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NM_001165963.4(SCN1A):c.835C>T (p.Gln279Ter) AND Severe myoclonic epilepsy in infancy

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 1, 2022
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:
RCV002283766.1

Allele description [Variation Report for NM_001165963.4(SCN1A):c.835C>T (p.Gln279Ter)]

NM_001165963.4(SCN1A):c.835C>T (p.Gln279Ter)

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.835C>T (p.Gln279Ter)
HGVS:
  • NC_000002.12:g.166051848G>A
  • NG_011906.1:g.26792C>T
  • NM_001165963.4:c.835C>TMANE SELECT
  • NM_001165964.3:c.835C>T
  • NM_001202435.3:c.835C>T
  • NM_001353948.2:c.835C>T
  • NM_001353949.2:c.835C>T
  • NM_001353950.2:c.835C>T
  • NM_001353951.2:c.835C>T
  • NM_001353952.2:c.835C>T
  • NM_001353954.2:c.835C>T
  • NM_001353955.2:c.835C>T
  • NM_001353957.2:c.835C>T
  • NM_001353958.2:c.835C>T
  • NM_001353960.2:c.835C>T
  • NM_001353961.2:c.-1591C>T
  • NM_006920.6:c.835C>T
  • NP_001159435.1:p.Gln279Ter
  • NP_001159436.1:p.Gln279Ter
  • NP_001189364.1:p.Gln279Ter
  • NP_001340877.1:p.Gln279Ter
  • NP_001340878.1:p.Gln279Ter
  • NP_001340879.1:p.Gln279Ter
  • NP_001340880.1:p.Gln279Ter
  • NP_001340881.1:p.Gln279Ter
  • NP_001340883.1:p.Gln279Ter
  • NP_001340884.1:p.Gln279Ter
  • NP_001340886.1:p.Gln279Ter
  • NP_001340887.1:p.Gln279Ter
  • NP_001340889.1:p.Gln279Ter
  • NP_008851.3:p.Gln279Ter
  • NP_008851.3:p.Gln279Ter
  • LRG_8t1:c.835C>T
  • LRG_8:g.26792C>T
  • LRG_8p1:p.Gln279Ter
  • NC_000002.11:g.166908358G>A
  • NM_006920.4:c.835C>T
  • NR_148667.2:n.1221C>T
Protein change:
Q279*
Molecular consequence:
  • NM_001353961.2:c.-1591C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NR_148667.2:n.1221C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001165963.4:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001165964.3:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001202435.3:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353948.2:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353949.2:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353950.2:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353951.2:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353952.2:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353954.2:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353955.2:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353957.2:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353958.2:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353960.2:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_006920.6:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0025728323billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Sep 1, 2022) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing

Citations

PubMed

Genotype-phenotype associations in SCN1A-related epilepsies.

Zuberi SM, Brunklaus A, Birch R, Reavey E, Duncan J, Forbes GH.

Neurology. 2011 Feb 15;76(7):594-600. doi: 10.1212/WNL.0b013e31820c309b. Epub 2011 Jan 19.

PubMed [citation]
PMID:
21248271

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 3billion, SCV002572832.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)

Description

The variant is not observed in the gnomAD v2.1.1 dataset. Stop-gained (nonsense) is predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported to be associated with SCN1A -related disorder (PMID: 21248271). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Aug 5, 2023