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COVID-19 research

Gene: AP1S3

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

4 reviews

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
Created: 25 Sep 2019, 1:49 p.m.
Last Modified: 25 Sep 2019, 1:49 p.m.
Panel version: Imported from Primary immunodeficiency 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
Created: 25 Sep 2019, 1:44 p.m.
Last Modified: 25 Sep 2019, 1:44 p.m.
Panel version: Imported from Primary immunodeficiency 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.
Created: 29 Jun 2018, 1:24 p.m.

Panel version: Imported from Primary immunodeficiency panel version 0.1370

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.
Created: 26 Jun 2018, 12:47 p.m.

Panel version: Imported from Primary immunodeficiency panel version 1.130

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • IUIS Classification February 2018
  • IUIS Classification December 2019
  • London North GLH
  • NHS GMS
  • North West GLH
  • Victorian Clinical Genetics Services
  • 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

2 Apr 2020, Gel status: 3

Added New Source, Set Phenotypes, Status Update

Ellen McDonagh (Genomics England Curator)

Source Expert Review Green was added to AP1S3. Added phenotypes Pustular psoriasis, 616106; Autoinflammatory Disorders; Pustular psoriasis for gene: AP1S3 Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

1 Apr 2020, Gel status: 2

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Ellen McDonagh (Genomics England Curator)

gene: AP1S3 was added gene: AP1S3 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,North West GLH,NHS GMS,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber Mode of inheritance for gene: AP1S3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: AP1S3 were set to 32086639; 32048120 Phenotypes for gene: AP1S3 were set to Pustular psoriasis, 616106; Autoinflammatory Disorders; Pustular psoriasis