Genes in panel
STRs in panel
Prev Next

Primary immunodeficiency

Gene: AP3B1

Green List (high evidence)

AP3B1 (adaptor related protein complex 3 beta 1 subunit)
EnsemblGeneIds (GRCh38): ENSG00000132842
EnsemblGeneIds (GRCh37): ENSG00000132842
OMIM: 603401, Gene2Phenotype
AP3B1 is in 13 panels

5 reviews

Eleanor Williams (Genomics England Curator)

Comment 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, 12:24 p.m. | Last Modified: 14 Oct 2020, 12:24 p.m.
Panel Version: 2.222
The following PubMed IDs were added to gene AP3B1 (OMIM gene MIM#603401): 10024875;16551969;30974211. These publications have been associated with the gene by the immunedysregulation 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)

Green List (high evidence)

agree with green gene
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Tracy Briggs (Manchester Genomic Medicine Centre)

Green List (high evidence)

YES- this is covered on our targeted exome
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

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): AP3B1 .PanelApp HGNC gene symbol check: AP3B1 . IUIS Disease: Hermansky-Pudlak syndrome, type 2 . IUIS Inheritance: AR .T cells: N/A, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Partial albinism, recurrent infections, pulmonary fibrosis, increased bleeding, neutropenia, HLH. IUIS Major category: Diseases of Immune Dysregulation. IUIS Subcategory: FHL Syndromes with Hypopigmentation
Created: 2 Jul 2018, 10:35 a.m.
Comment on list classification: Changed from Amber to Green more than 3 unrelated cases described in the literature with HSP2 of which neutropenia is a feature
Created: 11 May 2018, 10:59 a.m.
Comment on publications: Neutropenia and/or immune defects have been associated with AP3 deficient HPS, including individuals with pathogenic variants in AP3B1 (and AP3D1) PMID:16507770,28585318,26744459
Created: 11 May 2018, 10:49 a.m.
from orphanet: HPS-2 presents with features of HPS including oculocutaneous albinisim, reduced visual acuity, horizontal nystagmus, easy bruising of soft tissues, epistaxis, and prolonged bleeding after dental extraction, surgery or childbirth. Women may present with medically significant menstrual bleeding. In addition, HPS-2 patients present with recurrent infections due to neutropenia and impaired cytotoxic activity.
Created: 11 May 2018, 10:30 a.m.
Comment on phenotypes: expanded the phenotype to include PID association
Created: 11 May 2018, 10:25 a.m.
Comment on publications: added publications to support PID phenotype
Created: 11 May 2018, 10:24 a.m.
Comment on phenotypes: added OMIM MIMid
Created: 11 May 2018, 10:19 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: AP3B1, PanelApp HGNC gene symbol check: AP3B1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Diseases of immune dysregulation / Hemophagocytic Lymphohistiocytosis (HLH) / Hermansky-Pudlak syndrome
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: AP3B1, GRID_Gene_Symbol: AP3B1, GRID_Transcript_ENS_Community submitted: ENST00000519295, GRID_Transcript_RefSeq: NM_001271769, GRID_Transcript_ENS_used_on_Production: ENST00000519295
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Other
  • NHS GMS
  • North West GLH
  • London North GLH
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Hermansky-Pudlak syndrome 2
  • HPS2
  • Hermansky-Pudlak syndrome, 608233
  • Immunodeficient HPS
  • Hermansky-Pudlak syndrome with neutropenia
  • Partial albinism, recurrent infections, pulmonary fibrosis, increased bleeding, neutropenia, HLH
  • Diseases of Immune Dysregulation
OMIM
603401
Clinvar variants
Variants in AP3B1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

14 Oct 2020, Gel status: 3

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: ap3b1 has been classified as Green List (High Evidence).

13 Oct 2020, Gel status: 1

Added New Source, Set publications, Status Update

Eleanor Williams (Genomics England Curator)

Source Other was added to AP3B1. Publications for gene AP3B1 were updated from 10024875; 14566336; 8042664; 11809908; 16537806; 19679886; 23403622; 16507770; 28585318 to 19679886; 11809908; 10024875; 16551969; 16537806; 16507770; 28585318; 30974211; 23403622; 8042664; 14566336 Rating Changed from Green List (high evidence) to Red List (low evidence)

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to AP3B1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to AP3B1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to AP3B1.

12 Jul 2018, Gel status: 4

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.

1 Jul 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene AP3B1 were set to Hermansky-Pudlak syndrome 2, HPS2, Hermansky-Pudlak syndrome, 608233, Immunodeficient HPS, Hermansky-Pudlak syndrome with neutropenia, Partial albinism, recurrent infections, pulmonary fibrosis, increased bleeding, neutropenia, HLH, Diseases of Immune Dysregulation

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to AP3B1. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to AP3B1. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: ap3b1 has been classified as Green List (High Evidence).

11 May 2018, Gel status: 3

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

11 May 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for AP3B1 were set to 10024875; 14566336; 8042664; 11809908; 16537806; 19679886; 23403622; 16507770; 28585318

11 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for AP3B1 were set to Hermansky-Pudlak syndrome 2; HPS2; Hermansky-Pudlak syndrome, 608233; Immunodeficient HPS; Hermansky-Pudlak syndrome with neutropenia

11 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for AP3B1 were set to Hermansky-Pudlak syndrome 2; HPS2; Hermansky-Pudlak syndrome, 608233; Immunodeficient HPS

11 May 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for AP3B1 were set to 10024875; 14566336; 8042664; 11809908

11 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for AP3B1 were set to Hermansky-Pudlak syndrome 2; Hermansky-Pudlak syndrome, 608233

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to AP3B1. Panel: Primary immunodeficiency disorders

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to AP3B1. Panel: Primary immunodeficiency disorders Phenotypes for gene AP3B1 were set to Hermansky-Pudlak syndrome 2, Hermansky-Pudlak syndrome

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene AP3B1 were set to Hermansky-Pudlak syndrome 2

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

AP3B1 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

AP3B1 was created by Louise Daugherty