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NM_001165963.4(SCN1A):c.602C>T (p.Ala201Val) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 6, 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:
RCV001229412.9

Allele description [Variation Report for NM_001165963.4(SCN1A):c.602C>T (p.Ala201Val)]

NM_001165963.4(SCN1A):c.602C>T (p.Ala201Val)

Gene:
SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001165963.4(SCN1A):c.602C>T (p.Ala201Val)
HGVS:
  • NC_000002.12:g.166054638G>A
  • NG_011906.1:g.24002C>T
  • NM_001165963.4:c.602C>TMANE SELECT
  • NM_001165964.3:c.602C>T
  • NM_001202435.3:c.602C>T
  • NM_001353948.2:c.602C>T
  • NM_001353949.2:c.602C>T
  • NM_001353950.2:c.602C>T
  • NM_001353951.2:c.602C>T
  • NM_001353952.2:c.602C>T
  • NM_001353954.2:c.602C>T
  • NM_001353955.2:c.602C>T
  • NM_001353957.2:c.602C>T
  • NM_001353958.2:c.602C>T
  • NM_001353960.2:c.602C>T
  • NM_001353961.2:c.-1824C>T
  • NM_006920.6:c.602C>T
  • NP_001159435.1:p.Ala201Val
  • NP_001159436.1:p.Ala201Val
  • NP_001189364.1:p.Ala201Val
  • NP_001340877.1:p.Ala201Val
  • NP_001340878.1:p.Ala201Val
  • NP_001340879.1:p.Ala201Val
  • NP_001340880.1:p.Ala201Val
  • NP_001340881.1:p.Ala201Val
  • NP_001340883.1:p.Ala201Val
  • NP_001340884.1:p.Ala201Val
  • NP_001340886.1:p.Ala201Val
  • NP_001340887.1:p.Ala201Val
  • NP_001340889.1:p.Ala201Val
  • NP_008851.3:p.Ala201Val
  • LRG_8:g.24002C>T
  • NC_000002.11:g.166911148G>A
  • NM_001165963.1:c.602C>T
  • NR_148667.2:n.988C>T
Protein change:
A201V
Links:
dbSNP: rs1553551312
NCBI 1000 Genomes Browser:
rs1553551312
Molecular consequence:
  • NM_001353961.2:c.-1824C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001165963.4:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.988C>T - 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
SCV001401857Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Jun 6, 2023)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

SCN1A Gene Mutation and Adaptive Functioning in 18 Vietnamese Children with Dravet Syndrome.

Do TT, Vu DM, Huynh TT, Le TK, Sohn EH, Le TM, Ha HH, Bui CB.

J Clin Neurol. 2017 Jan;13(1):62-70. doi: 10.3988/jcn.2017.13.1.62.

PubMed [citation]
PMID:
28079314
PMCID:
PMC5242153

Assessment of parental mosaicism in SCN1A-related epilepsy by single-molecule molecular inversion probes and next-generation sequencing.

de Lange IM, Koudijs MJ, van 't Slot R, Sonsma ACM, Mulder F, Carbo EC, van Kempen MJA, Nijman IJ, Ernst RF, Savelberg SMC, Knoers NVAM, Brilstra EH, Koeleman BPC.

J Med Genet. 2019 Feb;56(2):75-80. doi: 10.1136/jmedgenet-2018-105672. Epub 2018 Oct 27.

PubMed [citation]
PMID:
30368457
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001401857.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 201 of the SCN1A protein (p.Ala201Val). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the p.Arg201 amino acid residue in SCN1A. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 28079314). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 956579). This missense change has been observed in individuals with clinical features of SCN1A-related conditions (PMID: 30368457; Invitae). This variant is not present in population databases (gnomAD no frequency).

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

Last Updated: Sep 29, 2024