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NM_001165963.4(SCN1A):c.1181_1182delinsGA (p.Ala394Gly) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 24, 2018
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:
RCV000702492.4

Allele description

NM_001165963.4(SCN1A):c.1181_1182delinsGA (p.Ala394Gly)

Gene:
SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001165963.4(SCN1A):c.1181_1182delinsGA (p.Ala394Gly)
HGVS:
  • NC_000002.12:g.166046965_166046966delinsTC
  • NG_011906.1:g.31674_31675delinsGA
  • NM_001165963.4:c.1181_1182delinsGAMANE SELECT
  • NM_001165964.3:c.1181_1182delinsGA
  • NM_001202435.3:c.1181_1182delinsGA
  • NM_001353948.2:c.1181_1182delinsGA
  • NM_001353949.2:c.1181_1182delinsGA
  • NM_001353950.2:c.1181_1182delinsGA
  • NM_001353951.2:c.1181_1182delinsGA
  • NM_001353952.2:c.1181_1182delinsGA
  • NM_001353954.2:c.1181_1182delinsGA
  • NM_001353955.2:c.1181_1182delinsGA
  • NM_001353957.2:c.1181_1182delinsGA
  • NM_001353958.2:c.1181_1182delinsGA
  • NM_001353960.2:c.1181_1182delinsGA
  • NM_001353961.2:c.-1245_-1244delinsGA
  • NM_006920.6:c.1181_1182delinsGA
  • NP_001159435.1:p.Ala394Gly
  • NP_001159436.1:p.Ala394Gly
  • NP_001189364.1:p.Ala394Gly
  • NP_001340877.1:p.Ala394Gly
  • NP_001340878.1:p.Ala394Gly
  • NP_001340879.1:p.Ala394Gly
  • NP_001340880.1:p.Ala394Gly
  • NP_001340881.1:p.Ala394Gly
  • NP_001340883.1:p.Ala394Gly
  • NP_001340884.1:p.Ala394Gly
  • NP_001340886.1:p.Ala394Gly
  • NP_001340887.1:p.Ala394Gly
  • NP_001340889.1:p.Ala394Gly
  • NP_008851.3:p.Ala394Gly
  • LRG_8:g.31674_31675delinsGA
  • NC_000002.11:g.166903475_166903476delinsTC
  • NM_001165963.1:c.1181_1182delinsGA
  • NR_148667.2:n.1567_1568delinsGA
Protein change:
A394G
Links:
dbSNP: rs1559226096
NCBI 1000 Genomes Browser:
rs1559226096
Molecular consequence:
  • NM_001353961.2:c.-1245_-1244delinsGA - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001165963.4:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.1181_1182delinsGA - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.1567_1568delinsGA - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000831348Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Apr 24, 2018)
germlineclinical testing

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

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 Invitae, SCV000831348.3

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

Description

This sequence change replaces alanine with glycine at codon 394 of the SCN1A protein (p.Ala394Gly). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and glycine. 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with SCN1A-related disease. This variant is not present in population databases (ExAC no frequency).

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

Last Updated: Feb 20, 2024