NM_001165963.4(SCN1A):c.5468T>C (p.Met1823Thr) AND Early infantile epileptic encephalopathy with suppression bursts

Clinical significance:Uncertain significance (Last evaluated: Jun 27, 2018)

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.5468T>C (p.Met1823Thr)]

NM_001165963.4(SCN1A):c.5468T>C (p.Met1823Thr)

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.5468T>C (p.Met1823Thr)
  • NC_000002.12:g.165991807A>G
  • NG_011906.1:g.86833T>C
  • NM_001165963.4:c.5468T>CMANE SELECT
  • NM_001165964.3:c.5384T>C
  • NM_001202435.3:c.5468T>C
  • NM_001353948.2:c.5468T>C
  • NM_001353949.2:c.5435T>C
  • NM_001353950.2:c.5435T>C
  • NM_001353951.2:c.5435T>C
  • NM_001353952.2:c.5435T>C
  • NM_001353954.2:c.5432T>C
  • NM_001353955.2:c.5432T>C
  • NM_001353957.2:c.5384T>C
  • NM_001353958.2:c.5384T>C
  • NM_001353960.2:c.5381T>C
  • NM_001353961.2:c.3026T>C
  • NM_006920.6:c.5435T>C
  • NP_001159435.1:p.Met1823Thr
  • NP_001159436.1:p.Met1795Thr
  • NP_001189364.1:p.Met1823Thr
  • NP_001340877.1:p.Met1823Thr
  • NP_001340878.1:p.Met1812Thr
  • NP_001340879.1:p.Met1812Thr
  • NP_001340880.1:p.Met1812Thr
  • NP_001340881.1:p.Met1812Thr
  • NP_001340883.1:p.Met1811Thr
  • NP_001340884.1:p.Met1811Thr
  • NP_001340886.1:p.Met1795Thr
  • NP_001340887.1:p.Met1795Thr
  • NP_001340889.1:p.Met1794Thr
  • NP_001340890.1:p.Met1009Thr
  • NP_008851.3:p.Met1812Thr
  • LRG_8:g.86833T>C
  • NC_000002.11:g.166848317A>G
  • NM_001165963.1:c.5468T>C
  • NR_148667.2:n.5885T>C
Protein change:
dbSNP: rs1559101839
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001165963.4:c.5468T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.5384T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.5468T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.5468T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.5435T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.5435T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.5435T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.5435T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.5432T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.5432T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.5384T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.5384T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.5381T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353961.2:c.3026T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.5435T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.5885T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]


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)
SCV000821506Invitaecriteria provided, single submitter
Uncertain significance
(Jun 27, 2018)
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



When is a child with status epilepticus likely to have Dravet syndrome?

Le Gal F, Lebon S, Ramelli GP, Datta AN, Mercati D, Maier O, Combescure C, Rodriguez MI, Seeck M, Roulet E, Korff CM.

Epilepsy Res. 2014 May;108(4):740-7. doi: 10.1016/j.eplepsyres.2014.02.019. Epub 2014 Mar 12.

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, SCV000821506.1

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


This sequence change replaces methionine with threonine at codon 1823 of the SCN1A protein (p.Met1823Thr). The methionine residue is highly conserved and there is a moderate physicochemical difference between methionine and threonine. This variant is not present in population databases (ExAC no frequency). This variant has been observed to be de novo in an individual affected with generalized epilepsy with febrile seizures plus spectrum (PMID: 24679980). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C65"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Nov 27, 2021

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