NM_000335.5(SCN5A):c.4289C>G (p.Ser1430Cys) AND Cardiac arrhythmia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 5, 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:: RCV001841913.11

Allele description [Variation Report for NM_000335.5(SCN5A):c.4289C>G (p.Ser1430Cys)]

NM_000335.5(SCN5A):c.4289C>G (p.Ser1430Cys)

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.4289C>G (p.Ser1430Cys)

HGVS:

NC_000003.12:g.38557238G>C
NG_008934.1:g.97435C>G
NM_000335.5:c.4289C>GMANE SELECT
NM_001099404.2:c.4292C>G
NM_001099405.2:c.4246-660C>G
NM_001160160.2:c.4289C>G
NM_001160161.2:c.4130C>G
NM_001354701.2:c.4243-660C>G
NM_198056.3:c.4292C>G
NP_000326.2:p.Ser1430Cys
NP_001092874.1:p.Ser1431Cys
NP_001153632.1:p.Ser1430Cys
NP_001153633.1:p.Ser1377Cys
NP_932173.1:p.Ser1431Cys
NP_932173.1:p.Ser1431Cys
LRG_289t1:c.4292C>G
LRG_289:g.97435C>G
LRG_289p1:p.Ser1431Cys
NC_000003.11:g.38598729G>C
NM_198056.2:c.4292C>G

Protein change:

S1377C

Links:

dbSNP: rs1226701514

NCBI 1000 Genomes Browser:

rs1226701514

Molecular consequence:

NM_001099405.2:c.4246-660C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354701.2:c.4243-660C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000335.5:c.4289C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.4292C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.4289C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.4130C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.4292C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cardiac arrhythmia
Synonyms:: Cardiac rhythm disease
Identifiers:: EFO: EFO_0004269; MONDO: MONDO:0007263; MedGen: C0003811; Human Phenotype Ontology: HP:0011675

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000907535	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 5, 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

SCV000907535

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 5, 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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Color Diagnostics, LLC DBA Color Health, SCV000907535.2

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

Description

Variant of Uncertain Significance due to insufficient evidence: This missense variant is located in the transmembrane domain DIII of the SCN5A protein. Computational prediction tools and conservation analyses suggest that this variant may have deleterious impact on the protein function. Computational splicing tools suggest that this variant may not impact the RNA splicing. To our knowledge, functional assays have not been performed for this variant nor has this variant been reported in individuals affected with cardiovascular disorders in the literature. This variant is rare in the general population and has been identified in 1/246180 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Available evidence is insufficient to determine the pathogenicity of this variant conclusively.

#	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: Jun 2, 2024

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