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NM_001040142.2(SCN2A):c.5645G>A (p.Arg1882Gln) AND Complex neurodevelopmental disorder

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Apr 6, 2018
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:
RCV001265414.3

Allele description [Variation Report for NM_001040142.2(SCN2A):c.5645G>A (p.Arg1882Gln)]

NM_001040142.2(SCN2A):c.5645G>A (p.Arg1882Gln)

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.5645G>A (p.Arg1882Gln)
Other names:
p.R1882Q:CGA>CAA
HGVS:
  • NC_000002.12:g.165389451G>A
  • NG_008143.1:g.155050G>A
  • NM_001040142.2:c.5645G>AMANE SELECT
  • NM_001040143.2:c.5645G>A
  • NM_001371246.1:c.5645G>A
  • NM_001371247.1:c.5645G>A
  • NM_021007.3:c.5645G>A
  • NP_001035232.1:p.Arg1882Gln
  • NP_001035233.1:p.Arg1882Gln
  • NP_001358175.1:p.Arg1882Gln
  • NP_001358176.1:p.Arg1882Gln
  • NP_066287.2:p.Arg1882Gln
  • NP_066287.2:p.Arg1882Gln
  • NC_000002.11:g.166245961G>A
  • NM_001040142.1:c.5645G>A
  • NM_001040142.2:c.5645G>A
  • NM_021007.2:c.5645G>A
Protein change:
R1882Q; ARG1882GLN
Links:
OMIM: 182390.0020; dbSNP: rs794727444
NCBI 1000 Genomes Browser:
rs794727444
Molecular consequence:
  • NM_001040142.2:c.5645G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001040143.2:c.5645G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371246.1:c.5645G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371247.1:c.5645G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021007.3:c.5645G>A - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
  • Increase in persistent current [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0040]
  • Increase in resurgent current [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0099]
  • Moderate depolarizing shift of voltage dependence of fast inactivation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0063]
  • Normal peak current [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0096]
  • Normal voltage dependence of activation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0032]
  • Slowing of fast inactivation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0048]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001443540GenomeConnect - Simons Searchlight
no assertion criteria provided
Pathogenic
(Apr 6, 2018) 		unknownprovider interpretation

SCV002605499Channelopathy-Associated Epilepsy Research Center
no classification provided
not providednot applicableliterature only

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes2not providednot provided2not providedprovider interpretation
not providednot applicablenot applicablenot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Resurgent and Gating Pore Currents Induced by De Novo SCN2A Epilepsy Mutations.

Mason ER, Wu F, Patel RR, Xiao Y, Cannon SC, Cummins TR.

eNeuro. 2019 Oct 16;6(5). doi:pii: ENEURO.0141-19.2019. 10.1523/ENEURO.0141-19.2019. Print 2019 Sep/Oct.

PubMed [citation]
PMID:
31558572
PMCID:
PMC6795554

Details of each submission

From GenomeConnect - Simons Searchlight, SCV001443540.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedprovider interpretationnot provided
2not provided1not providednot providedprovider interpretationnot provided

Description

Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2018-04-06 and interpreted as Pathogenic. The reporting laboratory might also submit to ClinVar. This variant was identified in multiple probands enrolled in Simons Searchlight.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyes1not providednot provided1not providednot providednot provided
2unknownyes1not providednot provided1not providednot providednot provided

From Channelopathy-Associated Epilepsy Research Center, SCV002605499.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not applicablenot applicablenot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 15, 2024