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NM_198056.2(SCN5A):c.86_87invCA (p.Ala29Val) AND Cardiovascular phenotype

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 3, 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:
RCV000249341.11

Allele description [Variation Report for NM_198056.2(SCN5A):c.86_87invCA (p.Ala29Val)]

NM_198056.2(SCN5A):c.86_87invCA (p.Ala29Val)

Gene:
SCN5A:sodium voltage-gated channel alpha subunit 5 [Gene - OMIM - HGNC]
Variant type:
Inversion
Cytogenetic location:
3p22.2
Genomic location:
Preferred name:
NM_198056.2(SCN5A):c.86_87invCA (p.Ala29Val)
HGVS:
  • NC_000003.12:g.38633221_38633222inv
  • NG_008934.1:g.21451_21452inv
  • NM_000335.5:c.86_87invMANE SELECT
  • NM_001099404.2:c.86_87inv
  • NM_001099405.2:c.86_87inv
  • NM_001160160.2:c.86_87inv
  • NM_001160161.2:c.86_87inv
  • NM_001354701.2:c.86_87inv
  • NM_198056.2:c.86_87inv
  • NM_198056.3:c.86_87inv
  • NP_000326.2:p.Ala29Val
  • NP_001092874.1:p.Ala29Val
  • NP_001092875.1:p.Ala29Val
  • NP_001153632.1:p.Ala29Val
  • NP_001153633.1:p.Ala29Val
  • NP_001341630.1:p.Ala29Val
  • NP_932173.1:p.Ala29Val
  • LRG_289t1:c.86_87inv
  • LRG_289:g.21451_21452inv
  • LRG_289p1:p.Ala29Val
  • NC_000003.11:g.38674712_38674713delinsCA
  • NC_000003.11:g.38674712_38674713inv
  • NM_001099404.1:c.86_87delinsTG
  • NM_198056.2:c.86_87delinsTG
  • NM_198056.2:c.86_87delinsTG
  • NM_198056.2:c.86_87inv
  • NM_198056.2:c.86_87invCA
  • NM_198056.3:c.86_87delinsTG
Protein change:
A29V
Molecular consequence:
  • NM_000335.5:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099404.2:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099405.2:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160160.2:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160161.2:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354701.2:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198056.3:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Cardiovascular phenotype
Identifiers:
MedGen: CN230736

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000320685Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Feb 3, 2022) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Founder mutations characterise the mutation panorama in 200 Swedish index cases referred for Long QT syndrome genetic testing.

Stattin EL, Boström IM, Winbo A, Cederquist K, Jonasson J, Jonsson BA, Diamant UB, Jensen SM, Rydberg A, Norberg A.

BMC Cardiovasc Disord. 2012 Oct 25;12:95. doi: 10.1186/1471-2261-12-95.

PubMed [citation]
PMID:
23098067
PMCID:
PMC3520728

Postmortem genetic screening for the identification, verification, and reporting of genetic variants contributing to the sudden death of the young.

Methner DN, Scherer SE, Welch K, Walkiewicz M, Eng CM, Belmont JW, Powell MC, Korchina V, Doddapaneni HV, Muzny DM, Gibbs RA, Wolf DA, Sanchez LA, Kahn R.

Genome Res. 2016 Sep;26(9):1170-7. doi: 10.1101/gr.195800.115. Epub 2016 Jul 19.

PubMed [citation]
PMID:
27435932
PMCID:
PMC5052040
See all PubMed Citations (4)

Details of each submission

From Ambry Genetics, SCV000320685.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

The c.86_87delCAinsTG variant (also known as p.A29V), located in coding exon 1 of the SCN5A gene, results from an in-frame deletion of CA and insertion of TG at nucleotide positions 86 to 87. This results in the substitution of the alanine residue for a valine residue at codon 29, an amino acid with similar properties. This alteration has been reported in a Brugada syndrome cohort; however, clinical details were limited (Ciconte G et al. Eur Heart J, 2021 03;42:1082-1090). Another alteration at the same codon, p.A29V (c.86C>T), has been described in individuals with a prolonged QT interval and a sudden unexplained infant death cohort (Stattin EL et al. BMC Cardiovasc Disord, 2012 Oct;12:95; Methner DN et al. Genome Res, 2016 09;26:1170-7; Haskell GT et al. Circ Cardiovasc Genet, 2017 Jun;10:[ePub ahead of print]). Based on data from gnomAD, the TG allele has an overall frequency of 0.008% (22/280148) total alleles studied. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be inconclusive by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

Last Updated: Sep 16, 2024