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:

Allele description

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

SCN2A:sodium voltage-gated channel alpha subunit 2 [Gene - OMIM - HGNC]
Variant type:
Cytogenetic location:
Genomic location:
Preferred name:
NM_021007.2(SCN2A):c.3391delA (p.Ser1131Alafs)
  • 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]


MedGen: CN221809

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000572697GeneDxcriteria provided, single submitter
(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


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.

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

Last Updated: Jun 5, 2017