NM_000335.5(SCN5A):c.5452G>A (p.Asp1818Asn) AND Cardiovascular phenotype

Germline classification:: Likely benign (1 submission)
Last evaluated:: Dec 15, 2019
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:: RCV002345238.9

Allele description [Variation Report for NM_000335.5(SCN5A):c.5452G>A (p.Asp1818Asn)]

NM_000335.5(SCN5A):c.5452G>A (p.Asp1818Asn)

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.5452G>A (p.Asp1818Asn)

Other names:

p.D1819N:GAT>AAT

HGVS:

NC_000003.12:g.38550917C>T
NG_008934.1:g.103756G>A
NM_000335.5:c.5452G>AMANE SELECT
NM_001099404.2:c.5455G>A
NM_001099405.2:c.5401G>A
NM_001160160.2:c.5356G>A
NM_001160161.2:c.5293G>A
NM_001354701.2:c.5398G>A
NM_198056.3:c.5455G>A
NP_000326.2:p.Asp1818Asn
NP_001092874.1:p.Asp1819Asn
NP_001092874.1:p.Asp1819Asn
NP_001092875.1:p.Asp1801Asn
NP_001153632.1:p.Asp1786Asn
NP_001153633.1:p.Asp1765Asn
NP_001341630.1:p.Asp1800Asn
NP_932173.1:p.Asp1819Asn
NP_932173.1:p.Asp1819Asn
LRG_289t1:c.5455G>A
LRG_289t3:c.5455G>A
LRG_289:g.103756G>A
LRG_289p1:p.Asp1819Asn
LRG_289p3:p.Asp1819Asn
NC_000003.11:g.38592408C>T
NM_001099404.1:c.5455G>A
NM_198056.2:c.5455G>A
Q14524:p.Asp1819Asn

Protein change:

D1765N; ASP1819ASN

Links:

UniProtKB: Q14524#VAR_036668; OMIM: 600163.0035; dbSNP: rs137854619

NCBI 1000 Genomes Browser:

rs137854619

Molecular consequence:

NM_000335.5:c.5452G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.5455G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.5401G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.5356G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.5293G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.5398G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.5455G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002649717	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Dec 15, 2019)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 16922724, 22685113, 23396983, 24606995, 28988457, 29728395 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002649717

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Dec 15, 2019)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

Citation Link

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

Spectrum of pathogenic mutations and associated polymorphisms in a cohort of 44 unrelated patients with long QT syndrome.

Millat G, Chevalier P, Restier-Miron L, Da Costa A, Bouvagnet P, Kugener B, Fayol L, Gonzàlez Armengod C, Oddou B, Chanavat V, Froidefond E, Perraudin R, Rousson R, Rodriguez-Lafrasse C.

Clin Genet. 2006 Sep;70(3):214-27.

PubMed [citation]

PMID:: 16922724

High prevalence of long QT syndrome-associated SCN5A variants in patients with early-onset lone atrial fibrillation.

Olesen MS, Yuan L, Liang B, Holst AG, Nielsen N, Nielsen JB, Hedley PL, Christiansen M, Olesen SP, Haunsø S, Schmitt N, Jespersen T, Svendsen JH.

Circ Cardiovasc Genet. 2012 Aug 1;5(4):450-9. doi: 10.1161/CIRCGENETICS.111.962597. Epub 2012 Jun 8.

PubMed [citation]

PMID:: 22685113

See all PubMed Citations (6)

Details of each submission

From Ambry Genetics, SCV002649717.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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 13, 2024

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