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NM_001040142.2(SCN2A):c.4025T>C (p.Leu1342Pro) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 11, 2012
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:
RCV000189147.1

Allele description [Variation Report for NM_001040142.2(SCN2A):c.4025T>C (p.Leu1342Pro)]

NM_001040142.2(SCN2A):c.4025T>C (p.Leu1342Pro)

Gene:
SCN2A:sodium voltage-gated channel alpha subunit 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001040142.2(SCN2A):c.4025T>C (p.Leu1342Pro)
Other names:
p.L1342P:CTG>CCG
HGVS:
  • NC_000002.12:g.165374737T>C
  • NG_008143.1:g.140336T>C
  • NM_001040142.2:c.4025T>CMANE SELECT
  • NM_001040143.2:c.4025T>C
  • NM_001371246.1:c.4025T>C
  • NM_001371247.1:c.4025T>C
  • NM_021007.3:c.4025T>C
  • NP_001035232.1:p.Leu1342Pro
  • NP_001035233.1:p.Leu1342Pro
  • NP_001358175.1:p.Leu1342Pro
  • NP_001358176.1:p.Leu1342Pro
  • NP_066287.2:p.Leu1342Pro
  • NP_066287.2:p.Leu1342Pro
  • NC_000002.11:g.166231247T>C
  • NM_001040142.1:c.4025T>C
  • NM_021007.2:c.4025T>C
Protein change:
L1342P
Links:
dbSNP: rs796053134
NCBI 1000 Genomes Browser:
rs796053134
Molecular consequence:
  • NM_001040142.2:c.4025T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001040143.2:c.4025T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371246.1:c.4025T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371247.1:c.4025T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021007.3:c.4025T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000242779GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Sep 11, 2012) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000242779.10

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

Description

p.Leu1342Pro (CTG>CCG):c.4025 T>C in exon 22 of the SCN2A gene (NM_021007.2). The Leu1342Pro missense change has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. The NHLBI ESP Exome Variant Project has not identified Leu1342Pro in approximately 6,500 individuals of European or African American ethnicity, indicating that it is not a common benign variant in these populations. Although Leucine and Proline are both uncharged, non-polar amino acids, the gain of a bulky Proline residue could alter the secondary structure of the protein. Leu1342Pro alters a highly conserved position in the S5 segment of the third transmembrane domain, and multiple in silico algorithms predict it is damaging to protein structure/function. Therefore, based on the currently available information, Leu1342Pro is a strong candidate for a disease-causing mutation, although the possibility that it is a benign variant cannot be excluded. The variant is found in INFANT-EPI panel(s).

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

Last Updated: Aug 3, 2025