NM_001165963.4(SCN1A):c.5591G>C (p.Cys1864Ser) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 22, 2020
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:: RCV002344824.2

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5591G>C (p.Cys1864Ser)]

NM_001165963.4(SCN1A):c.5591G>C (p.Cys1864Ser)

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.5591G>C (p.Cys1864Ser)

HGVS:

NC_000002.12:g.165991684C>G
NG_011906.1:g.86956G>C
NM_001165963.4:c.5591G>CMANE SELECT
NM_001165964.3:c.5507G>C
NM_001202435.3:c.5591G>C
NM_001353948.2:c.5591G>C
NM_001353949.2:c.5558G>C
NM_001353950.2:c.5558G>C
NM_001353951.2:c.5558G>C
NM_001353952.2:c.5558G>C
NM_001353954.2:c.5555G>C
NM_001353955.2:c.5555G>C
NM_001353957.2:c.5507G>C
NM_001353958.2:c.5507G>C
NM_001353960.2:c.5504G>C
NM_001353961.2:c.3149G>C
NM_006920.6:c.5558G>C
NP_001159435.1:p.Cys1864Ser
NP_001159436.1:p.Cys1836Ser
NP_001189364.1:p.Cys1864Ser
NP_001340877.1:p.Cys1864Ser
NP_001340878.1:p.Cys1853Ser
NP_001340879.1:p.Cys1853Ser
NP_001340880.1:p.Cys1853Ser
NP_001340881.1:p.Cys1853Ser
NP_001340883.1:p.Cys1852Ser
NP_001340884.1:p.Cys1852Ser
NP_001340886.1:p.Cys1836Ser
NP_001340887.1:p.Cys1836Ser
NP_001340889.1:p.Cys1835Ser
NP_001340890.1:p.Cys1050Ser
NP_008851.3:p.Cys1853Ser
NP_008851.3:p.Cys1853Ser
LRG_8t1:c.5558G>C
LRG_8:g.86956G>C
LRG_8p1:p.Cys1853Ser
NC_000002.11:g.166848194C>G
NM_001165963.1:c.5591G>C
NM_006920.4:c.5558G>C
NR_148667.2:n.6008G>C

Protein change:

C1050S

Molecular consequence:

NM_001165963.4:c.5591G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.5507G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.5591G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.5591G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.5558G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.5558G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.5558G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.5558G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.5555G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.5555G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.5507G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.5507G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.5504G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353961.2:c.3149G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.5558G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.6008G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002649151	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jun 22, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002649151

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jun 22, 2020)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV002649151.2

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

Description

The p.C1864S variant (also known as c.5591G>C), located in coding exon 26 of the SCN1A gene, results from a G to C substitution at nucleotide position 5591. The cysteine at codon 1864 is replaced by serine, an amino acid with dissimilar properties. This variant has been determined to be the result of a de novo mutation or germline mosaicism in one individual with intractable focal epilepsy (Ambry internal data). 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.

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

Last Updated: May 1, 2024

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