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 [Variation Report for NM_001165963.4(SCN1A):c.1181_1182delinsGA (p.Ala394Gly)]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000831348	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 24, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000831348

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 24, 2018)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

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