NM_001165963.4(SCN1A):c.5911G>C (p.Glu1971Gln) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 20, 2017
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:: RCV000523148.1

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5911G>C (p.Glu1971Gln)]

NM_001165963.4(SCN1A):c.5911G>C (p.Glu1971Gln)

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.5911G>C (p.Glu1971Gln)

HGVS:

NC_000002.12:g.165991364C>G
NG_011906.1:g.87276G>C
NM_001165963.4:c.5911G>CMANE SELECT
NM_001165964.3:c.5827G>C
NM_001202435.3:c.5911G>C
NM_001353948.2:c.5911G>C
NM_001353949.2:c.5878G>C
NM_001353950.2:c.5878G>C
NM_001353951.2:c.5878G>C
NM_001353952.2:c.5878G>C
NM_001353954.2:c.5875G>C
NM_001353955.2:c.5875G>C
NM_001353957.2:c.5827G>C
NM_001353958.2:c.5827G>C
NM_001353960.2:c.5824G>C
NM_001353961.2:c.3469G>C
NM_006920.6:c.5878G>C
NP_001159435.1:p.Glu1971Gln
NP_001159436.1:p.Glu1943Gln
NP_001189364.1:p.Glu1971Gln
NP_001340877.1:p.Glu1971Gln
NP_001340878.1:p.Glu1960Gln
NP_001340879.1:p.Glu1960Gln
NP_001340880.1:p.Glu1960Gln
NP_001340881.1:p.Glu1960Gln
NP_001340883.1:p.Glu1959Gln
NP_001340884.1:p.Glu1959Gln
NP_001340886.1:p.Glu1943Gln
NP_001340887.1:p.Glu1943Gln
NP_001340889.1:p.Glu1942Gln
NP_001340890.1:p.Glu1157Gln
NP_008851.3:p.Glu1960Gln
LRG_8:g.87276G>C
NC_000002.11:g.166847874C>G
NM_001165963.1:c.5911G>C
NR_148667.2:n.6328G>C

Protein change:

E1157Q

Links:

dbSNP: rs1553519738

NCBI 1000 Genomes Browser:

rs1553519738

Molecular consequence:

NM_001165963.4:c.5911G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.5827G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.5911G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.5911G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.5878G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.5878G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.5878G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.5878G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.5875G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.5875G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.5827G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.5827G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.5824G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353961.2:c.3469G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.5878G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.6328G>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
SCV000619198	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Jul 20, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000619198

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Jul 20, 2017)

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, SCV000619198.2

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

Description

A variant of uncertain significance has been identified in the SCN1A gene. The E1971Q variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The E1971Q variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The E1971Q variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. However, this substitution is predicted to be within the C-terminal cytoplasmic domain, where amino acids with similar properties to Glutamic acid are tolerated across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

#	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: Apr 23, 2022

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