.Ala29Val). This variant is present in population databases (rs562675882, gnomAD 0.04%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with KCNQ1-related conditions (PMID: 23098067, 28611029, 33221895). ClinVar contains an entry for this variant (Variation ID: 201428). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C55"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Jun 22, 2025

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