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NM_001165963.4(SCN1A):c.472G>C (p.Glu158Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Sep 30, 2021)
Last evaluated:
Jan 6, 2021
Accession:
VCV000206928.4
Variation ID:
206928
Description:
single nucleotide variant
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NM_001165963.4(SCN1A):c.472G>C (p.Glu158Gln)

Allele ID
201624
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 166056412 (GRCh38) GRCh38 UCSC
2: 166912922 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.166912922C>G
NC_000002.12:g.166056412C>G
NG_011906.1:g.22228G>C
... more HGVS
Protein change
E158Q
Other names
p.E158Q:GAA>CAA
Canonical SPDI
NC_000002.12:166056411:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA317752
dbSNP: rs796053090
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Jan 6, 2021 RCV000189072.3
Uncertain significance 1 criteria provided, single submitter Sep 25, 2017 RCV000636394.1
Likely pathogenic 1 no assertion criteria provided Jan 1, 2019 RCV001252613.1
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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
1308 2631

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Sep 25, 2017)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Allele origin: germline
Invitae
Accession: SCV000757833.1
Submitted: (Apr 02, 2018)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces glutamic acid with glutamine at codon 158 of the SCN1A protein (p.Glu158Gln). The glutamic acid residue is highly conserved and there … (more)
Likely pathogenic
(Jan 06, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000242703.12
Submitted: (Sep 30, 2021)
Evidence details
Comment:
Not observed in large population cohorts (Lek et al., 2016); Missense variants in this gene are often considered pathogenic (Stenson et al., 2014); In silico … (more)
Likely pathogenic
(Jan 01, 2019)
no assertion criteria provided
Method: clinical testing
Severe myoclonic epilepsy in infancy
Allele origin: unknown
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille
Accession: SCV001428372.1
Submitted: (May 05, 2020)
Evidence details
Publications
PubMed (1)

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
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

Text-mined citations for rs796053090...

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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