NM_000335.5(SCN5A):c.3539T>C (p.Val1180Ala) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 18, 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:: RCV003654243.2

Allele description [Variation Report for NM_000335.5(SCN5A):c.3539T>C (p.Val1180Ala)]

NM_000335.5(SCN5A):c.3539T>C (p.Val1180Ala)

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.3539T>C (p.Val1180Ala)

HGVS:

NC_000003.12:g.38575421A>G
NG_008934.1:g.79252T>C
NM_000335.5:c.3539T>CMANE SELECT
NM_001099404.2:c.3542T>C
NM_001099405.2:c.3542T>C
NM_001160160.2:c.3539T>C
NM_001160161.2:c.3380T>C
NM_001354701.2:c.3539T>C
NM_198056.3:c.3542T>C
NP_000326.2:p.Val1180Ala
NP_001092874.1:p.Val1181Ala
NP_001092875.1:p.Val1181Ala
NP_001153632.1:p.Val1180Ala
NP_001153633.1:p.Val1127Ala
NP_001341630.1:p.Val1180Ala
NP_932173.1:p.Val1181Ala
NP_932173.1:p.Val1181Ala
LRG_289t1:c.3542T>C
LRG_289:g.79252T>C
LRG_289p1:p.Val1181Ala
NC_000003.11:g.38616912A>G
NM_000335.5:c.3539T>C
NM_198056.2:c.3542T>C

Protein change:

V1127A

Links:

dbSNP: rs376965389

NCBI 1000 Genomes Browser:

rs376965389

Molecular consequence:

NM_000335.5:c.3539T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.3542T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.3542T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.3539T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.3380T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.3539T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.3542T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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1162751[uid] (1)
Taxonomy
313558[uid] (1)
Taxonomy
6-Methyluracil (4708097)
BioSample
Homo sapiens Ly6/neurotoxin 1 (LYNX1), transcript variant 1, mRNA
Homo sapiens Ly6/neurotoxin 1 (LYNX1), transcript variant 1, mRNA
gi|212286119|ref|NM_023946.2|

Nucleotide
Combined low LDL and fibrinogen
Combined low LDL and fibrinogen

MedGen

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000291804	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 18, 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

SCV000291804

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 18, 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, SCV000291804.7

#	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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C25"). ClinVar contains an entry for this variant (Variation ID: 242196). This variant has not been reported in the literature in individuals affected with SCN5A-related conditions. This variant is present in population databases (rs376965389, gnomAD 0.03%). This sequence change replaces valine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 1181 of the SCN5A protein (p.Val1181Ala).

#	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

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