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NM_001165963.4(SCN1A):c.3538T>C (p.Cys1180Arg) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 21, 2018
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001822144.4

Allele description [Variation Report for NM_001165963.4(SCN1A):c.3538T>C (p.Cys1180Arg)]

NM_001165963.4(SCN1A):c.3538T>C (p.Cys1180Arg)

Genes:
SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
LOC102724058:uncharacterized LOC102724058 [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001165963.4(SCN1A):c.3538T>C (p.Cys1180Arg)
HGVS:
  • NC_000002.12:g.166015619A>G
  • NG_011906.1:g.63021T>C
  • NM_001165963.4:c.3538T>CMANE SELECT
  • NM_001165964.3:c.3454T>C
  • NM_001202435.3:c.3538T>C
  • NM_001353948.2:c.3538T>C
  • NM_001353949.2:c.3505T>C
  • NM_001353950.2:c.3505T>C
  • NM_001353951.2:c.3505T>C
  • NM_001353952.2:c.3505T>C
  • NM_001353954.2:c.3502T>C
  • NM_001353955.2:c.3502T>C
  • NM_001353957.2:c.3454T>C
  • NM_001353958.2:c.3454T>C
  • NM_001353960.2:c.3451T>C
  • NM_001353961.2:c.1096T>C
  • NM_006920.6:c.3505T>C
  • NP_001159435.1:p.Cys1180Arg
  • NP_001159436.1:p.Cys1152Arg
  • NP_001189364.1:p.Cys1180Arg
  • NP_001340877.1:p.Cys1180Arg
  • NP_001340878.1:p.Cys1169Arg
  • NP_001340879.1:p.Cys1169Arg
  • NP_001340880.1:p.Cys1169Arg
  • NP_001340881.1:p.Cys1169Arg
  • NP_001340883.1:p.Cys1168Arg
  • NP_001340884.1:p.Cys1168Arg
  • NP_001340886.1:p.Cys1152Arg
  • NP_001340887.1:p.Cys1152Arg
  • NP_001340889.1:p.Cys1151Arg
  • NP_001340890.1:p.Cys366Arg
  • NP_008851.3:p.Cys1169Arg
  • LRG_8:g.63021T>C
  • NC_000002.11:g.166872129A>G
  • NM_001165963.1:c.3538T>C
  • NR_110598.1:n.182A>G
  • NR_148667.2:n.3891T>C
Protein change:
C1151R
Links:
dbSNP: rs1574069096
NCBI 1000 Genomes Browser:
rs1574069096
Molecular consequence:
  • NM_001165963.4:c.3538T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.3454T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.3538T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.3538T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.3505T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.3505T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.3505T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.3505T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.3502T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.3502T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.3454T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.3454T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.3451T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353961.2:c.1096T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.3505T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_110598.1:n.182A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148667.2:n.3891T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002064460Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Nov 21, 2018) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV002064460.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

DNA sequence analysis of the SCN1A gene demonstrated a sequence change, c.3538T>C, in exon 17 that results in an amino acid change, p.Cys1180Arg. The p.Cys1180Arg change affects a highly conserved amino acid residue located in a domain of the SCN1A protein that is known to be functional. The p.Cys1180Arg substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL, CADD). This sequence change is the likely cause of this phenotype, however functional studies have not been performed to prove this conclusively.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 24, 2023