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NM_001040142.2(SCN2A):c.1269G>A (p.Val423=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(5);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000130211.9
Variation ID:
130211
Description:
single nucleotide variant
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NM_001040142.2(SCN2A):c.1269G>A (p.Val423=)

Allele ID
135658
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 165313994 (GRCh38) GRCh38 UCSC
2: 166170504 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.166170504G>A
NC_000002.12:g.165313994G>A
NG_008143.1:g.79593G>A
... more HGVS
Protein change
-
Other names
p.V423V:GTG>GTA
Canonical SPDI
NC_000002.12:165313993:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.01078 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00662
Trans-Omics for Precision Medicine (TOPMed) 0.00699
The Genome Aggregation Database (gnomAD) 0.00599
Trans-Omics for Precision Medicine (TOPMed) 0.00688
1000 Genomes Project 0.01078
The Genome Aggregation Database (gnomAD), exomes 0.00168
Exome Aggregation Consortium (ExAC) 0.00228
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00753
Links
ClinGen: CA289013
dbSNP: rs139815570
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Jun 26, 2020 RCV000212987.2
Uncertain significance 1 criteria provided, single submitter Apr 15, 2013 RCV000118245.7
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000267564.2
Benign 1 criteria provided, single submitter Jun 18, 2016 RCV000716197.1
Benign 1 criteria provided, single submitter Dec 3, 2020 RCV001079874.2
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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
Uncertain significance
(Apr 15, 2013)
criteria provided, single submitter
Method: clinical testing
not provided
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000152612.1
Submitted: (Apr 30, 2014)
Evidence details
Benign
(Jan 15, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000171527.10
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Seizures, benign familial infantile, 3
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000417401.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Jun 18, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000847034.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Benign
(Jun 26, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV001475475.1
Submitted: (Dec 30, 2020)
Evidence details
Benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Seizures, benign familial infantile, 3
Early infantile epileptic encephalopathy 11
Allele origin: germline
Invitae
Accession: SCV000562153.6
Submitted: (Jan 07, 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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs139815570...

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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 27, 2021