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NM_003978.5(PSTPIP1):c.59C>T (p.Thr20Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Apr 17, 2020
Accession:
VCV000317170.5
Variation ID:
317170
Description:
single nucleotide variant
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NM_003978.5(PSTPIP1):c.59C>T (p.Thr20Met)

Allele ID
323408
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q24.3
Genomic location
15: 77018170 (GRCh38) GRCh38 UCSC
15: 77310511 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.77018170C>T
NC_000015.9:g.77310511C>T
NG_007526.1:g.28047C>T
... more HGVS
Protein change
T20M, T11M, T85M
Other names
-
Canonical SPDI
NC_000015.10:77018169:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00006
1000 Genomes Project 0.00040
Links
ClinGen: CA7675689
dbSNP: rs553718554
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Apr 17, 2020 RCV000299645.5
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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
Likely benign
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
Pyogenic arthritis-pyoderma gangrenosum-acne syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000393987.3
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 17, 2020)
criteria provided, single submitter
Method: clinical testing
Pyogenic arthritis-pyoderma gangrenosum-acne syndrome
Allele origin: germline
Invitae
Accession: SCV000932754.3
Submitted: (Jan 07, 2021)
Evidence details
Comment:
This sequence change replaces threonine with methionine at codon 20 of the PSTPIP1 protein (p.Thr20Met). The threonine residue is moderately conserved and there is a … (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 rs553718554...

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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