NM_001040142.2(SCN2A):c.2942dup (p.Leu981fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 29, 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:
RCV000520679.1

Allele description [Variation Report for NM_001040142.2(SCN2A):c.2942dup (p.Leu981fs)]

NM_001040142.2(SCN2A):c.2942dup (p.Leu981fs)

Gene:
SCN2A:sodium voltage-gated channel alpha subunit 2 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001040142.2(SCN2A):c.2942dup (p.Leu981fs)
HGVS:
  • NC_000002.12:g.165354214dup
  • NG_008143.1:g.119813dup
  • NM_001040142.2:c.2942dupMANE SELECT
  • NM_001040143.2:c.2942dup
  • NM_001371246.1:c.2942dup
  • NM_001371247.1:c.2942dup
  • NM_021007.3:c.2942dup
  • NP_001035232.1:p.Leu981fs
  • NP_001035233.1:p.Leu981fs
  • NP_001358175.1:p.Leu981fs
  • NP_001358176.1:p.Leu981fs
  • NP_066287.2:p.Leu981fs
  • NC_000002.11:g.166210724dup
  • NM_021007.2:c.2942dupT
Protein change:
L981fs
Links:
dbSNP: rs1553583550
NCBI 1000 Genomes Browser:
rs1553583550
Molecular consequence:
  • NM_001040142.2:c.2942dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001040143.2:c.2942dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001371246.1:c.2942dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001371247.1:c.2942dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_021007.3:c.2942dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000618664GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Jun 29, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000618664.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.2942dupT variant in the SCN2A gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.2942dupT variant causes a frameshift starting with codon Leucine 981, changes this amino acid to a Phenylalanine residue, and creates a premature Stop codon at position 9 of the new reading frame, denoted p.Leu981PhefsX9. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.2942dupT variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.2942dupT as a pathogenic variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 17, 2022