NM_001040142.2(SCN2A):c.632G>A (p.Gly211Asp) AND Complex neurodevelopmental disorder

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Apr 25, 2016
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV001265408.2

Allele description [Variation Report for NM_001040142.2(SCN2A):c.632G>A (p.Gly211Asp)]

NM_001040142.2(SCN2A):c.632G>A (p.Gly211Asp)

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.632G>A (p.Gly211Asp)

HGVS:

NC_000002.12:g.165309378G>A
NG_008143.1:g.74977G>A
NM_001040142.2:c.632G>AMANE SELECT
NM_001040143.2:c.697+122G>A
NM_001371246.1:c.697+122G>A
NM_001371247.1:c.632G>A
NM_021007.3:c.632G>A
NP_001035232.1:p.Gly211Asp
NP_001358176.1:p.Gly211Asp
NP_066287.2:p.Gly211Asp
NC_000002.11:g.166165888G>A
NM_021007.2:c.632G>A

Protein change:

G211D

Links:

dbSNP: rs1697311700

NCBI 1000 Genomes Browser:

rs1697311700

Molecular consequence:

NM_001040143.2:c.697+122G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001371246.1:c.697+122G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001040142.2:c.632G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001371247.1:c.632G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_021007.3:c.632G>A - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

Mild hyperpolarizing shift of voltage dependence of fast inactivation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0067]
Moderate hyperpolarizing shift of voltage dependence of activation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0030]
Normal fast inactivation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0047]
Normal peak current [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0096]
Normal persistent current [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0044]
Normal ramp current [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0131]
Normal rate of recovery from fast inactivation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0054]
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]
Slowing of recovery from slow inactivation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0109]

Condition(s)

Name:: Complex neurodevelopmental disorder
Identifiers:: MONDO: MONDO:0100038; MedGen: C5568766

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001443534	GenomeConnect - Simons Searchlight	no assertion criteria provided	Likely pathogenic (Apr 25, 2016)	de novo	provider interpretation
SCV004232400	Channelopathy-Associated Epilepsy Research Center	no classification provided	not provided	not applicable	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001443534

GenomeConnect - Simons Searchlight

no assertion criteria provided

Likely pathogenic
(Apr 25, 2016)

de novo

provider interpretation

SCV004232400

Channelopathy-Associated Epilepsy Research Center

no classification provided

not provided

not applicable

literature only

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	not applicable	not applicable	not provided	not provided	not provided	not provided	not provided	literature only
not provided	de novo	yes	not provided	not provided	not provided	not provided	not provided	provider interpretation

Citations

PubMed

Epilepsy-associated SCN2A (NaV1.2) variants exhibit diverse and complex functional properties.

Thompson CH, Potet F, Abramova TV, DeKeyser JM, Ghabra NF, Vanoye CG, Millichap JJ, George AL.

J Gen Physiol. 2023 Oct 2;155(10). doi:pii: e202313375. 10.1085/jgp.202313375. Epub 2023 Aug 14.

PubMed [citation]

PMID:: 37578743
PMCID:: PMC10424433

Details of each submission

From GenomeConnect - Simons Searchlight, SCV001443534.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	provider interpretation	not provided

Description

Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2016-04-25 and interpreted as Likely Pathogenic. Variant was initially reported on 2015-03-27 by GTR ID of laboratory name 26957. The reporting laboratory might also submit to ClinVar.

#	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		not provided	not provided	not provided	not provided

From Channelopathy-Associated Epilepsy Research Center, SCV004232400.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine