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NM_001330260.2(SCN8A):c.5938T>A (p.Cys1980Ser) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 18, 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:
RCV002047028.7

Allele description [Variation Report for NM_001330260.2(SCN8A):c.5938T>A (p.Cys1980Ser)]

NM_001330260.2(SCN8A):c.5938T>A (p.Cys1980Ser)

Gene:
SCN8A:sodium voltage-gated channel alpha subunit 8 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q13.13
Genomic location:
Preferred name:
NM_001330260.2(SCN8A):c.5938T>A (p.Cys1980Ser)
HGVS:
  • NC_000012.12:g.51807424T>A
  • NG_021180.3:g.222467T>A
  • NM_001177984.3:c.5815T>A
  • NM_001330260.2:c.5938T>AMANE SELECT
  • NM_001369788.1:c.5815T>A
  • NM_014191.4:c.5938T>A
  • NP_001171455.1:p.Cys1939Ser
  • NP_001317189.1:p.Cys1980Ser
  • NP_001356717.1:p.Cys1939Ser
  • NP_055006.1:p.Cys1980Ser
  • LRG_1389t1:c.5938T>A
  • LRG_1389t2:c.5938T>A
  • LRG_1389:g.222467T>A
  • LRG_1389p1:p.Cys1980Ser
  • LRG_1389p2:p.Cys1980Ser
  • NC_000012.11:g.52201208T>A
Protein change:
C1939S
Links:
dbSNP: rs1322359113
NCBI 1000 Genomes Browser:
rs1322359113
Molecular consequence:
  • NM_001177984.3:c.5815T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330260.2:c.5938T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369788.1:c.5815T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014191.4:c.5938T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Early infantile epileptic encephalopathy with suppression bursts (EIEE)
Synonyms:
Early infantile epileptic encephalopathy; Ohtahara syndrome; Developmental and epileptic encephalopathy
Identifiers:
MONDO: MONDO:0100062; MedGen: C0393706; Orphanet: 1934; OMIM: PS308350

Recent activity

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002109083Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 18, 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, SCV002109083.3

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

Description

This sequence change replaces cysteine, which is neutral and slightly polar, with serine, which is neutral and polar, at codon 1980 of the SCN8A protein (p.Cys1980Ser). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SCN8A-related conditions. ClinVar contains an entry for this variant (Variation ID: 1349586). 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 not expected to disrupt SCN8A protein function with a negative predictive value of 95%. 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.

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

Last Updated: Sep 29, 2024