NM_000335.5(SCN5A):c.3535G>A (p.Ala1179Thr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 17, 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:: RCV003655286.2

Allele description [Variation Report for NM_000335.5(SCN5A):c.3535G>A (p.Ala1179Thr)]

NM_000335.5(SCN5A):c.3535G>A (p.Ala1179Thr)

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.3535G>A (p.Ala1179Thr)

HGVS:

NC_000003.12:g.38575425C>T
NG_008934.1:g.79248G>A
NM_000335.5:c.3535G>AMANE SELECT
NM_001099404.2:c.3538G>A
NM_001099405.2:c.3538G>A
NM_001160160.2:c.3535G>A
NM_001160161.2:c.3376G>A
NM_001354701.2:c.3535G>A
NM_198056.3:c.3538G>A
NP_000326.2:p.Ala1179Thr
NP_001092874.1:p.Ala1180Thr
NP_001092875.1:p.Ala1180Thr
NP_001153632.1:p.Ala1179Thr
NP_001153633.1:p.Ala1126Thr
NP_001341630.1:p.Ala1179Thr
NP_932173.1:p.Ala1180Thr
NP_932173.1:p.Ala1180Thr
LRG_289t1:c.3538G>A
LRG_289:g.79248G>A
LRG_289p1:p.Ala1180Thr
NC_000003.11:g.38616916C>T
NM_198056.2:c.3538G>A

Protein change:

A1126T

Links:

dbSNP: rs1575749176

NCBI 1000 Genomes Browser:

rs1575749176

Molecular consequence:

NM_000335.5:c.3535G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.3538G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.3538G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.3535G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.3376G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.3535G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.3538G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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MAG TPA_asm: Candidatus Thalassarchaeaceae archaeon isolate UBA12570, whole geno...
MAG TPA_asm: Candidatus Thalassarchaeaceae archaeon isolate UBA12570, whole genome shotgun sequencing project
gi|1851982472|tpg|DUIL00000000.1|DU 00000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000953231	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 17, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000953231

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 17, 2022)

germline

clinical testing

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

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000953231.3

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 656471). This variant has not been reported in the literature in individuals affected with SCN5A-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1180 of the SCN5A protein (p.Ala1180Thr).

#	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: Oct 26, 2024

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