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NM_001040142.2(SCN2A):c.4303C>T (p.Arg1435Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Nov 19, 2021)
Last evaluated:
Oct 23, 2020
Accession:
VCV000419721.6
Variation ID:
419721
Description:
single nucleotide variant
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NM_001040142.2(SCN2A):c.4303C>T (p.Arg1435Ter)

Allele ID
405354
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 165377645 (GRCh38) GRCh38 UCSC
2: 166234155 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.166234155C>T
NC_000002.12:g.165377645C>T
NG_008143.1:g.143244C>T
... more HGVS
Protein change
R1435*
Other names
-
Canonical SPDI
NC_000002.12:165377644:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA16617269
dbSNP: rs796053138
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 criteria provided, multiple submitters, no conflicts Oct 23, 2020 RCV000485232.3
Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Jan 1, 2018 RCV000585884.2
Pathogenic 1 criteria provided, single submitter Nov 8, 2018 RCV000640630.2
Likely pathogenic 1 criteria provided, single submitter Apr 20, 2020 RCV001257715.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SCN2A Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1416 1474

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jan 01, 2018)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy 11
Allele origin: unknown
NeuroMeGen,Hospital Clinico Santiago de Compostela
Accession: SCV000693773.1
Submitted: (Mar 07, 2018)
Evidence details
Likely pathogenic
(Sep 13, 2017)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy 11
Allele origin: de novo
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
Study: Clinvar_gadteam_Clinical_exome_analysis_3
Accession: SCV000803822.1
Submitted: (Feb 06, 2018)
Evidence details
Pathogenic
(Sep 01, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000567713.4
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The R1435X nonsense variant in the SCN2A gene has not been reported previously as a pathogenic variant nor as a benign polymorphism, to our knowledge. … (more)
Pathogenic
(Nov 08, 2018)
criteria provided, single submitter
Method: clinical testing
Benign familial neonatal-infantile seizures
Early infantile epileptic encephalopathy 11
Allele origin: germline
Invitae
Accession: SCV000762224.2
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change creates a premature translational stop signal (p.Arg1435*) in the SCN2A gene. It is expected to result in an absent or disrupted protein … (more)
Likely pathogenic
(Apr 20, 2020)
criteria provided, single submitter
Method: clinical testing
Intellectual disability
(Autosomal dominant inheritance)
Allele origin: de novo
Diagnostic Laboratory, Strasbourg University Hospital
Accession: SCV001434526.1
Submitted: (May 30, 2020)
Evidence details
Pathogenic
(Oct 23, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
(Unknown mechanism)
Allele origin: germline
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001448115.1
Submitted: (Oct 23, 2020)
Evidence details
Pathogenic
(Oct 04, 2021)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
PerkinElmer Genomics
Accession: SCV002020013.1
Submitted: (Nov 19, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Genetic and phenotypic heterogeneity suggest therapeutic implications in SCN2A-related disorders. Wolff M Brain : a journal of neurology 2017 PMID: 28379373
Improving diagnosis and broadening the phenotypes in early-onset seizure and severe developmental delay disorders through gene panel analysis. Trump N Journal of medical genetics 2016 PMID: 26993267

Text-mined citations for rs796053138...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 28, 2021