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NM_001365536.1(SCN9A):c.4143A>G (p.Arg1381=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Feb 20, 2020)
Last evaluated:
May 16, 2017
Accession:
VCV000471123.2
Variation ID:
471123
Description:
single nucleotide variant
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NM_001365536.1(SCN9A):c.4143A>G (p.Arg1381=)

Allele ID
449072
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 166228754 (GRCh38) GRCh38 UCSC
2: 167085264 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_369:g.152234A>G
NC_000002.11:g.167085264T>C
NC_000002.12:g.166228754T>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:166228753:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00000
Links
ClinGen: CA59810250
dbSNP: rs200610689
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter May 16, 2017 RCV000540930.1
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001128930.1
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001128932.1
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001128931.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SCN1A-AS1 - - - GRCh38 - 1165
SCN9A - - GRCh38
GRCh37
235 1427

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(May 16, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary sensory and autonomic neuropathy type IIA
Generalized epilepsy with febrile seizures plus, type 7
Allele origin: germline
Invitae
Accession: SCV000649337.1
Submitted: (Oct 05, 2017)
Evidence details
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Primary erythromelalgia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001288426.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Paroxysmal extreme pain disorder
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001288427.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Indifference to pain, congenital, autosomal recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001288428.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)

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 rs200610689...

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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 Oct 08, 2021