NM_000335.5(SCN5A):c.5713A>G (p.Met1905Val) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 26, 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:: RCV003542328.3

Allele description [Variation Report for NM_000335.5(SCN5A):c.5713A>G (p.Met1905Val)]

NM_000335.5(SCN5A):c.5713A>G (p.Met1905Val)

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.5713A>G (p.Met1905Val)

HGVS:

NC_000003.12:g.38550656T>C
NG_008934.1:g.104017A>G
NM_000335.5:c.5713A>GMANE SELECT
NM_001099404.2:c.5716A>G
NM_001099405.2:c.5662A>G
NM_001160160.2:c.5617A>G
NM_001160161.2:c.5554A>G
NM_001354701.2:c.5659A>G
NM_198056.3:c.5716A>G
NP_000326.2:p.Met1905Val
NP_001092874.1:p.Met1906Val
NP_001092875.1:p.Met1888Val
NP_001153632.1:p.Met1873Val
NP_001153633.1:p.Met1852Val
NP_001341630.1:p.Met1887Val
NP_932173.1:p.Met1906Val
LRG_289t1:c.5716A>G
LRG_289:g.104017A>G
NC_000003.11:g.38592147T>C
NC_000003.11:g.38592147T>C
NM_198056.2:c.5716A>G

Protein change:

M1852V

Links:

dbSNP: rs923779348

NCBI 1000 Genomes Browser:

rs923779348

Molecular consequence:

NM_000335.5:c.5713A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.5716A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.5662A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.5617A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.5554A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.5659A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.5716A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003452565	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 26, 2023)	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

SCV003452565

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 26, 2023)

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, SCV003452565.2

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

Description

This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1906 of the SCN5A protein (p.Met1906Val). This variant has not been reported in the literature in individuals affected with SCN5A-related conditions. 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 919315).

#	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

ClinVar

Relating variation to medicine