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NM_001165963.4(SCN1A):c.3637C>T (p.Arg1213Ter)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Jul 4, 2021)
Last evaluated:
Jul 1, 2019
Accession:
VCV000189861.10
Variation ID:
189861
Description:
single nucleotide variant
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NM_001165963.4(SCN1A):c.3637C>T (p.Arg1213Ter)

Allele ID
187772
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 166013812 (GRCh38) GRCh38 UCSC
2: 166870322 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_8:g.64828C>T
LRG_8t1:c.3604C>T
NC_000002.11:g.166870322G>A
... more HGVS
Protein change
R1202*, R1213*, R1201*, R399*, R1184*, R1185*
Other names
p.R1213*:CGA>TGA
Canonical SPDI
NC_000002.12:166013811:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA303131
dbSNP: rs794726710
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 4 criteria provided, multiple submitters, no conflicts Sep 5, 2017 RCV000180814.4
Pathogenic 2 criteria provided, multiple submitters, no conflicts Jul 1, 2019 RCV000189082.4
Pathogenic 1 criteria provided, single submitter Sep 14, 2017 RCV000585684.1
Pathogenic 1 criteria provided, single submitter Aug 10, 2018 RCV000808766.1
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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
Pathogenic
(Dec 20, 2014)
criteria provided, single submitter
Method: research
Dravet syndrome
Allele origin: de novo
Center for Bioinformatics, Peking University
Additional submitter:
Pediatric Department, Peking University First Hospital
Study: University Clinical Cooperation “985 Project” PKU-2014-1-1
Accession: SCV000221776.1
Submitted: (Mar 07, 2015)
Comment:
Dravet syndrome (DS) probands were recruited from the outpatient and inpatient child neurology units of Peking University First Hospital from 2005 till present. The study … (more)
Evidence details
Publications
PubMed (1)
Other databases
http://www.openbioinformatics.or…
Pathogenic
(Jun 10, 2014)
criteria provided, single submitter
Method: clinical testing
Severe myoclonic epilepsy in infancy
(Autosomal dominant inheritance)
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000255823.2
Submitted: (Oct 06, 2015)
Evidence details
Publications
PubMed (2)
Pathogenic
(Nov 04, 2014)
criteria provided, single submitter
Method: research
Severe myoclonic epilepsy in infancy
Allele origin: de novo
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology
Study: CSER-HudsonAlpha
Accession: SCV000265529.2
Submitted: (Mar 03, 2016)
Evidence details
Pathogenic
(Nov 09, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000242713.11
Submitted: (Jan 29, 2019)
Evidence details
Comment:
p.Arg1213Ter (CGA>TGA): c.3637 C>T in exon 18 of the SCN1A gene (NM_001165963.1) The R1213X nonsense mutation in the SCN1A gene has been reported previously in … (more)
Pathogenic
(Sep 14, 2017)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: de novo
Center of Genomic medicine, Geneva,University Hospital of Geneva
Accession: SCV000693448.1
Submitted: (Nov 15, 2017)
Evidence details
Comment:
This pathogenic mutation in the SCN1A gene was found in a child with epilepsy since the age of 5 months.
Pathogenic
(Aug 10, 2018)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Allele origin: germline
Invitae
Accession: SCV000948885.1
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change creates a premature translational stop signal (p.Arg1213*) in the SCN1A gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Sep 05, 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: SCV001428929.1
Submitted: (Apr 20, 2020)
Evidence details
Pathogenic
(Jul 01, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001247846.6
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
Amplicon Resequencing Identified Parental Mosaicism for Approximately 10% of "de novo" SCN1A Mutations in Children with Dravet Syndrome. Xu X Human mutation 2015 PMID: 26096185
De novo mutations in epileptic encephalopathies. Epi4K Consortium. Nature 2013 PMID: 23934111
Prevalence of SCN1A mutations in children with suspected Dravet syndrome and intractable childhood epilepsy. Wang JW Epilepsy research 2012 PMID: 23195492
Spectrum of SCN1A gene mutations associated with Dravet syndrome: analysis of 333 patients. Depienne C Journal of medical genetics 2009 PMID: 18930999
Mutations of sodium channel alpha subunit type 1 (SCN1A) in intractable childhood epilepsies with frequent generalized tonic-clonic seizures. Fujiwara T Brain : a journal of neurology 2003 PMID: 12566275
http://www.openbioinformatics.org/annovar/annovar_startup.html - - - -

Text-mined citations for rs794726710...

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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