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NM_003978.5(PSTPIP1):c.908C>T (p.Pro303Leu)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 26, 2020
Accession:
VCV000138828.6
Variation ID:
138828
Description:
single nucleotide variant
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NM_003978.5(PSTPIP1):c.908C>T (p.Pro303Leu)

Allele ID
142531
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q24.3
Genomic location
15: 77032931 (GRCh38) GRCh38 UCSC
15: 77325272 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.77032931C>T
NC_000015.9:g.77325272C>T
NM_003978.5:c.908C>T MANE Select NP_003969.2:p.Pro303Leu missense
... more HGVS
Protein change
P303L, P294L, P368L
Other names
p.P303L:CCG>CTG
Canonical SPDI
NC_000015.10:77032930:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00200 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00333
The Genome Aggregation Database (gnomAD) 0.00271
The Genome Aggregation Database (gnomAD), exomes 0.00067
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00353
1000 Genomes Project 0.00200
Exome Aggregation Consortium (ExAC) 0.00120
Links
ClinGen: CA292944
dbSNP: rs189773500
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Nov 26, 2020 RCV000273267.6
Benign 1 criteria provided, single submitter Dec 28, 2012 RCV000127638.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
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
Benign
(Dec 28, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000171217.10
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
(Nov 26, 2020)
criteria provided, single submitter
Method: clinical testing
Pyogenic arthritis-pyoderma gangrenosum-acne syndrome
Allele origin: germline
Invitae
Accession: SCV000764075.4
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Pyogenic arthritis-pyoderma gangrenosum-acne syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000394009.3
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
(Jun 08, 2020)
criteria provided, single submitter
Method: clinical testing
Pyogenic arthritis-pyoderma gangrenosum-acne syndrome
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV000604958.3
Submitted: (Dec 11, 2020)
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 rs189773500...

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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