Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: AP1S3Comment on list classification: Changed rating of gene from Red to Amber. This gene was rated as Amber 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, 12:10 p.m. | Last Modified: 14 Oct 2020, 12:10 p.m.
Panel Version: 2.210
The following PubMed IDs were added to entity AP1S3: 24791904. These publications have been associated with OMIM phenotype MIM#616106, 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 all the Amber genesCreated: 25 Sep 2019, 1:49 p.m. | Last Modified: 25 Sep 2019, 1:49 p.m.
Panel Version: 1.115
The amber genes are covered on our targeted exome, we feel that these should be covered in the testingCreated: 25 Sep 2019, 1:44 p.m. | Last Modified: 25 Sep 2019, 1:44 p.m.
Panel Version: 1.114
linked to pustular psoriasis but status as an immune disorder in some doubtCreated: 29 Jun 2018, 1:24 p.m.
Pustular psoriasis susceptibility: variant seen in cases > controls. Is this a relevant phenotype / is this clinically useful?Created: 26 Sep 2019, 3:49 p.m. | Last Modified: 26 Sep 2019, 3:49 p.m.
Panel Version: 1.130
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 only enough evidence to rate this gene Amber.Created: 25 Sep 2019, 3 p.m. | Last Modified: 25 Sep 2019, 3 p.m.
Panel Version: 1.116
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 only enough evidence to rate this gene AmberCreated: 25 Sep 2019, 3 p.m. | Last Modified: 25 Sep 2019, 3 p.m.
Panel Version: 1.116
Keep Amber until more info on gene and disease association.Created: 2 Jul 2018, 3:45 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): AP1S3 .PanelApp HGNC gene symbol check: AP1S3 . IUIS Disease: AP1S3 deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: N/A, .IUIS Other affected cells: Keratinocytes. IUIS Associated features: Pustular psoriasis. IUIS Major category: Autoinflammatory Disorders. IUIS Subcategory: Non-Inflammasome Related ConditionsCreated: 2 Jul 2018, 10:35 a.m.
Comment on list classification: 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 from Victorian Clinical Genetics Services. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1. No disorder or MOI was listed in the submitted list.Created: 26 Jun 2018, 12:47 p.m.
Gene: ap1s3 has been classified as Amber List (Moderate Evidence).
Source Other was added to AP1S3. Publications for gene AP1S3 were updated from 32048120; 32086639 to 32086639; 24791904; 32048120 Rating Changed from Amber List (moderate evidence) to Red List (low evidence)
Source IUIS Classification December 2019 was added to AP1S3. Added phenotypes Pustular psoriasis; Autoinflammatory Disorders for gene: AP1S3 Publications for gene AP1S3 were updated from to 32048120; 32086639
Source North West GLH was added to AP1S3.
Source London North GLH was added to AP1S3.
Source NHS GMS was added to AP1S3.
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.
Gene: ap1s3 has been classified as Amber List (Moderate Evidence).
Phenotypes for gene: AP1S3 were set to Pustular psoriasis, 616106; Autoinflammatory Disorders
Mode of inheritance for gene: AP1S3 was changed from to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene AP1S3 were set to Pustular psoriasis, Autoinflammatory Disorders
IUIS Classification February 2018 was added to AP1S3. Panel: Primary immunodeficiency disorders
Gene: ap1s3 has been classified as Amber List (Moderate Evidence).
AP1S3 was added to Primary immunodeficiency disorders panel. Sources: Victorian Clinical Genetics Services
AP1S3 was created by Louise Daugherty