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NM_001040142.2(SCN2A):c.629T>A (p.Leu210Gln) AND Inborn genetic diseases

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 7, 2023
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:
RCV003163525.2

Allele description [Variation Report for NM_001040142.2(SCN2A):c.629T>A (p.Leu210Gln)]

NM_001040142.2(SCN2A):c.629T>A (p.Leu210Gln)

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.629T>A (p.Leu210Gln)
HGVS:
  • NC_000002.12:g.165309375T>A
  • NG_008143.1:g.74974T>A
  • NM_001040142.2:c.629T>AMANE SELECT
  • NM_001040143.2:c.697+119T>A
  • NM_001371246.1:c.697+119T>A
  • NM_001371247.1:c.629T>A
  • NM_021007.3:c.629T>A
  • NP_001035232.1:p.Leu210Gln
  • NP_001358176.1:p.Leu210Gln
  • NP_066287.2:p.Leu210Gln
  • NC_000002.11:g.166165885T>A
  • NM_021007.2:c.629T>A
Protein change:
L210Q
Links:
dbSNP: rs1559352517
NCBI 1000 Genomes Browser:
rs1559352517
Molecular consequence:
  • NM_001040143.2:c.697+119T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001371246.1:c.697+119T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001040142.2:c.629T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371247.1:c.629T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021007.3:c.629T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003902444Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Mar 7, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV003902444.2

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

Description

The c.629T>A (p.L210Q) alteration is located in exon 6 (coding exon 5) of the SCN2A gene. This alteration results from a T to A substitution at nucleotide position 629, causing the leucine (L) at amino acid position 210 to be replaced by a glutamine (Q). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic.

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

Last Updated: Sep 29, 2024