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NM_000335.5(SCN5A):c.127C>T (p.Arg43Ter) AND Cardiac arrhythmia

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 20, 2020
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:
RCV001843273.10

Allele description [Variation Report for NM_000335.5(SCN5A):c.127C>T (p.Arg43Ter)]

NM_000335.5(SCN5A):c.127C>T (p.Arg43Ter)

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.127C>T (p.Arg43Ter)
HGVS:
  • NC_000003.12:g.38633181G>A
  • NG_008934.1:g.21492C>T
  • NM_000335.5:c.127C>TMANE SELECT
  • NM_001099404.2:c.127C>T
  • NM_001099405.2:c.127C>T
  • NM_001160160.2:c.127C>T
  • NM_001160161.2:c.127C>T
  • NM_001354701.2:c.127C>T
  • NM_198056.3:c.127C>T
  • NP_000326.2:p.Arg43Ter
  • NP_001092874.1:p.Arg43Ter
  • NP_001092875.1:p.Arg43Ter
  • NP_001153632.1:p.Arg43Ter
  • NP_001153633.1:p.Arg43Ter
  • NP_001341630.1:p.Arg43Ter
  • NP_932173.1:p.Arg43Ter
  • LRG_289t1:c.127C>T
  • LRG_289:g.21492C>T
  • NC_000003.11:g.38674672G>A
  • NM_198056.2:c.127C>T
Protein change:
R43*
Links:
dbSNP: rs1553607597
NCBI 1000 Genomes Browser:
rs1553607597
Molecular consequence:
  • NM_000335.5:c.127C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001099404.2:c.127C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001099405.2:c.127C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001160160.2:c.127C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001160161.2:c.127C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354701.2:c.127C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_198056.3:c.127C>T - nonsense - [Sequence Ontology: SO:0001587]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001352351Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Mar 20, 2020) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV001352351.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant changes 1 nucleotide in exon 2 of the SCN5A gene, creating a premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, functional assays have not been performed for this variant. This variant has been reported in an individual affected with Brugada syndrome (PMID: 22840528). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of SCN5A function is a known mechanism of disease. Based on available evidence, this variant is classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024