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NM_001165963.4(SCN1A):c.638C>T (p.Ser213Leu) AND Inborn genetic diseases

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 12, 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:
RCV002363173.2

Allele description [Variation Report for NM_001165963.4(SCN1A):c.638C>T (p.Ser213Leu)]

NM_001165963.4(SCN1A):c.638C>T (p.Ser213Leu)

Gene:
SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001165963.4(SCN1A):c.638C>T (p.Ser213Leu)
HGVS:
  • NC_000002.12:g.166052908G>A
  • NG_011906.1:g.25732C>T
  • NM_001165963.4:c.638C>TMANE SELECT
  • NM_001165964.3:c.638C>T
  • NM_001202435.3:c.638C>T
  • NM_001353948.2:c.638C>T
  • NM_001353949.2:c.638C>T
  • NM_001353950.2:c.638C>T
  • NM_001353951.2:c.638C>T
  • NM_001353952.2:c.638C>T
  • NM_001353954.2:c.638C>T
  • NM_001353955.2:c.638C>T
  • NM_001353957.2:c.638C>T
  • NM_001353958.2:c.638C>T
  • NM_001353960.2:c.638C>T
  • NM_001353961.2:c.-1788C>T
  • NM_006920.6:c.638C>T
  • NP_001159435.1:p.Ser213Leu
  • NP_001159436.1:p.Ser213Leu
  • NP_001189364.1:p.Ser213Leu
  • NP_001340877.1:p.Ser213Leu
  • NP_001340878.1:p.Ser213Leu
  • NP_001340879.1:p.Ser213Leu
  • NP_001340880.1:p.Ser213Leu
  • NP_001340881.1:p.Ser213Leu
  • NP_001340883.1:p.Ser213Leu
  • NP_001340884.1:p.Ser213Leu
  • NP_001340886.1:p.Ser213Leu
  • NP_001340887.1:p.Ser213Leu
  • NP_001340889.1:p.Ser213Leu
  • NP_008851.3:p.Ser213Leu
  • LRG_8:g.25732C>T
  • NC_000002.11:g.166909418G>A
  • NM_001165963.1:c.638C>T
  • NR_148667.2:n.1024C>T
Protein change:
S213L
Links:
dbSNP: rs754661378
NCBI 1000 Genomes Browser:
rs754661378
Molecular consequence:
  • NM_001353961.2:c.-1788C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001165963.4:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.638C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.1024C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002657915Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Oct 12, 2018) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV002657915.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The p.S213L variant (also known as c.638C>T), located in coding exon 5 of the SCN1A gene, results from a C to T substitution at nucleotide position 638. The serine at codon 213 is replaced by leucine, an amino acid with dissimilar properties. A different alteration located at the same position, p.S213W, was detected in an individual with febrile and afebrile seizures and developmental delay (Butler KM et al. Pediatr. Neurol., 2017 Dec;77:61-66). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

Last Updated: May 1, 2024