NM_001165963.4(SCN1A):c.5146T>C (p.Cys1716Arg) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 4, 2014
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:: RCV000188987.2

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5146T>C (p.Cys1716Arg)]

NM_001165963.4(SCN1A):c.5146T>C (p.Cys1716Arg)

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.5146T>C (p.Cys1716Arg)

Other names:

p.C1716R:TGC>CGC

HGVS:

NC_000002.12:g.165992129A>G
NG_011906.1:g.86511T>C
NM_001165963.4:c.5146T>CMANE SELECT
NM_001165964.3:c.5062T>C
NM_001202435.3:c.5146T>C
NM_001353948.2:c.5146T>C
NM_001353949.2:c.5113T>C
NM_001353950.2:c.5113T>C
NM_001353951.2:c.5113T>C
NM_001353952.2:c.5113T>C
NM_001353954.2:c.5110T>C
NM_001353955.2:c.5110T>C
NM_001353957.2:c.5062T>C
NM_001353958.2:c.5062T>C
NM_001353960.2:c.5059T>C
NM_001353961.2:c.2704T>C
NM_006920.6:c.5113T>C
NP_001159435.1:p.Cys1716Arg
NP_001159436.1:p.Cys1688Arg
NP_001189364.1:p.Cys1716Arg
NP_001340877.1:p.Cys1716Arg
NP_001340878.1:p.Cys1705Arg
NP_001340879.1:p.Cys1705Arg
NP_001340880.1:p.Cys1705Arg
NP_001340881.1:p.Cys1705Arg
NP_001340883.1:p.Cys1704Arg
NP_001340884.1:p.Cys1704Arg
NP_001340886.1:p.Cys1688Arg
NP_001340887.1:p.Cys1688Arg
NP_001340889.1:p.Cys1687Arg
NP_001340890.1:p.Cys902Arg
NP_008851.3:p.Cys1705Arg
LRG_8t1:c.5113T>C
LRG_8:g.86511T>C
NC_000002.11:g.166848639A>G
NM_001165963.1:c.5146T>C
NM_006920.4:c.5113T>C
NR_148667.2:n.5563T>C

Protein change:

C1687R

Links:

UniProtKB/Swiss-Prot: VAR_064327; dbSNP: rs121917926

NCBI 1000 Genomes Browser:

rs121917926

Molecular consequence:

NM_001165963.4:c.5146T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.5062T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.5146T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.5146T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.5113T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.5113T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.5113T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.5113T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.5110T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.5110T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.5062T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.5062T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.5059T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353961.2:c.2704T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.5113T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.5563T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000242618	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Aug 4, 2014)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000242618

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Aug 4, 2014)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000242618.11

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

p.Cys1716Arg (TGC>CGC): c.5146 T>C in exon 26 of the SCN1A gene (NM_001165963.1) The C1716R missense mutation in the SCN1A gene has been reported as a de novo mutation in a patient with severe myoclonic epilepsy of infancy boarderline (SMEB) (Marini et al., 2007). This substitution occurs at a conserved position in the extracellular loop between the S5 and S6 transmembrane segments of the 4th homologous domain. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Therefore, based on the currently available information, C17176R is considered a disease-causing mutation. The variant is found in EPILEPSY panel(s).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Aug 5, 2023

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