NM_000335.5(SCN5A):c.5318del (p.Asn1773fs) AND Arrhythmia

Clinical significance:Likely pathogenic (Last evaluated: Feb 12, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001190118.1

Allele description [Variation Report for NM_000335.5(SCN5A):c.5318del (p.Asn1773fs)]

NM_000335.5(SCN5A):c.5318del (p.Asn1773fs)

Gene:
SCN5A:sodium voltage-gated channel alpha subunit 5 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
3p22.2
Genomic location:
Preferred name:
NM_000335.5(SCN5A):c.5318del (p.Asn1773fs)
HGVS:
  • NC_000003.12:g.38551052del
  • NG_008934.1:g.103622del
  • NM_000335.5:c.5318delMANE SELECT
  • NM_001099404.2:c.5321del
  • NM_001099405.2:c.5267del
  • NM_001160160.2:c.5222del
  • NM_001160161.2:c.5159del
  • NM_001354701.2:c.5264del
  • NM_198056.3:c.5321del
  • NP_000326.2:p.Asn1773fs
  • NP_001092874.1:p.Asn1774fs
  • NP_001092875.1:p.Asn1756fs
  • NP_001153632.1:p.Asn1741fs
  • NP_001153633.1:p.Asn1720fs
  • NP_001341630.1:p.Asn1755fs
  • NP_932173.1:p.Asn1774fs
  • LRG_289t1:c.5321del
  • LRG_289:g.103622del
  • NC_000003.11:g.38592543del
  • NM_198056.2:c.5321del
Protein change:
N1720fs
Molecular consequence:
  • NM_000335.5:c.5318del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001099404.2:c.5321del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001099405.2:c.5267del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001160160.2:c.5222del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001160161.2:c.5159del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354701.2:c.5264del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_198056.3:c.5321del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Arrhythmia
Synonyms:
Abnormal electrocardiogram; Arrhythmias; Cardiac arrhythmias; See all synonyms [MedGen]
Identifiers:
EFO: EFO_0004269; MedGen: C0855329; Human Phenotype Ontology: HP:0011675

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001357534Color Health, Inccriteria provided, single submitter
Likely pathogenic
(Feb 12, 2020)
germlineclinical testing

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

Description

This variant deletes 1 nucleotide in exon 28 of the SCN5A gene, creating a frameshift and premature translation stop signal in the last exon. This mutant transcript is predicted to escape nonsense-mediated decay and be expressed as a truncated protein. To our knowledge, this variant has not been reported in individuals affected with cardiovascular disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Truncating variants occurring downstream of this variant have been reported in individuals affected with long QT syndrome (Clinvar). Loss of SCN5A function is a known mechanism of disease. Based on the available evidence, this variant is classified as Likely Pathogenic.

SCV001357534

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 Health, Inc, SCV001357534.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 3, 2021

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