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NM_000335.5(SCN5A):c.4296+1del AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 17, 2022
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:
RCV003542346.2

Allele description [Variation Report for NM_000335.5(SCN5A):c.4296+1del]

NM_000335.5(SCN5A):c.4296+1del

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.4296+1del
HGVS:
  • NC_000003.12:g.38557235del
  • NG_008934.1:g.97443del
  • NM_000335.5:c.4296+1delMANE SELECT
  • NM_001099404.2:c.4299+1del
  • NM_001099405.2:c.4246-652del
  • NM_001160160.2:c.4296+1del
  • NM_001160161.2:c.4137+1del
  • NM_001354701.2:c.4243-652del
  • NM_198056.3:c.4299+1del
  • LRG_289t1:c.4299+1del
  • LRG_289t3:c.4299+1del
  • LRG_289:g.97443del
  • NC_000003.11:g.38598721del
  • NC_000003.11:g.38598726del
  • NM_001099404.1:c.4299+1del
  • NM_198056.2:c.4299+1delG
Links:
dbSNP: rs1450434935
NCBI 1000 Genomes Browser:
rs1450434935
Molecular consequence:
  • NM_001099405.2:c.4246-652del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354701.2:c.4243-652del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000335.5:c.4296+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001099404.2:c.4299+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001160160.2:c.4296+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001160161.2:c.4137+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_198056.3:c.4299+1del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003525426Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 17, 2022)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

An international compendium of mutations in the SCN5A-encoded cardiac sodium channel in patients referred for Brugada syndrome genetic testing.

Kapplinger JD, Tester DJ, Alders M, Benito B, Berthet M, Brugada J, Brugada P, Fressart V, Guerchicoff A, Harris-Kerr C, Kamakura S, Kyndt F, Koopmann TT, Miyamoto Y, Pfeiffer R, Pollevick GD, Probst V, Zumhagen S, Vatta M, Towbin JA, Shimizu W, Schulze-Bahr E, et al.

Heart Rhythm. 2010 Jan;7(1):33-46. doi: 10.1016/j.hrthm.2009.09.069. Epub 2009 Oct 8.

PubMed [citation]
PMID:
20129283
PMCID:
PMC2822446

Brugada syndrome 2012.

Berne P, Brugada J.

Circ J. 2012;76(7):1563-71. Epub 2012 Jun 13. Review.

PubMed [citation]
PMID:
22789973
See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003525426.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr1434Metfs*29) in the SCN5A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SCN5A are known to be pathogenic (PMID: 20129283, 22789973). This premature translational stop signal has been observed in individual(s) with Brugada syndrome and/or noncompaction cardiomyopathy (PMID: 19251209, 29447731, 30193851). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 1327132).

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

Last Updated: Oct 26, 2024