Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_001165963.4(SCN1A):c.3481G>A (p.Ala1161Thr)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 20, 2020
Accession:
VCV000194721.5
Variation ID:
194721
Description:
single nucleotide variant
Help

NM_001165963.4(SCN1A):c.3481G>A (p.Ala1161Thr)

Allele ID
191884
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 166015676 (GRCh38) GRCh38 UCSC
2: 166872186 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.166872186C>T
NC_000002.12:g.166015676C>T
NG_011906.1:g.62964G>A
... more HGVS
Protein change
A1150T, A1161T, A1133T, A1132T, A1149T, A347T
Other names
p.A1161T:GCA>ACA
Canonical SPDI
NC_000002.12:166015675:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00006
The Genome Aggregation Database (gnomAD), exomes 0.00038
Exome Aggregation Consortium (ExAC) 0.00040
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Trans-Omics for Precision Medicine (TOPMed) 0.00015
Links
ClinGen: CA240854
dbSNP: rs201079458
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter May 10, 2017 RCV000188914.5
Uncertain significance 1 criteria provided, single submitter May 23, 2017 RCV000515245.1
SCN1A-Related Disorders
Benign 1 criteria provided, single submitter Apr 28, 2017 RCV001132318.1
Likely benign 1 criteria provided, single submitter Nov 20, 2020 RCV001444749.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jan 28, 2019 RCV000724750.2
Help
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
1309 2632
LOC102724058 - - - GRCh38 - 1287

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(May 10, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000242544.11
Submitted: (Jul 13, 2017)
Evidence details
Comment:
The A1161T missense substitution was previously identified on the same chromosome (in cis) with the R604H variant in a patient with juvenile myoclonic epilepsy (JME); … (more)
Uncertain significance
(Apr 22, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000226591.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(May 23, 2017)
criteria provided, single submitter
Method: clinical testing
Generalized epilepsy with febrile seizures plus, type 2
Severe myoclonic epilepsy in infancy
Familial hemiplegic migraine type 3
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000611519.1
Submitted: (May 23, 2017)
Evidence details
Likely benign
(Jan 28, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000559690.4
Submitted: (Mar 14, 2019)
Evidence details
Benign
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
SCN1A-Related Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001291977.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Nov 20, 2020)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Allele origin: germline
Invitae
Accession: SCV001647760.1
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

Help
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

Help
Title Author Journal Year Link
A novel SCN1A mutation associated with generalized epilepsy with febrile seizures plus--and prevalence of variants in patients with epilepsy. Escayg A American journal of human genetics 2001 PMID: 11254445
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SCN1A - - - -

Text-mined citations for rs201079458...

Help
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