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Primary immunodeficiency

Gene: AP1S3

Amber List (moderate evidence)

AP1S3 (adaptor related protein complex 1 sigma 3 subunit)
EnsemblGeneIds (GRCh38): ENSG00000152056
EnsemblGeneIds (GRCh37): ENSG00000152056
OMIM: 615781, Gene2Phenotype
AP1S3 is in 3 panels

5 reviews

Eleanor Williams (Genomics England Curator)

Comment 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

Kimberly Gilmour (Great Ormond Street Hopsital)

I don't know

agree with all the Amber genes
Created: 25 Sep 2019, 1:49 p.m. | Last Modified: 25 Sep 2019, 1:49 p.m.
Panel Version: 1.115

Tracy Briggs (Manchester Genomic Medicine Centre)

I don't know

The amber genes are covered on our targeted exome, we feel that these should be covered in the testing
Created: 25 Sep 2019, 1:44 p.m. | Last Modified: 25 Sep 2019, 1:44 p.m.
Panel Version: 1.114

Sophie Hambleton (Newcastle University)

I don't know

linked to pustular psoriasis but status as an immune disorder in some doubt
Created: 29 Jun 2018, 1:24 p.m.

Louise Daugherty (Genomics England Curator)

I don't know

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 Amber
Created: 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 Conditions
Created: 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.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Other
  • IUIS Classification December 2019
  • North West GLH
  • London North GLH
  • NHS GMS
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
Phenotypes
  • Pustular psoriasis, 616106
  • Pustular psoriasis
  • Autoinflammatory Disorders
OMIM
615781
Clinvar variants
Variants in AP1S3
Penetrance
None
Publications
Panels with this gene

History Filter Activity

14 Oct 2020, Gel status: 2

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: ap1s3 has been classified as Amber List (Moderate Evidence).

13 Oct 2020, Gel status: 1

Added New Source, Set publications, Status Update

Eleanor Williams (Genomics England Curator)

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)

28 Feb 2020, Gel status: 2

Added New Source, Set Phenotypes, Set publications

Louise Daugherty (Genomics England Curator)

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

17 Sep 2019, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to AP1S3.

17 Sep 2019, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to AP1S3.

17 Sep 2019, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to AP1S3.

12 Jul 2018, Gel status: 2

Panel promoted to version 1.0

Louise Daugherty (Genomics England Curator)

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.

2 Jul 2018, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: ap1s3 has been classified as Amber List (Moderate Evidence).

2 Jul 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: AP1S3 were set to Pustular psoriasis, 616106; Autoinflammatory Disorders

2 Jul 2018, Gel status: 2

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: AP1S3 was changed from to BIALLELIC, autosomal or pseudoautosomal

1 Jul 2018, Gel status: 2

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene AP1S3 were set to Pustular psoriasis, Autoinflammatory Disorders

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to AP1S3. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: ap1s3 has been classified as Amber List (Moderate Evidence).

26 Jun 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

AP1S3 was added to Primary immunodeficiency disorders panel. Sources: Victorian Clinical Genetics Services

26 Jun 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

AP1S3 was created by Louise Daugherty