NM_001165963.4(SCN1A):c.5656C>T (p.Arg1886Ter) AND Early infantile epileptic encephalopathy with suppression bursts

Clinical significance:Pathogenic (Last evaluated: Jan 3, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000692766.4

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5656C>T (p.Arg1886Ter)]

NM_001165963.4(SCN1A):c.5656C>T (p.Arg1886Ter)

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.5656C>T (p.Arg1886Ter)
Other names:
p.R1886*:CGA>TGA
HGVS:
  • NC_000002.12:g.165991619G>A
  • NG_011906.1:g.87021C>T
  • NM_001165963.4:c.5656C>TMANE SELECT
  • NM_001165964.3:c.5572C>T
  • NM_001202435.3:c.5656C>T
  • NM_001353948.2:c.5656C>T
  • NM_001353949.2:c.5623C>T
  • NM_001353950.2:c.5623C>T
  • NM_001353951.2:c.5623C>T
  • NM_001353952.2:c.5623C>T
  • NM_001353954.2:c.5620C>T
  • NM_001353955.2:c.5620C>T
  • NM_001353957.2:c.5572C>T
  • NM_001353958.2:c.5572C>T
  • NM_001353960.2:c.5569C>T
  • NM_001353961.2:c.3214C>T
  • NM_006920.6:c.5623C>T
  • NP_001159435.1:p.Arg1886Ter
  • NP_001159436.1:p.Arg1858Ter
  • NP_001189364.1:p.Arg1886Ter
  • NP_001340877.1:p.Arg1886Ter
  • NP_001340878.1:p.Arg1875Ter
  • NP_001340879.1:p.Arg1875Ter
  • NP_001340880.1:p.Arg1875Ter
  • NP_001340881.1:p.Arg1875Ter
  • NP_001340883.1:p.Arg1874Ter
  • NP_001340884.1:p.Arg1874Ter
  • NP_001340886.1:p.Arg1858Ter
  • NP_001340887.1:p.Arg1858Ter
  • NP_001340889.1:p.Arg1857Ter
  • NP_001340890.1:p.Arg1072Ter
  • NP_008851.3:p.Arg1875Ter
  • LRG_8:g.87021C>T
  • NC_000002.11:g.166848129G>A
  • NM_001165963.1:c.5656C>T
  • NR_148667.2:n.6073C>T
  • p.Arg1886*
  • AB093548.1:c.5656C>T;p.Arg1886*
Protein change:
R1072*
Links:
dbSNP: rs779614747
NCBI 1000 Genomes Browser:
rs779614747
Molecular consequence:
  • NR_148667.2:n.6073C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001165963.4:c.5656C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001165964.3:c.5572C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001202435.3:c.5656C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353948.2:c.5656C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353949.2:c.5623C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353950.2:c.5623C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353951.2:c.5623C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353952.2:c.5623C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353954.2:c.5620C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353955.2:c.5620C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353957.2:c.5572C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353958.2:c.5572C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353960.2:c.5569C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353961.2:c.3214C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_006920.6:c.5623C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000820608Invitaecriteria provided, single submitter
Pathogenic
(Jan 3, 2020)
germlineclinical testing

PubMed (5)
[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

Progressive gait deterioration in adolescents with Dravet syndrome.

Rodda JM, Scheffer IE, McMahon JM, Berkovic SF, Graham HK.

Arch Neurol. 2012 Jul;69(7):873-8.

PubMed [citation]
PMID:
22409937

The spectrum of SCN1A-related infantile epileptic encephalopathies.

Harkin LA, McMahon JM, Iona X, Dibbens L, Pelekanos JT, Zuberi SM, Sadleir LG, Andermann E, Gill D, Farrell K, Connolly M, Stanley T, Harbord M, Andermann F, Wang J, Batish SD, Jones JG, Seltzer WK, Gardner A; Infantile Epileptic Encephalopathy Referral Consortium., Sutherland G, Berkovic SF, et al.

Brain. 2007 Mar;130(Pt 3):843-52.

PubMed [citation]
PMID:
17347258
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000820608.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change results in a premature translational stop signal in the SCN1A gene (p.Arg1886*). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 124 amino acids of the SCN1A protein. This variant is not present in population databases (ExAC no frequency). This variant has been reported in individuals affected with severe myoclonic epilepsy of infancy (SMEI) or Dravet syndrome (PMID: 17054684, 18930999, 22409937, 17347258). In a number of these individuals, the variant was reported to be de novo (PMID: 17054684, 18930999). ClinVar contains an entry for this variant (Variation ID: 189912). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Dec 2, 2021

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