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NM_001165963.4(SCN1A):c.4762T>C (p.Cys1588Arg)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3
First in ClinVar:
Oct 31, 2013
Most recent Submission:
May 16, 2022
Last evaluated:
Aug 27, 2021
Accession:
VCV000068552.4
Variation ID:
68552
Description:
single nucleotide variant
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NM_001165963.4(SCN1A):c.4762T>C (p.Cys1588Arg)

Allele ID
79444
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 165994236 (GRCh38) GRCh38 UCSC
2: 166850746 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001165963.4:c.4762T>C MANE Select NP_001159435.1:p.Cys1588Arg missense
NM_001165964.3:c.4678T>C NP_001159436.1:p.Cys1560Arg missense
NM_001202435.3:c.4762T>C NP_001189364.1:p.Cys1588Arg missense
... more HGVS
Protein change
C1577R, C1588R, C1560R, C1576R, C774R, C1559R
Other names
p.C1588R:TGT>CGT
Canonical SPDI
NC_000002.12:165994235:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA284979
UniProtKB/Swiss-Prot: VAR_064319
dbSNP: rs121917919
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 Dec 21, 2016 RCV000188974.4
Pathogenic 1 criteria provided, single submitter Aug 27, 2021 RCV000636318.4
not provided 1 no assertion provided - RCV000059426.2
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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
1646 3367
LOC102724058 - - - GRCh38 - 1673

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Likely pathogenic
(Dec 21, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Affected status: yes
Allele origin: germline
GeneDx
Accession: SCV000242605.12
First in ClinVar: Aug 07, 2015
Last updated: Mar 08, 2017
Comment:
p.Cys1588Arg (TGT>CGT): c.4762 T>C in exon 25 of the SCN1A gene (NM_001165963.1) A C1588R variant that is likely pathogenic has been identified in the SCN1A … (more)
Pathogenic
(Aug 27, 2021)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV000757757.3
First in ClinVar: May 28, 2018
Last updated: May 16, 2022
Publications:
PubMed (1)
PubMed: 28492532
not provided
(-)
no assertion provided
Method: not provided
Severe myoclonic epilepsy in infancy
Affected status: not provided
Allele origin: unknown
UniProtKB/Swiss-Prot
Accession: SCV000090950.1
First in ClinVar: Oct 31, 2013
Last updated: Oct 31, 2013

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
Idiopathic epilepsies with seizures precipitated by fever and SCN1A abnormalities. Marini C Epilepsia 2007 PMID: 17561957

Text-mined citations for rs121917919...

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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 Jun 24, 2022