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NM_001165963.4(SCN1A):c.4168G>A (p.Val1390Met)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Sep 23, 2021)
Last evaluated:
Sep 10, 2018
Accession:
VCV000068537.7
Variation ID:
68537
Description:
single nucleotide variant
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NM_001165963.4(SCN1A):c.4168G>A (p.Val1390Met)

Allele ID
79429
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 166002588 (GRCh38) GRCh38 UCSC
2: 166859098 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_8:g.76052G>A
LRG_8t1:c.4135G>A
NC_000002.11:g.166859098C>T
... more HGVS
Protein change
V1379M, V1390M, V1378M, V1362M, V1361M, V576M
Other names
-
Canonical SPDI
NC_000002.12:166002587:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA284940
UniProtKB/Swiss-Prot: VAR_029699
dbSNP: rs121917986
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, single submitter Dec 20, 2014 RCV000059411.2
Pathogenic 3 criteria provided, single submitter Jan 12, 2018 RCV000254970.4
Pathogenic 1 criteria provided, single submitter Sep 10, 2018 RCV000804975.1
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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
(Sep 10, 2018)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Allele origin: germline
Invitae
Accession: SCV000944916.1
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (7)
Comment:
This sequence change replaces valine with methionine at codon 1390 of the SCN1A protein (p.Val1390Met). The valine residue is highly conserved and there is a … (more)
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: SCV000221778.1
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
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000322269.6
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The V1390M missense pathogenic variant in the SCN1A gene has been reported previously as a de novo pathogenic variant in association with Dravet syndrome and … (more)
Pathogenic
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001931131.1
Submitted: (Sep 23, 2021)
Evidence details
Pathogenic
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001740812.3
Submitted: (Sep 02, 2021)
Evidence details
not provided
(-)
no assertion provided
Method: not provided
Severe myoclonic epilepsy in infancy
Allele origin: unknown
UniProtKB/Swiss-Prot
Accession: SCV000090935.1
Submitted: (Apr 28, 2011)
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
Efficacy of Stiripentol in Dravet Syndrome with or without SCN1A Mutations. Cho MJ Journal of clinical neurology (Seoul, Korea) 2018 PMID: 29141279
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
UniProt: a hub for protein information. UniProt Consortium. Nucleic acids research 2015 PMID: 25348405
Prevalence of SCN1A-related dravet syndrome among children reported with seizures following vaccination: a population-based ten-year cohort study. Verbeek NE PloS one 2013 PMID: 23762420
Dravet syndrome: seizure control and gait in adults with different SCN1A mutations. Rilstone JJ Epilepsia 2012 PMID: 22780858
Analysis of SCN1A mutation and parental origin in patients with Dravet syndrome. Sun H Journal of human genetics 2010 PMID: 20431604
A catalog of SCN1A variants. Lossin C Brain & development 2009 PMID: 18804930
The spectrum of SCN1A-related infantile epileptic encephalopathies. Harkin LA Brain : a journal of neurology 2007 PMID: 17347258
Significant correlation of the SCN1A mutations and severe myoclonic epilepsy in infancy. Ohmori I Biochemical and biophysical research communications 2002 PMID: 12083760
http://www.openbioinformatics.org/annovar/annovar_startup.html - - - -

Text-mined citations for rs121917986...

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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 Sep 24, 2021