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NM_001165963.4(SCN1A):c.3879+1G>A AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 15, 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:
RCV002651543.3

Allele description [Variation Report for NM_001165963.4(SCN1A):c.3879+1G>A]

NM_001165963.4(SCN1A):c.3879+1G>A

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.3879+1G>A
HGVS:
  • NC_000002.12:g.166012108C>T
  • NG_011906.1:g.66532G>A
  • NM_001165963.4:c.3879+1G>AMANE SELECT
  • NM_001165964.3:c.3795+1G>A
  • NM_001202435.3:c.3879+1G>A
  • NM_001353948.2:c.3879+1G>A
  • NM_001353949.2:c.3846+1G>A
  • NM_001353950.2:c.3846+1G>A
  • NM_001353951.2:c.3846+1G>A
  • NM_001353952.2:c.3846+1G>A
  • NM_001353954.2:c.3843+1G>A
  • NM_001353955.2:c.3843+1G>A
  • NM_001353957.2:c.3795+1G>A
  • NM_001353958.2:c.3795+1G>A
  • NM_001353960.2:c.3792+1G>A
  • NM_001353961.2:c.1437+1G>A
  • NM_006920.6:c.3846+1G>A
  • LRG_8:g.66532G>A
  • NC_000002.11:g.166868618C>T
Molecular consequence:
  • NM_001165963.4:c.3879+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001165964.3:c.3795+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001202435.3:c.3879+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353948.2:c.3879+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353949.2:c.3846+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353950.2:c.3846+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353951.2:c.3846+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353952.2:c.3846+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353954.2:c.3843+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353955.2:c.3843+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353957.2:c.3795+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353958.2:c.3795+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353960.2:c.3792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353961.2:c.1437+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_006920.6:c.3846+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003524844Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 15, 2022) 		germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Genotype-phenotype associations in SCN1A-related epilepsies.

Zuberi SM, Brunklaus A, Birch R, Reavey E, Duncan J, Forbes GH.

Neurology. 2011 Feb 15;76(7):594-600. doi: 10.1212/WNL.0b013e31820c309b. Epub 2011 Jan 19.

PubMed [citation]
PMID:
21248271

Prevalence of SCN1A mutations in children with suspected Dravet syndrome and intractable childhood epilepsy.

Wang JW, Shi XY, Kurahashi H, Hwang SK, Ishii A, Higurashi N, Kaneko S, Hirose S; Epilepsy Genetic Study Group Japan..

Epilepsy Res. 2012 Dec;102(3):195-200. doi: 10.1016/j.eplepsyres.2012.06.006. Epub 2012 Jul 20.

PubMed [citation]
PMID:
23195492
See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003524844.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant is also known as IVS19+1G>A. Disruption of this splice site has been observed in individual(s) with Dravet syndrome (PMID: 18930999, 21248271, 23195492). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 19 of the SCN1A gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SCN1A are known to be pathogenic (PMID: 17347258, 18930999).

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

Last Updated: Sep 29, 2024