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NM_001040142.2(SCN2A):c.4435C>A (p.Gln1479Lys) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 26, 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:
RCV001865623.7

Allele description [Variation Report for NM_001040142.2(SCN2A):c.4435C>A (p.Gln1479Lys)]

NM_001040142.2(SCN2A):c.4435C>A (p.Gln1479Lys)

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.4435C>A (p.Gln1479Lys)
HGVS:
  • NC_000002.12:g.165380718C>A
  • NG_008143.1:g.146317C>A
  • NM_001040142.2:c.4435C>AMANE SELECT
  • NM_001040143.2:c.4435C>A
  • NM_001371246.1:c.4435C>A
  • NM_001371247.1:c.4435C>A
  • NM_021007.3:c.4435C>A
  • NP_001035232.1:p.Gln1479Lys
  • NP_001035233.1:p.Gln1479Lys
  • NP_001358175.1:p.Gln1479Lys
  • NP_001358176.1:p.Gln1479Lys
  • NP_066287.2:p.Gln1479Lys
  • NP_066287.2:p.Gln1479Lys
  • NC_000002.11:g.166237228C>A
  • NM_021007.2:c.4435C>A
Protein change:
Q1479K
Links:
dbSNP: rs1553462134
NCBI 1000 Genomes Browser:
rs1553462134
Molecular consequence:
  • NM_001040142.2:c.4435C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001040143.2:c.4435C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371246.1:c.4435C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371247.1:c.4435C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021007.3:c.4435C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Seizures, benign familial infantile, 3 (BFIS3)
Synonyms:
CONVULSIONS, BENIGN FAMILIAL INFANTILE, 3; Familial neonatal seizures
Identifiers:
MONDO: MONDO:0011904; MedGen: C1843140; Orphanet: 140927; Orphanet: 306; OMIM: 607745
Name:
Developmental and epileptic encephalopathy, 11 (DEE11)
Synonyms:
Early infantile epileptic encephalopathy 11
Identifiers:
MONDO: MONDO:0013388; MedGen: C3150987; Orphanet: 1934; OMIM: 613721

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002216817Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Apr 26, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002216817.3

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

Description

ClinVar contains an entry for this variant (Variation ID: 436661). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SCN2A protein function. This variant has not been reported in the literature in individuals affected with SCN2A-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamine, which is neutral and polar, with lysine, which is basic and polar, at codon 1479 of the SCN2A protein (p.Gln1479Lys).

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

Last Updated: Sep 29, 2024