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NM_001165963.4(SCN1A):c.3879+5G>C AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 25, 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:
RCV002796511.3

Allele description [Variation Report for NM_001165963.4(SCN1A):c.3879+5G>C]

NM_001165963.4(SCN1A):c.3879+5G>C

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+5G>C
HGVS:
  • NC_000002.12:g.166012104C>G
  • NG_011906.1:g.66536G>C
  • NM_001165963.4:c.3879+5G>CMANE SELECT
  • NM_001165964.3:c.3795+5G>C
  • NM_001202435.3:c.3879+5G>C
  • NM_001353948.2:c.3879+5G>C
  • NM_001353949.2:c.3846+5G>C
  • NM_001353950.2:c.3846+5G>C
  • NM_001353951.2:c.3846+5G>C
  • NM_001353952.2:c.3846+5G>C
  • NM_001353954.2:c.3843+5G>C
  • NM_001353955.2:c.3843+5G>C
  • NM_001353957.2:c.3795+5G>C
  • NM_001353958.2:c.3795+5G>C
  • NM_001353960.2:c.3792+5G>C
  • NM_001353961.2:c.1437+5G>C
  • NM_006920.6:c.3846+5G>C
  • LRG_8:g.66536G>C
  • NC_000002.11:g.166868614C>G
Molecular consequence:
  • NM_001165963.4:c.3879+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001165964.3:c.3795+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001202435.3:c.3879+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353948.2:c.3879+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353949.2:c.3846+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353950.2:c.3846+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353951.2:c.3846+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353952.2:c.3846+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353954.2:c.3843+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353955.2:c.3843+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353957.2:c.3795+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353958.2:c.3795+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353960.2:c.3792+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353961.2:c.1437+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_006920.6:c.3846+5G>C - intron variant - [Sequence Ontology: SO:0001627]

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
SCV003197969Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Oct 25, 2022) 		germlineclinical testing

PubMed (4)
[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

Defining Dravet syndrome: An essential pre-requisite for precision medicine trials.

Li W, Schneider AL, Scheffer IE.

Epilepsia. 2021 Sep;62(9):2205-2217. doi: 10.1111/epi.17015. Epub 2021 Aug 2.

PubMed [citation]
PMID:
34338318
PMCID:
PMC9291974

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003197969.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 19 of the SCN1A gene. It does not directly change the encoded amino acid sequence of the SCN1A protein. It affects a nucleotide within the consensus splice site. This variant has been observed in individual(s) with epilepsy (Invitae). In at least one individual the variant was observed to be de novo. For these reasons, this variant has been classified as Pathogenic. This variant disrupts the c.3879+5G nucleotide in the SCN1A gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 34338318). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site.

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

Last Updated: Sep 29, 2024