Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_001365536.1(SCN9A):c.3343A>G (p.Ser1115Gly)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 2, 2020
Accession:
VCV000331972.6
Variation ID:
331972
Description:
single nucleotide variant
Help

NM_001365536.1(SCN9A):c.3343A>G (p.Ser1115Gly)

Allele ID
285359
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 166272407 (GRCh38) GRCh38 UCSC
2: 167128917 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_369:g.108581A>G
LRG_369t1:c.3310A>G LRG_369p1:p.Ser1104Gly
NC_000002.11:g.167128917T>C
... more HGVS
Protein change
S1104G, S1115G
Other names
-
Canonical SPDI
NC_000002.12:166272406:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00014
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00042
The Genome Aggregation Database (gnomAD) 0.00048
The Genome Aggregation Database (gnomAD) 0.00025
The Genome Aggregation Database (gnomAD), exomes 0.00036
Exome Aggregation Consortium (ExAC) 0.00110
Links
ClinGen: CA1944092
dbSNP: rs201984007
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000293562.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000329282.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000335564.2
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000388955.2
Likely benign 1 criteria provided, single submitter Dec 2, 2020 RCV000647806.4
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SCN1A-AS1 - - - GRCh38 - 1176
SCN9A - - GRCh38
GRCh37
236 1439

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Small Fiber Neuropathy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000418489.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Primary erythromelalgia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000418493.3
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)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Indifference to pain, congenital, autosomal recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000418491.3
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
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Paroxysmal extreme pain disorder
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000418487.3
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)
Likely benign
(Dec 02, 2020)
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: SCV000769609.4
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

Help
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

Help
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 rs201984007...

Help
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