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NM_001040142.2(SCN2A):c.1058G>A (p.Cys353Tyr) AND Developmental and epileptic encephalopathy, 11

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 23, 2021
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:
RCV002275571.1

Allele description [Variation Report for NM_001040142.2(SCN2A):c.1058G>A (p.Cys353Tyr)]

NM_001040142.2(SCN2A):c.1058G>A (p.Cys353Tyr)

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.1058G>A (p.Cys353Tyr)
HGVS:
  • NC_000002.12:g.165313643G>A
  • NG_008143.1:g.79242G>A
  • NM_001040142.2:c.1058G>AMANE SELECT
  • NM_001040143.2:c.1058G>A
  • NM_001371246.1:c.1058G>A
  • NM_001371247.1:c.1058G>A
  • NM_021007.3:c.1058G>A
  • NP_001035232.1:p.Cys353Tyr
  • NP_001035233.1:p.Cys353Tyr
  • NP_001358175.1:p.Cys353Tyr
  • NP_001358176.1:p.Cys353Tyr
  • NP_066287.2:p.Cys353Tyr
  • NC_000002.11:g.166170153G>A
Protein change:
C353Y
Links:
dbSNP: rs1697566111
NCBI 1000 Genomes Browser:
rs1697566111
Molecular consequence:
  • NM_001040142.2:c.1058G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001040143.2:c.1058G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371246.1:c.1058G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371247.1:c.1058G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021007.3:c.1058G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

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
SCV002564184New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Oct 23, 2021) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV002564184.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The heterozygous missense variant c.1058G>A (p.Cys353Tyr) identified in exon 9 (of 27) of the SCN2A gene has not been reported in affected individuals in the literature. The variant is absent from the gnomAD(v3) database suggesting it is not a common benign variant in the populations represented in that database. This variant affects a highly conserved residue (Cys353) of the SCN2A gene and is predicted deleterious by multiple in silico prediction tools (CADD score= 28.7, REVEL score = 0.902). Due to the lack of compelling evidence for its pathogenicity, the heterozygous c.1058G>A (p.Cys353Tyr) missense variant identified inthe SCN2A gene is reported as a Variant of Uncertain Significance.

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

Last Updated: Dec 24, 2023