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

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jul 4, 2021)
Last evaluated:
Nov 1, 2020
Accession:
VCV000572287.6
Variation ID:
572287
Description:
single nucleotide variant
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NM_001165963.4(SCN1A):c.5468T>C (p.Met1823Thr)

Allele ID
557604
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 165991807 (GRCh38) GRCh38 UCSC
2: 166848317 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.166848317A>G
NC_000002.12:g.165991807A>G
NG_011906.1:g.86833T>C
... more HGVS
Protein change
M1812T, M1823T, M1009T, M1795T, M1811T, M1794T
Other names
-
Canonical SPDI
NC_000002.12:165991806:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs1559101839
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jun 27, 2018 RCV000693631.1
Pathogenic 1 criteria provided, single submitter Nov 3, 2017 RCV001253286.1
Likely pathogenic 1 criteria provided, single submitter Nov 1, 2020 RCV001200252.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SCN1A Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1341 2698
LOC102724058 - - - GRCh38 - 1321

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 27, 2018)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy
Allele origin: germline
Invitae
Accession: SCV000821506.1
Submitted: (Aug 29, 2018)
Evidence details
Publications
PubMed (2)
Comment:
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 … (more)
Pathogenic
(Nov 03, 2017)
criteria provided, single submitter
Method: clinical testing
Severe myoclonic epilepsy in infancy
Allele origin: germline
Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001428932.1
Submitted: (Apr 20, 2020)
Evidence details
Likely pathogenic
(Nov 01, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001371157.4
Submitted: (Jul 04, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
When is a child with status epilepticus likely to have Dravet syndrome? Le Gal F Epilepsy research 2014 PMID: 24679980

Text-mined citations for rs1559101839...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021