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NM_003978.5(PSTPIP1):c.856A>G (p.Asn286Asp)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Mar 17, 2020
Accession:
VCV000317181.5
Variation ID:
317181
Description:
single nucleotide variant
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NM_003978.5(PSTPIP1):c.856A>G (p.Asn286Asp)

Allele ID
323421
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q24.3
Genomic location
15: 77032879 (GRCh38) GRCh38 UCSC
15: 77325220 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_172:g.42756A>G
LRG_172t1:c.856A>G
NC_000015.10:g.77032879A>G
... more HGVS
Protein change
N286D, N277D, N351D
Other names
-
Canonical SPDI
NC_000015.10:77032878:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00035
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00017
Trans-Omics for Precision Medicine (TOPMed) 0.00012
The Genome Aggregation Database (gnomAD) 0.00003
Links
ClinGen: CA7676052
dbSNP: rs377437961
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 2 criteria provided, multiple submitters, no conflicts Mar 17, 2020 RCV000303879.5
Uncertain significance 1 criteria provided, single submitter Aug 5, 2016 RCV000412772.1
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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
(Aug 05, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000490748.1
Submitted: (Dec 21, 2016)
Evidence details
Comment:
To our knowledge, the N286D missense substitution has neither been published as a pathogenic variant, nor as a benign polymorphism. N286D represents a non-conservative amino … (more)
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: SCV000394007.3
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
(Mar 17, 2020)
criteria provided, single submitter
Method: clinical testing
Pyogenic arthritis-pyoderma gangrenosum-acne syndrome
Allele origin: germline
Invitae
Accession: SCV000764084.4
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 rs377437961...

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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