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NM_000335.4(SCN5A):c.3296C>T (p.Ala1099Val) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 10, 2018
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:
RCV000183030.2

Allele description

NM_000335.4(SCN5A):c.3296C>T (p.Ala1099Val)

Genes:
LOC110121269:VISTA enhancer hs2177 [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_000335.4(SCN5A):c.3296C>T (p.Ala1099Val)
Other names:
p.A1100V:GCG>GTG
HGVS:
  • NC_000003.12:g.38579425G>A
  • NG_008934.1:g.75248C>T
  • NM_000335.4:c.3296C>T
  • NM_001099404.1:c.3299C>T
  • NM_001160161.1:c.3228+1506C>T
  • NM_198056.2:c.3299C>T
  • NP_000326.2:p.Ala1099Val
  • NP_001092874.1:p.Ala1100Val
  • NP_932173.1:p.Ala1100Val
  • LRG_289t1:c.3299C>T
  • LRG_289t2:c.3296C>T
  • LRG_289t3:c.3299C>T
  • LRG_289:g.75248C>T
  • LRG_289p1:p.Ala1100Val
  • LRG_289p2:p.Ala1099Val
  • LRG_289p3:p.Ala1100Val
  • NC_000003.11:g.38620916G>A
Protein change:
A1099V
Links:
dbSNP: rs199473192
NCBI 1000 Genomes Browser:
rs199473192
Molecular consequence:
  • NM_001160161.1:c.3228+1506C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000335.4:c.3296C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000235438GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Apr 10, 2018) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000235438.11

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

Description

The A1100V variant of uncertain significance in the SCN5A gene (also reported as A1099V due to alternate nomenclature) has been reported previously in one individual who was referred for LQTS genetic testing; however, no detailed clinical information was provided (Kapplinger et al., 2009). Additionally, the A1100V variant was identified in a 2-month-old female with sudden unexplained death while co-sleeping (Wang et al., 2014). Nevertheless, the A1100V variant is observed in 12/23,660 (0.05%) alleles from individuals of African ancestry in large population cohorts (Lek et al., 2016). The A1100V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. Moreover, in-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function.

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

Last Updated: Mar 31, 2019