NM_000335.5(SCN5A):c.3732G>T (p.Met1244Ile) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 19, 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:: RCV003660867.3

Allele description [Variation Report for NM_000335.5(SCN5A):c.3732G>T (p.Met1244Ile)]

NM_000335.5(SCN5A):c.3732G>T (p.Met1244Ile)

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.3732G>T (p.Met1244Ile)

HGVS:

NC_000003.12:g.38566514C>A
NG_008934.1:g.88159G>T
NM_000335.5:c.3732G>TMANE SELECT
NM_001099404.2:c.3735G>T
NM_001099405.2:c.3735G>T
NM_001160160.2:c.3732G>T
NM_001160161.2:c.3573G>T
NM_001354701.2:c.3732G>T
NM_198056.3:c.3735G>T
NP_000326.2:p.Met1244Ile
NP_001092874.1:p.Met1245Ile
NP_001092875.1:p.Met1245Ile
NP_001153632.1:p.Met1244Ile
NP_001153633.1:p.Met1191Ile
NP_001341630.1:p.Met1244Ile
NP_932173.1:p.Met1245Ile
LRG_289t1:c.3735G>T
LRG_289:g.88159G>T
NC_000003.11:g.38608005C>A
NC_000003.11:g.38608005C>A
NM_198056.2:c.3735G>T

Protein change:

M1191I

Links:

dbSNP: rs753677814

NCBI 1000 Genomes Browser:

rs753677814

Molecular consequence:

NM_000335.5:c.3732G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.3735G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.3735G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.3732G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.3573G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.3732G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.3735G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Smp_155700 [Schistosoma mansoni]
Smp_155700 [Schistosoma mansoni]
Gene ID:8347668

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003795995	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 19, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 27554632, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003795995

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 19, 2023)

germline

clinical testing

PubMed (2)
[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

Analysis of SCN5A Gene Variants in East Slovak Patients with Cardiomyopathy.

Priganc M, Zigová M, Boroňová I, Bernasovská J, Dojčáková D, Szabadosová V, Mydlárová Blaščáková M, Tóthová I, Kmec J, Bernasovský I.

J Clin Lab Anal. 2017 Mar;31(2). doi: 10.1002/jcla.22037. Epub 2016 Aug 24.

PubMed [citation]

PMID:: 27554632
PMCID:: PMC6816823

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, SCV003795995.3

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

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. 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: 924677). This missense change has been observed in individual(s) with SCN5A-related conditions (PMID: 27554632). 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 isoleucine, which is neutral and non-polar, at codon 1245 of the SCN5A protein (p.Met1245Ile).

#	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: Nov 10, 2024

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