NM_001040142.2(SCN2A):c.2995G>A (p.Glu999Lys) AND Developmental and epileptic encephalopathy, 11

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Feb 6, 2020
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000496128.3

Allele description [Variation Report for NM_001040142.2(SCN2A):c.2995G>A (p.Glu999Lys)]

NM_001040142.2(SCN2A):c.2995G>A (p.Glu999Lys)

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.2995G>A (p.Glu999Lys)

Other names:

p.E999K:GAA>AAA

HGVS:

NC_000002.12:g.165354267G>A
NG_008143.1:g.119866G>A
NM_001040142.2:c.2995G>AMANE SELECT
NM_001040143.2:c.2995G>A
NM_001371246.1:c.2995G>A
NM_001371247.1:c.2995G>A
NM_021007.3:c.2995G>A
NP_001035232.1:p.Glu999Lys
NP_001035233.1:p.Glu999Lys
NP_001358175.1:p.Glu999Lys
NP_001358176.1:p.Glu999Lys
NP_066287.2:p.Glu999Lys
NP_066287.2:p.Glu999Lys
NC_000002.11:g.166210777G>A
NM_001040142.1:c.2995G>A
NM_021007.2:c.2995G>A
Q99250:p.Glu999Lys

Protein change:

E999K

Links:

UniProtKB: Q99250#VAR_070003; dbSNP: rs796053126

Molecular consequence:

NM_001040142.2:c.2995G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001040143.2:c.2995G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001371246.1:c.2995G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001371247.1:c.2995G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_021007.3:c.2995G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000586737	NeuroMeGen, Hospital Clinico Santiago de Compostela	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23935176, 25741868
SCV001520569	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 6, 2020)	unknown	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

SCV000586737

NeuroMeGen, Hospital Clinico Santiago de Compostela

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001520569

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 6, 2020)

unknown

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	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical spectrum of SCN2A mutations expanding to Ohtahara syndrome.

Nakamura K, Kato M, Osaka H, Yamashita S, Nakagawa E, Haginoya K, Tohyama J, Okuda M, Wada T, Shimakawa S, Imai K, Takeshita S, Ishiwata H, Lev D, Lerman-Sagie T, Cervantes-Barragán DE, Villarroel CE, Ohfu M, Writzl K, Gnidovec Strazisar B, Hirabayashi S, Chitayat D, et al.

Neurology. 2013 Sep 10;81(11):992-8. doi: 10.1212/WNL.0b013e3182a43e57. Epub 2013 Aug 9.

PubMed [citation]

PMID:: 23935176

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 NeuroMeGen, Hospital Clinico Santiago de Compostela, SCV000586737.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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

From Baylor Genetics, SCV001520569.1

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

Description

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

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

Last Updated: Feb 23, 2026

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