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NM_001165963.4(SCN1A):c.5870A>G (p.Glu1957Gly)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 24, 2021)
Last evaluated:
Feb 14, 2020
Accession:
VCV000068671.4
Variation ID:
68671
Description:
single nucleotide variant
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NM_001165963.4(SCN1A):c.5870A>G (p.Glu1957Gly)

Allele ID
79563
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 165991405 (GRCh38) GRCh38 UCSC
2: 166847915 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.166847915T>C
NC_000002.12:g.165991405T>C
NG_011906.1:g.87235A>G
... more HGVS
Protein change
E1946G, E1957G, E1143G, E1929G, E1945G, E1928G
Other names
p.E1957G:GAA>GGA
Canonical SPDI
NC_000002.12:165991404:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00006
Exome Aggregation Consortium (ExAC) 0.00009
The Genome Aggregation Database (gnomAD), exomes 0.00014
Trans-Omics for Precision Medicine (TOPMed) 0.00015
The Genome Aggregation Database (gnomAD) 0.00016
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00038
Links
ClinGen: CA213190
UniProtKB/Swiss-Prot: VAR_029731
dbSNP: rs121918802
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 Aug 25, 2018 RCV000537890.3
Uncertain significance 1 criteria provided, single submitter Oct 31, 2018 RCV000764283.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Feb 14, 2020 RCV000416094.2
not provided 1 no assertion provided - RCV000059551.1
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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
1348 2705
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
(Jul 31, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000493672.6
Submitted: (Oct 23, 2018)
Evidence details
Uncertain significance
(Aug 25, 2018)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Allele origin: germline
Invitae
Accession: SCV000633877.3
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change replaces glutamic acid with glycine at codon 1957 of the SCN1A protein (p.Glu1957Gly). The glutamic acid residue is highly conserved and there … (more)
Benign
(Feb 14, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000242655.12
Submitted: (Sep 24, 2021)
Evidence details
Comment:
Reported previously an individual with infantile spasms and mild intellectual disability; however, family studies were not performed (Wallace et al., 2003); This substitution is within … (more)
Uncertain significance
(Oct 31, 2018)
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: SCV000895302.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
not provided
(-)
no assertion provided
Method: not provided
not provided
Allele origin: not provided
UniProtKB/Swiss-Prot
Accession: SCV000091083.1
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
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
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
UniProt: a hub for protein information. UniProt Consortium. Nucleic acids research 2015 PMID: 25348405
A catalog of SCN1A variants. Lossin C Brain & development 2009 PMID: 18804930
Sodium channel alpha1-subunit mutations in severe myoclonic epilepsy of infancy and infantile spasms. Wallace RH Neurology 2003 PMID: 14504318

Text-mined citations for rs121918802...

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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 Nov 27, 2021