NM_001165963.4(SCN1A):c.1702C>T (p.Arg568Ter) AND Early infantile epileptic encephalopathy with suppression bursts

Clinical significance:Pathogenic (Last evaluated: Sep 24, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001382872.1

Allele description [Variation Report for NM_001165963.4(SCN1A):c.1702C>T (p.Arg568Ter)]

NM_001165963.4(SCN1A):c.1702C>T (p.Arg568Ter)

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.1702C>T (p.Arg568Ter)
HGVS:
  • NC_000002.12:g.166044010G>A
  • NG_011906.1:g.34630C>T
  • NM_001165963.4:c.1702C>TMANE SELECT
  • NM_001165964.3:c.1702C>T
  • NM_001202435.3:c.1702C>T
  • NM_001353948.2:c.1702C>T
  • NM_001353949.2:c.1702C>T
  • NM_001353950.2:c.1702C>T
  • NM_001353951.2:c.1702C>T
  • NM_001353952.2:c.1702C>T
  • NM_001353954.2:c.1699C>T
  • NM_001353955.2:c.1699C>T
  • NM_001353957.2:c.1702C>T
  • NM_001353958.2:c.1702C>T
  • NM_001353960.2:c.1699C>T
  • NM_001353961.2:c.-724C>T
  • NM_006920.6:c.1702C>T
  • NP_001159435.1:p.Arg568Ter
  • NP_001159436.1:p.Arg568Ter
  • NP_001189364.1:p.Arg568Ter
  • NP_001340877.1:p.Arg568Ter
  • NP_001340878.1:p.Arg568Ter
  • NP_001340879.1:p.Arg568Ter
  • NP_001340880.1:p.Arg568Ter
  • NP_001340881.1:p.Arg568Ter
  • NP_001340883.1:p.Arg567Ter
  • NP_001340884.1:p.Arg567Ter
  • NP_001340886.1:p.Arg568Ter
  • NP_001340887.1:p.Arg568Ter
  • NP_001340889.1:p.Arg567Ter
  • NP_008851.3:p.Arg568Ter
  • LRG_8:g.34630C>T
  • NC_000002.11:g.166900520G>A
  • NM_001165963.1:c.1702C>T
  • NM_001165963.3:c.1702C>T
  • NR_148667.2:n.2088C>T
Protein change:
R567*
Links:
dbSNP: rs886039430
NCBI 1000 Genomes Browser:
rs886039430
Molecular consequence:
  • NM_001353961.2:c.-724C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NR_148667.2:n.2088C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001165963.4:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001165964.3:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001202435.3:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353948.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353949.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353950.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353951.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353952.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353954.2:c.1699C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353955.2:c.1699C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353957.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353958.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353960.2:c.1699C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_006920.6:c.1702C>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
SCV001581826Invitaecriteria provided, single submitter
Pathogenic
(Sep 24, 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

Significant correlation of the SCN1A mutations and severe myoclonic epilepsy in infancy.

Ohmori I, Ouchida M, Ohtsuka Y, Oka E, Shimizu K.

Biochem Biophys Res Commun. 2002 Jul 5;295(1):17-23.

PubMed [citation]
PMID:
12083760

Diagnostic yield of targeted massively parallel sequencing in children with epileptic encephalopathy.

Kothur K, Holman K, Farnsworth E, Ho G, Lorentzos M, Troedson C, Gupta S, Webster R, Procopis PG, Menezes MP, Antony J, Ardern-Holmes S, Dale RC, Christodoulou J, Gill D, Bennetts B.

Seizure. 2018 Jul;59:132-140. doi: 10.1016/j.seizure.2018.05.005. Epub 2018 May 28.

PubMed [citation]
PMID:
29852413
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001581826.1

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

Description

This sequence change creates a premature translational stop signal (p.Arg568*) in the SCN1A gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with Dravet syndrome (PMID: 12083760, 29852413). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 265254). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. Loss-of-function variants in SCN1A are known to be pathogenic (PMID: 17347258, 18930999). 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: Oct 8, 2021

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