NM_021007.2(SCN2A):c.3391delA (p.Ser1131Alafs) AND not provided

Clinical significance:Pathogenic (Last evaluated: Jan 30, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000487276.1

Allele description

NM_021007.2(SCN2A):c.3391delA (p.Ser1131Alafs)

Gene:
SCN2A:sodium voltage-gated channel alpha subunit 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_021007.2(SCN2A):c.3391delA (p.Ser1131Alafs)
HGVS:
  • NC_000002.12:g.165354663delA
  • NG_008143.1:g.120262delA
  • NM_001040142.1:c.3391delA
  • NM_021007.2:c.3391delA
  • NP_001035232.1:p.Ser1131Alafs
  • NP_066287.2:p.Ser1131Alafs
  • NC_000002.11:g.166211173delA
Molecular consequence:
  • NM_001040142.1:c.3391delA - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Identifiers:
MedGen: CN221809

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000572697GeneDxcriteria provided, single submitter
Pathogenic
(Jan 30, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000572697.1

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

Description

The c.3391delA variant in the SCN2A gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.3391delA variant causes a frameshift starting with codon Serine 1131, changes this amino acid to an Alanine residue, and creates a premature Stop codon at position 5 of the new reading frame, denoted p.Ser1131AlafsX5. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.3391delA variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret c.3391delA as a pathogenic variant.

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

Last Updated: Jun 5, 2017