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NM_000335.5(SCN5A):c.4717G>T (p.Glu1573Ter) AND Cardiac arrhythmia

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 10, 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:
RCV001842017.9

Allele description [Variation Report for NM_000335.5(SCN5A):c.4717G>T (p.Glu1573Ter)]

NM_000335.5(SCN5A):c.4717G>T (p.Glu1573Ter)

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.4717G>T (p.Glu1573Ter)
HGVS:
  • NC_000003.12:g.38554372C>A
  • NG_008934.1:g.100301G>T
  • NM_000335.5:c.4717G>TMANE SELECT
  • NM_001099404.2:c.4720G>T
  • NM_001099405.2:c.4666G>T
  • NM_001160160.2:c.4714+3G>T
  • NM_001160161.2:c.4558G>T
  • NM_001354701.2:c.4663G>T
  • NM_198056.3:c.4720G>T
  • NP_000326.2:p.Glu1573Ter
  • NP_001092874.1:p.Glu1574Ter
  • NP_001092875.1:p.Glu1556Ter
  • NP_001153633.1:p.Glu1520Ter
  • NP_001341630.1:p.Glu1555Ter
  • NP_932173.1:p.Glu1574Ter
  • NP_932173.1:p.Glu1574Ter
  • LRG_289t1:c.4720G>T
  • LRG_289:g.100301G>T
  • LRG_289p1:p.Glu1574Ter
  • NC_000003.11:g.38595863C>A
  • NM_198056.2:c.4720G>T
  • p.E1574*
Protein change:
E1520*
Links:
dbSNP: rs199473620
NCBI 1000 Genomes Browser:
rs199473620
Molecular consequence:
  • NM_001160160.2:c.4714+3G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000335.5:c.4717G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001099404.2:c.4720G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001099405.2:c.4666G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001160161.2:c.4558G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354701.2:c.4663G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_198056.3:c.4720G>T - nonsense - [Sequence Ontology: SO:0001587]
Functional consequence:
protein truncation [Variation Ontology: 0015]

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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001372360Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Jun 10, 2020) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001372360.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: SCN5A c.4720G>T (p.Glu1574X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Loss-of-function mutations in SCN5A cause Brugada syndrome. The variant was absent in 249326 control chromosomes. To our knowledge, no occurrence of c.4720G>T in individuals affected with Arrhythmia/Brugada syndrome and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: May 1, 2024