NM_001165963.4(SCN1A):c.3697G>A (p.Gly1233Ser) AND Severe myoclonic epilepsy in infancy

Germline classification:: Uncertain significance (1 submission)
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:: RCV003340675.2

Allele description [Variation Report for NM_001165963.4(SCN1A):c.3697G>A (p.Gly1233Ser)]

NM_001165963.4(SCN1A):c.3697G>A (p.Gly1233Ser)

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.3697G>A (p.Gly1233Ser)

HGVS:

NC_000002.12:g.166013752C>T
NG_011906.1:g.64888G>A
NM_001165963.4:c.3697G>AMANE SELECT
NM_001165964.3:c.3613G>A
NM_001202435.3:c.3697G>A
NM_001353948.2:c.3697G>A
NM_001353949.2:c.3664G>A
NM_001353950.2:c.3664G>A
NM_001353951.2:c.3664G>A
NM_001353952.2:c.3664G>A
NM_001353954.2:c.3661G>A
NM_001353955.2:c.3661G>A
NM_001353957.2:c.3613G>A
NM_001353958.2:c.3613G>A
NM_001353960.2:c.3610G>A
NM_001353961.2:c.1255G>A
NM_006920.6:c.3664G>A
NP_001159435.1:p.Gly1233Ser
NP_001159436.1:p.Gly1205Ser
NP_001189364.1:p.Gly1233Ser
NP_001340877.1:p.Gly1233Ser
NP_001340878.1:p.Gly1222Ser
NP_001340879.1:p.Gly1222Ser
NP_001340880.1:p.Gly1222Ser
NP_001340881.1:p.Gly1222Ser
NP_001340883.1:p.Gly1221Ser
NP_001340884.1:p.Gly1221Ser
NP_001340886.1:p.Gly1205Ser
NP_001340887.1:p.Gly1205Ser
NP_001340889.1:p.Gly1204Ser
NP_001340890.1:p.Gly419Ser
NP_008851.3:p.Gly1222Ser
NP_008851.3:p.Gly1222Ser
LRG_8t1:c.3664G>A
LRG_8:g.64888G>A
LRG_8p1:p.Gly1222Ser
NC_000002.11:g.166870262C>T
NM_001165963.1:c.3697G>A
NM_006920.4:c.3664G>A
NR_148667.2:n.4050G>A

Protein change:

G1204S

Molecular consequence:

NM_001165963.4:c.3697G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.3613G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.3697G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.3697G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.3664G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.3664G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.3664G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.3664G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.3661G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.3661G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.3613G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.3613G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.3610G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353961.2:c.1255G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.3664G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.4050G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Severe myoclonic epilepsy in infancy (DRVT)
Synonyms:: Epilepsy, Myoclonic, Infantile, Severe; Dravet syndrome; Epileptic encephalopathy, early infantile, 6 (Dravet syndrome); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0100135; MedGen: C0751122; Orphanet: 33069; OMIM: 607208

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004047943	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004047943

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

germline

clinical testing

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

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

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 Neuberg Centre For Genomic Medicine, NCGM, SCV004047943.1

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

Description

The missense variant c.3697G>A (p.Gly1233Ser) in SCN1A gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Gly1233Ser variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. The amino acid Gly at position 1233 is changed to a Ser changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Gly1233Ser in SCN1A is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance (VUS).

#	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 6, 2024

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