NM_001040142.2(SCN2A):c.605C>T (p.Ala202Val) AND History of neurodevelopmental disorder

Clinical significance:Uncertain significance (Last evaluated: Feb 15, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000720902.1

Allele description [Variation Report for NM_001040142.2(SCN2A):c.605C>T (p.Ala202Val)]

NM_001040142.2(SCN2A):c.605C>T (p.Ala202Val)

Gene:
SCN2A:sodium voltage-gated channel alpha subunit 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001040142.2(SCN2A):c.605C>T (p.Ala202Val)
HGVS:
  • NC_000002.12:g.165308794C>T
  • NG_008143.1:g.74393C>T
  • NM_001040142.2:c.605C>TMANE SELECT
  • NM_001040143.2:c.605C>T
  • NM_001371246.1:c.605C>T
  • NM_001371247.1:c.605C>T
  • NM_021007.3:c.605C>T
  • NP_001035232.1:p.Ala202Val
  • NP_001035233.1:p.Ala202Val
  • NP_001358175.1:p.Ala202Val
  • NP_001358176.1:p.Ala202Val
  • NP_066287.2:p.Ala202Val
  • NP_066287.2:p.Ala202Val
  • NC_000002.11:g.166165304C>T
  • NM_021007.2:c.605C>T
Protein change:
A202V
Links:
Molecular consequence:
  • NM_001040142.2:c.605C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001040143.2:c.605C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371246.1:c.605C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371247.1:c.605C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021007.3:c.605C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
History of neurodevelopmental disorder
Identifiers:
MedGen: C2711754

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000851786Ambry Geneticscriteria provided, single submitter
Uncertain significance
(Feb 15, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Details of each submission

From Ambry Genetics, SCV000851786.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The c.605C>T variant (also known as p.A202V), located in coding exon 4 of the SCN2A gene, results from a C to T substitution at nucleotide position 605. The amino acid change results in alanine to valine at codon 202, an amino acid with similar properties. However, this change occurs in the last base pair of coding exon 4, which makes it likely to have some effect on normal mRNA splicing. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6498 samples (12996 alleles) with coverage at this position. This amino acid position is highly conserved in available vertebrate species. This amino acid alteration is predicted to be possibly damaging and deleterious by PolyPhen and SIFT in silico analyses, respectively. In addition, using theBDGPandESEfindersplice site prediction tools, this nucleotidealteration is not predicted to have any significant effect on this splice donor site; however, direct evidence is unavailable.Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

Last Updated: Dec 4, 2021

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