NM_001165963.4(SCN1A):c.3106C>T (p.Gln1036Ter) AND Early infantile epileptic encephalopathy with suppression bursts

Clinical significance:Pathogenic (Last evaluated: Sep 5, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_001165963.4(SCN1A):c.3106C>T (p.Gln1036Ter)]

NM_001165963.4(SCN1A):c.3106C>T (p.Gln1036Ter)

SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
LOC102724058:uncharacterized LOC102724058 [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001165963.4(SCN1A):c.3106C>T (p.Gln1036Ter)
  • NC_000002.12:g.166036371G>A
  • NG_011906.1:g.42269C>T
  • NM_001165963.4:c.3106C>TMANE SELECT
  • NM_001165964.3:c.3022C>T
  • NM_001202435.3:c.3106C>T
  • NM_001353948.2:c.3106C>T
  • NM_001353949.2:c.3073C>T
  • NM_001353950.2:c.3073C>T
  • NM_001353951.2:c.3073C>T
  • NM_001353952.2:c.3073C>T
  • NM_001353954.2:c.3070C>T
  • NM_001353955.2:c.3070C>T
  • NM_001353957.2:c.3022C>T
  • NM_001353958.2:c.3022C>T
  • NM_001353960.2:c.3019C>T
  • NM_001353961.2:c.664C>T
  • NM_006920.6:c.3073C>T
  • NP_001159435.1:p.Gln1036Ter
  • NP_001159436.1:p.Gln1008Ter
  • NP_001189364.1:p.Gln1036Ter
  • NP_001340877.1:p.Gln1036Ter
  • NP_001340878.1:p.Gln1025Ter
  • NP_001340879.1:p.Gln1025Ter
  • NP_001340880.1:p.Gln1025Ter
  • NP_001340881.1:p.Gln1025Ter
  • NP_001340883.1:p.Gln1024Ter
  • NP_001340884.1:p.Gln1024Ter
  • NP_001340886.1:p.Gln1008Ter
  • NP_001340887.1:p.Gln1008Ter
  • NP_001340889.1:p.Gln1007Ter
  • NP_001340890.1:p.Gln222Ter
  • NP_008851.3:p.Gln1025Ter
  • LRG_8:g.42269C>T
  • NC_000002.11:g.166892881G>A
  • NM_001165963.1:c.3106C>T
  • NR_110598.1:n.711G>A
  • NR_148667.2:n.3459C>T
Protein change:
dbSNP: rs542420576
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NR_110598.1:n.711G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148667.2:n.3459C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001165963.4:c.3106C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001165964.3:c.3022C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001202435.3:c.3106C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353948.2:c.3106C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353949.2:c.3073C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353950.2:c.3073C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353951.2:c.3073C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353952.2:c.3073C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353954.2:c.3070C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353955.2:c.3070C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353957.2:c.3022C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353958.2:c.3022C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353960.2:c.3019C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353961.2:c.664C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_006920.6:c.3073C>T - nonsense - [Sequence Ontology: SO:0001587]


Early infantile epileptic encephalopathy with suppression bursts (EIEE)
Early infantile epileptic encephalopathy; Ohtahara syndrome; Developmental and epileptic encephalopathy
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)
SCV000757763Invitaecriteria provided, single submitter
(Sep 5, 2017)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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



SCN1A mutational analysis in Korean patients with Dravet syndrome.

Lim BC, Hwang H, Chae JH, Choi JE, Hwang YS, Kang SH, Ki CS, Kim KJ.

Seizure. 2011 Dec;20(10):789-94. doi: 10.1016/j.seizure.2011.08.002. Epub 2011 Aug 24.

PubMed [citation]

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

Details of each submission

From Invitae, SCV000757763.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)


This sequence change creates a premature translational stop signal (p.Gln1036*) 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 reported to be de novo in an individual affected with Dravet syndrome (PMID: 21868258). ClinVar contains an entry for this variant (Variation ID: 189975). Loss-of-function variants in SCN1A are known to be pathogenic (PMID: 17347258, 18930999). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Nov 27, 2021

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