NM_001040142.2(SCN2A):c.4025T>C (p.Leu1342Pro) AND Developmental and epileptic encephalopathy, 11

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 21, 2019
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:: RCV001252986.1

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]

Functional consequence:

Effect on use dependence [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0132]
Normal peak current [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0096]
Normal slope of activation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0036]
Normal slope of fast inactivation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0074]
Overall mixed or unclear functional effect not able to be clearly categorized as Gain- or Loss-of-Function [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0145]
Severe hyperpolarizing shift of voltage dependence of activation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0031]
Severe hyperpolarizing shift of voltage dependence of fast inactivation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0069]
Slowing of recovery from fast inactivation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0055]

Observations:

Condition(s)

Name:: Developmental and epileptic encephalopathy, 11 (DEE11)
Synonyms:: Early infantile epileptic encephalopathy 11
Identifiers:: MONDO: MONDO:0013388; MedGen: C3150987; Orphanet: 1934; OMIM: 613721

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001428474	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 21, 2019)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001428474

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 21, 2019)

de novo

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Institute of Human Genetics, University of Leipzig Medical Center, SCV001428474.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

Description

This variant was identified as de novo (maternity and paternity confirmed).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Mar 16, 2025

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