Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: PSTPIP1Comment on list classification: Changed rating of gene from Red to Green. This gene was rated as Green in v2.208 and incorrectly automatically demoted to Red in v2.209. This was due to a defect in the automatic PanelApp uploading tool when a set of publications was added to the panel with the source ‘Other’, and under certain conditions associated to previous sources listed, resulted in the rating of the gene being automatically changed when it should not have been.Created: 14 Oct 2020, 1:42 p.m. | Last Modified: 14 Oct 2020, 1:42 p.m.
Panel Version: 2.298
The following PubMed IDs were added to entity PSTPIP1: 9212761;22161697;21532836. These publications have been associated with OMIM phenotype MIM#604416, which is listed for this entity, by the autoinflammation subgroup of the Human Phenotype Ontology Immune Mediated Disorders Consortium (https://hpo-immune-mediated-disorders.groups.io/g/update) in August 2020.Created: 13 Oct 2020, 9:36 a.m. | Last Modified: 13 Oct 2020, 9:36 a.m.
Panel Version: 2.208
Publications
agree with green geneCreated: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
YES- this is covered on our targeted exomeCreated: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes
PAPA syndrome; Hyperzincaemia hypercalprotectinaemia
Publications
Mode of pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Comment on list classification: Associated with phenotype in OMIM and not in Gen2Phen. At least 4 variants identified in unrelated cases.Created: 9 May 2018, 1:56 p.m.
Gene rating submitted by Kimberly Gilmour and Austen Worth on behalf of London North GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email 6th September the Specialist Test Group all agreed there is enough evidence to rate this gene Green.Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Gene rating submitted by Tracy Briggs, David Gokhale and Abigal Rousseau on behalf of North West GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email on 20th June the Specialist Test Group all agreed there is enough evidence to rate this gene Green.Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): PSTPIP1 (also called C2BP1) .PanelApp HGNC gene symbol check: PSTPIP1 . IUIS Disease: Pyogenic sterile arthritis, pyoderma gangrenosum, acne (PAPA) syndrome, hyperzincemia and hypercalprotectinemia . IUIS Inheritance: AD .T cells: Normal, .B cells: N/A, .IUIS Other affected cells: Hematopoietic tissues, upregulated in activated T-cells. IUIS Associated features: Destructive arthritis, inflammatory skin rash, myositis. IUIS Major category: Autoinflammatory Disorders. IUIS Subcategory: Non-Inflammasome Related ConditionsCreated: 2 Jul 2018, 10:35 a.m.
Comment on phenotypes: Added phenotypes suggested from external expert review.Created: 13 Jun 2018, 11:36 a.m.
Comment on publications: added further publication suggested from expert review PMID:26025129Created: 13 Jun 2018, 11:36 a.m.
This gene was absent from the original PanelApp PID panel dataset (review April 2018). However it was listed in external expert immunodeficiency diagnostic gene list(s) GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.Created: 20 Apr 2018, 12:25 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: PSTPIP1, PanelApp HGNC gene symbol check: PSTPIP1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Autoinflammatory disorders / Pyogenic sterile arthritis pyoderma gangrenosum and acne / Proline/serine/threonine phosphatase-interacting protein 1 deficiency (PSTPIP1)Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: PSTPIP1, GRID_Gene_Symbol: PSTPIP1, GRID_Transcript_ENS_Community submitted: ENST00000558012, GRID_Transcript_RefSeq: NM_003978.3, GRID_Transcript_ENS_used_on_Production: ENST00000558012Created: 17 Apr 2018, 12:12 p.m.
Phenotypes for gene: PSTPIP1 were changed from Pyogenic sterile arthritis, pyoderma gangrenosum, and acne 604416; Proline/serine/threonine phosphatase-interacting protein 1 deficiency (PSTPIP1); PAPA syndrome; Hyperzincaemia hypercalprotectinaemia; Destructive arthritis, inflammatory skin rash, myositis; Autoinflammatory Disorders to Pyogenic sterile arthritis, pyoderma gangrenosum, and acne, OMIM:604416; Destructive arthritis, inflammatory skin rash, myositis; Hyperzincaemia hypercalprotectinaemia; Autoinflammatory Disorders
Gene: pstpip1 has been classified as Green List (High Evidence).
Source Other was added to PSTPIP1. Publications for gene PSTPIP1 were updated from 28251506; 28628471; 28960754; 29575118; 26025129 to 21532836; 9212761; 28628471; 28251506; 28960754; 22161697; 26025129; 29575118 Rating Changed from Green List (high evidence) to Red List (low evidence)
Source NHS GMS was added to PSTPIP1.
Source North West GLH was added to PSTPIP1.
Source London North GLH was added to PSTPIP1.
2018-07-12 Louise Daugherty (Genomics England Curator) promoted panel to v1.0. Reviews were assessed, and panel was revised according to expert reviews and further in-house curation based on PanelApp guidelines. Previous panels (A- or hypo-gammaglobulinaemia, Congenital neutropaenia, Agranulocytosis, Combined B and T cell defect, Inherited complement deficiency and SCID panels) that were merged with this panel, were checked again for any changes/new reviews prior to versioning of this panel, these merged panels are now retired/made internal.
Phenotypes for gene PSTPIP1 were set to Pyogenic sterile arthritis, pyoderma gangrenosum, and acne 604416, Proline/serine/threonine phosphatase-interacting protein 1 deficiency (PSTPIP1), PAPA syndrome, Hyperzincaemia hypercalprotectinaemia, Destructive arthritis, inflammatory skin rash, myositis, Autoinflammatory Disorders
IUIS Classification February 2018 was added to PSTPIP1. Panel: Primary immunodeficiency disorders
Victorian Clinical Genetics Services was added to PSTPIP1. Panel: Primary immunodeficiency disorders
Gene: pstpip1 has been classified as Green List (High Evidence).
Phenotypes for gene: PSTPIP1 were set to Pyogenic sterile arthritis, pyoderma gangrenosum, and acne 604416; Proline/serine/threonine phosphatase-interacting protein 1 deficiency (PSTPIP1); PAPA syndrome; Hyperzincaemia hypercalprotectinaemia
Publications for gene: PSTPIP1 were set to 28251506; 28628471; 28960754; 29575118; 26025129
Mode of pathogenicity for gene: PSTPIP1 was changed to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Mode of inheritance for PSTPIP1 was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
This gene has been classified as Green List (High Evidence).
Publications for PSTPIP1 were set to 28251506; 28628471; 28960754; 29575118
Phenotypes for PSTPIP1 were set to Pyogenic sterile arthritis, pyoderma gangrenosum, and acne 604416; Proline/serine/threonine phosphatase-interacting protein 1 deficiency (PSTPIP1)
Expert Review Amber was added to PSTPIP1. Panel: Primary immunodeficiency disorders
ESID Registry 20171117 was added to PSTPIP1. Panel: Primary immunodeficiency disorders Phenotypes for gene PSTPIP1 were set to Pyogenic sterile arthritis, pyoderma gangrenosum, and acne, Proline/serine/threonine phosphatase-interacting protein 1 deficiency (PSTPIP1)
Phenotypes for gene PSTPIP1 were set to Pyogenic sterile arthritis, pyoderma gangrenosum, and acne
PSTPIP1 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0
PSTPIP1 was created by Louise Daugherty