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NM_001165963.4(SCN1A):c.5674C>T (p.Arg1892Ter)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jul 4, 2021)
Last evaluated:
Sep 30, 2019
Accession:
VCV000189896.11
Variation ID:
189896
Description:
single nucleotide variant
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NM_001165963.4(SCN1A):c.5674C>T (p.Arg1892Ter)

Allele ID
187701
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 166848111 (GRCh37) GRCh37 UCSC
2: 165991601 (GRCh38) GRCh38 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_8:g.87039C>T
NC_000002.11:g.166848111G>A
NC_000002.12:g.165991601G>A
... more HGVS
Protein change
R1881*, R1892*, R1078*, R1880*, R1863*, R1864*
Other names
p.R1892*:CGA>TGA
Canonical SPDI
NC_000002.12:165991600:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA303237
dbSNP: rs794726739
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, multiple submitters, no conflicts Jul 1, 2019 RCV000189004.3
Pathogenic 1 criteria provided, single submitter Dec 20, 2014 RCV000180848.1
Pathogenic 1 criteria provided, single submitter Oct 31, 2018 RCV000805798.1
Pathogenic 1 criteria provided, single submitter Sep 30, 2019 RCV000995637.2
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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: SCV000221813.1
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
(Mar 13, 2014)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000242635.11
Submitted: (Jan 29, 2019)
Evidence details
Comment:
p.Arg1892Stop (CGA>TGA): c.5674 C>T in exon 26 of the SCN1A gene (NM_001165963.1) The R1892X nonsense mutation in the SCN1A gene has been reported in multiple … (more)
Pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Allele origin: germline
Invitae
Accession: SCV000945767.1
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change results in a premature translational stop signal in the SCN1A gene (p.Arg1892*). While this is not anticipated to result in nonsense mediated … (more)
Pathogenic
(Sep 30, 2019)
criteria provided, single submitter
Method: clinical testing
Generalized epilepsy with febrile seizures plus, type 2
(Autosomal dominant inheritance)
Allele origin: de novo
Institute of Human Genetics, Klinikum rechts der Isar
Accession: SCV001149920.1
Submitted: (Jan 21, 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: SCV001245861.6
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
Pitfalls in genetic testing: the story of missed SCN1A mutations. Djémié T Molecular genetics & genomic medicine 2016 PMID: 27465585
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
Familial occurrence of febrile seizures and epilepsy in severe myoclonic epilepsy of infancy (SMEI) patients with SCN1A mutations. Mancardi MM Epilepsia 2006 PMID: 17054684
http://www.openbioinformatics.org/annovar/annovar_startup.html - - - -

Text-mined citations for rs794726739...

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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 16, 2021