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Primary immunodeficiency

Gene: TAP1

Green List (high evidence)

TAP1 (transporter 1, ATP binding cassette subfamily B member)
EnsemblGeneIds (GRCh38): ENSG00000168394
EnsemblGeneIds (GRCh37): ENSG00000168394
OMIM: 170260, Gene2Phenotype
TAP1 is in 3 panels

5 reviews

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)

Eleanor Williams (Genomics England Curator)

Green List (high evidence)

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, 4:40 p.m. | Last Modified: 14 Oct 2020, 4:40 p.m.
Panel Version: 2.321
The following PubMed IDs were added to gene TAP1 (OMIM gene MIM#170260): 20083708;7517574;10560675;10074494;11529920. These publications have been associated with the gene by the immunodeficiencies 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
Comment on list classification: There are plausable disease-causing mutations in TAP1 more than three unrelated cases so changing this gene from Amber to Green.
Created: 9 May 2018, 11:24 a.m.
TAP1 is associated with Bare lymphocyte syndrome, type I (MIM 604571) in OMIM and Genetics Home Reference. ATP-binding cassette transporter TAP translocates peptides from the cytosol to awaiting major histocompatibility complex (MHC) class I molecules in the endoplasmic reticulum. TAP is made up of the TAP1 and TAP2 (170261) polypeptides. Furukawa et al. (1999) (PMID: 10074494) identified homozygosity for a splice site mutation in intron 1 of the TAP1 gene in a Japanese woman with type I bare lymphocyte syndrome (patient originally reported in Maeda et al. (1985) (PMID: 3891604). de la Salle (1999) (PMID: 10074495) report an analysis of cell lines derived from the Japanese patient (patient2) reported in Furukawa et al (1999) and another patient (patient 1) originally reported in Plebani A, et al (1996) (PMID: 8912593). Patient 1 presented with low expression of HLA class I molecules on peripheral blood mononuclear cells and no expression of CD 1 a molecules on lesional skin and a Marfan-like phenotype. A deletion of one cytosine in exon 2, at nucleotide 819 of the coding sequence was found in the cells from patient1. Functional studies showed cells from both patients had low expression of HLA class I molecules. Moins-Teisserenc et al (1999) (PMID: 10560675) report 3 patients with TAP-1 mutations and a severe decrease in cell-surface expression of HLA class-I molecule but the genes were not sequenced. Caversaccio etl 2008 (PMID: 18283480) report two siblings from Italy with chronic rhinosinusitis and conductive hearing loss and a variant in the TAP1 gene leading to a premature stop codon (parents from same region as the patient reported by Plebani et al, variant the same). Villa-Forte et al 2008 (PMID:18668571) report a 20 year old patient with multiple skin ulcers on her legs, severe pansinusitis, and chronic lung disease found to have a TAP1 mutation generating a premature stop codon. Hanalioglu et al 2017 (PMID: 28161407 ) report 2 siblings with MHC class I deficiency and a homozygous insertion of a cytosine nucleotide in exon 10 to TAP1 which results in a premature stop codon. This publication includes a table showing cases of TAP1 variants found to date. There are plausable disease-causing mutations in TAP1 more than three unrelated cases so rating this gene green.
Created: 9 May 2018, 11:20 a.m.
Comment on phenotypes: Added MIM number to first phenotype
Created: 8 May 2018, 3:49 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
HLA CLASS I DEFICIENCY

Publications

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): TAP1 .PanelApp HGNC gene symbol check: TAP1 . IUIS Disease: MHC class I deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Vasculitis, pyoderma gangrenosum. IUIS Major category: Immunodeficiencies affecting cellular and humoral immunity. IUIS Subcategory: Combined Immunodeficiencies Generally Less Profound than Severe Combined Immunodeficiency
Created: 2 Jul 2018, 10:35 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: 19 Apr 2018, 1:56 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: TAP1, PanelApp HGNC gene symbol check: TAP1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Combined immunodeficiencies / HLA class I deficiency / HLA class I deficiency
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: TAP1, GRID_Gene_Symbol: TAP1, GRID_Transcript_ENS_Community submitted: ENST00000354258, GRID_Transcript_RefSeq: NM_000593.5, GRID_Transcript_ENS_used_on_Production: ENST00000354258
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
  • GOSH PID v.8.0
Phenotypes
  • Bare lymphocyte syndrome, type I 604571
  • HLA class I deficiency
  • Vasculitis, pyoderma gangrenosum
  • Immunodeficiencies affecting cellular and humoral immunity
OMIM
170260
Clinvar variants
Variants in TAP1
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: tap1 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 TAP1. Publications for gene TAP1 were updated from to 11529920; 7517574; 10560675; 20083708; 10074494 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 TAP1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to TAP1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to TAP1.

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 TAP1 were set to Bare lymphocyte syndrome, type I 604571, HLA class I deficiency, Vasculitis, pyoderma gangrenosum, Immunodeficiencies affecting cellular and humoral immunity

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to TAP1. 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 TAP1. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: tap1 has been classified as Green List (High Evidence).

9 May 2018, Gel status: 3

Gene classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

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

8 May 2018, Gel status: 2

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for TAP1 were set to Bare lymphocyte syndrome, type I 604571; HLA class I deficiency

19 Apr 2018, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to TAP1. Panel: Primary immunodeficiency disorders Phenotypes for gene TAP1 were set to Bare lymphocyte syndrome, type I, HLA class I deficiency

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene TAP1 were set to Bare lymphocyte syndrome, type I

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to TAP1. Panel: Primary immunodeficiency disorders Phenotypes for gene TAP1 were set to Bare lymphocyte syndrome, type I

6 Apr 2018, Gel status: 1

Clear Sources

Louise Daugherty (Genomics England Curator)

TAP1 Source: GOSH PID 20171200 was removed from gene: TAP1

6 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

GOSH PID v.8.0 was added to TAP1. Panel: Primary immunodeficiency disorders

29 Mar 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

TAP1 was added to Primary immunodeficiency disorders panel. Sources: GOSH PID 20171200

29 Mar 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

TAP1 was created by Louise Daugherty