NM_001165963.4(SCN1A):c.3655T>A (p.Trp1219Arg) AND Early infantile epileptic encephalopathy with suppression bursts

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 1, 2022
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:: RCV000540121.7

Allele description

NM_001165963.4(SCN1A):c.3655T>A (p.Trp1219Arg)

Genes:

SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
LOC102724058:uncharacterized LOC102724058 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001165963.4(SCN1A):c.3655T>A (p.Trp1219Arg)

HGVS:

NC_000002.12:g.166013794A>T
NG_011906.1:g.64846T>A
NM_001165963.4:c.3655T>AMANE SELECT
NM_001165964.3:c.3571T>A
NM_001202435.3:c.3655T>A
NM_001353948.2:c.3655T>A
NM_001353949.2:c.3622T>A
NM_001353950.2:c.3622T>A
NM_001353951.2:c.3622T>A
NM_001353952.2:c.3622T>A
NM_001353954.2:c.3619T>A
NM_001353955.2:c.3619T>A
NM_001353957.2:c.3571T>A
NM_001353958.2:c.3571T>A
NM_001353960.2:c.3568T>A
NM_001353961.2:c.1213T>A
NM_006920.6:c.3622T>A
NP_001159435.1:p.Trp1219Arg
NP_001159436.1:p.Trp1191Arg
NP_001189364.1:p.Trp1219Arg
NP_001340877.1:p.Trp1219Arg
NP_001340878.1:p.Trp1208Arg
NP_001340879.1:p.Trp1208Arg
NP_001340880.1:p.Trp1208Arg
NP_001340881.1:p.Trp1208Arg
NP_001340883.1:p.Trp1207Arg
NP_001340884.1:p.Trp1207Arg
NP_001340886.1:p.Trp1191Arg
NP_001340887.1:p.Trp1191Arg
NP_001340889.1:p.Trp1190Arg
NP_001340890.1:p.Trp405Arg
NP_008851.3:p.Trp1208Arg
LRG_8:g.64846T>A
NC_000002.11:g.166870304A>T
NM_001165963.1:c.3655T>A
NR_148667.2:n.4008T>A

Protein change:

W1190R

Links:

dbSNP: rs1553532599

NCBI 1000 Genomes Browser:

rs1553532599

Molecular consequence:

NM_001165963.4:c.3655T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.3571T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.3655T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.3655T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.3622T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.3622T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.3622T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.3622T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.3619T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.3619T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.3571T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.3571T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.3568T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353961.2:c.1213T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.3622T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.4008T>A - 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
SCV000633849	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 1, 2022)	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

SCV000633849

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 1, 2022)

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, SCV000633849.4

#	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 tryptophan, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 1219 of the SCN1A protein (p.Trp1219Arg). 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 sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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 SCN1A protein function. ClinVar contains an entry for this variant (Variation ID: 461265). This variant has not been reported in the literature in individuals affected with SCN1A-related conditions. This variant is not present in population databases (gnomAD 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 28, 2024

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Relating variation to medicine