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NM_003978.5(PSTPIP1):c.37T>G (p.Cys13Gly)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 24, 2020
Accession:
VCV000242299.3
Variation ID:
242299
Description:
single nucleotide variant
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NM_003978.5(PSTPIP1):c.37T>G (p.Cys13Gly)

Allele ID
243845
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q24.3
Genomic location
15: 77018148 (GRCh38) GRCh38 UCSC
15: 77310489 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.77018148T>G
NC_000015.9:g.77310489T>G
NM_003978.5:c.37T>G MANE Select NP_003969.2:p.Cys13Gly missense
... more HGVS
Protein change
C13G, C4G, C78G
Other names
-
Canonical SPDI
NC_000015.10:77018147:T:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00016
Exome Aggregation Consortium (ExAC) 0.00015
The Genome Aggregation Database (gnomAD), exomes 0.00015
Trans-Omics for Precision Medicine (TOPMed) 0.00006
The Genome Aggregation Database (gnomAD) 0.00029
Links
ClinGen: CA7675687
dbSNP: rs376128040
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Mar 4, 2014 RCV000231124.1
Benign 1 criteria provided, single submitter Sep 24, 2020 RCV001514746.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PSTPIP1 - - GRCh38
GRCh37
348 368

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Mar 04, 2014)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000291948.6
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The C13G variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. The C13G variant … (more)
Benign
(Sep 24, 2020)
criteria provided, single submitter
Method: clinical testing
Pyogenic arthritis-pyoderma gangrenosum-acne syndrome
Allele origin: germline
Invitae
Accession: SCV001722665.1
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 rs376128040...

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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 Jun 14, 2021