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Primary immunodeficiency

Gene: TAPBP

Amber List (moderate evidence)

TAPBP (TAP binding protein)
EnsemblGeneIds (GRCh38): ENSG00000231925
EnsemblGeneIds (GRCh37): ENSG00000231925
OMIM: 601962, Gene2Phenotype
TAPBP is in 3 panels

3 reviews

Sophie Hambleton (Newcastle University)

I don't know

One patient but high confidence in pathogenicity
Created: 29 Jun 2018, 3:28 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Eleanor Williams (Genomics England Curator)

I don't know

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, 12:15 p.m. | Last Modified: 14 Oct 2020, 12:15 p.m.
Panel Version: 2.215
The following PubMed IDs were added to gene TAPBP (OMIM gene MIM#601962): 12149238. 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
Added 'deletion tag'. Only reported case of association with Bare lymphocyte syndrome, type I is in a patient with a 7.4 kb deletion in TAPBP.
Created: 9 May 2018, 2:25 p.m.
In OMIM TAPBP is associated with Bare lymphocyte syndrome, type I. Evidence comes from Yabe et al. (2002) (PMID: 12149238) who report that a patient with tapasin deficiency and type I bare lymphocyte syndrome with an Alu-mediated homozygous 7.4-kb deletion, encompassing exons 4 through 7, in the TAPBP gene. Nothing found in Gene2Phenotype.
No other reports of cases of variants in TAPBP associated with Bare lymphocyte syndrome, type I were found in PubMed.
TAPBP is listed in the Genetics Test registry as a Clinical Test on several immune deficiency panels https://www.ncbi.nlm.nih.gov/gtr/all/tests/?term=6892[geneid]. Rating as amber as insufficient evidence to classify as green.
Created: 9 May 2018, 2:17 p.m.
Comment on phenotypes: Added MIM number to Bare lymphocyte syndrome, type I
Created: 9 May 2018, 1:52 p.m.

Publications

Louise Daugherty (Genomics England Curator)

I don't know

Keep Amber until more info on gene and disease association, request evidences from GOSH, GRID and Victorian Clinical Genetics Services
Created: 5 Jul 2018, 12:55 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): TAPBP .PanelApp HGNC gene symbol check: TAPBP . 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, 1:46 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: TAPBP, PanelApp HGNC gene symbol check: TAPBP, 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: TAPBP, GRID_Gene_Symbol: TAPBP, GRID_Transcript_ENS_Community submitted: ENST00000426633, GRID_Transcript_RefSeq: NM_003190.4, GRID_Transcript_ENS_used_on_Production: ENST00000426633
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Other
  • IUIS Classification December 2019
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
  • GOSH PID v.8.0
Phenotypes
  • Vasculitis, pyoderma gangrenosum
  • Bare lymphocyte syndrome, type I 604571
  • HLA class I deficiency
  • Immunodeficiencies affecting cellular and humoral immunity
  • Vasculitis,pyoderma gangrenosum
Tags
deletions
OMIM
601962
Clinvar variants
Variants in TAPBP
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: tapbp 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 TAPBP. Publications for gene TAPBP were updated from 32048120; 12149238; 32086639 to 32086639; 12149238; 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 TAPBP. Added phenotypes Vasculitis,pyoderma gangrenosum; Immunodeficiencies affecting cellular and humoral immunity for gene: TAPBP Publications for gene TAPBP were updated from 12149238 to 32048120; 12149238; 32086639

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.

5 Jul 2018, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

5 Jul 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: TAPBP were set to Bare lymphocyte syndrome, type I 604571; HLA class I deficiency; Vasculitis, pyoderma gangrenosum; Immunodeficiencies affecting cellular and humoral immunity

5 Jul 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: TAPBP were set to 12149238

1 Jul 2018, Gel status: 2

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene TAPBP 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: 2

Added New Source

Louise Daugherty (Genomics England Curator)

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

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

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

9 May 2018, Gel status: 2

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for TAPBP 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 TAPBP. Panel: Primary immunodeficiency disorders Phenotypes for gene TAPBP 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 TAPBP 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 TAPBP. Panel: Primary immunodeficiency disorders Phenotypes for gene TAPBP were set to Bare lymphocyte syndrome, type I

6 Apr 2018, Gel status: 1

Clear Sources

Louise Daugherty (Genomics England Curator)

TAPBP Source: GOSH PID 20171202 was removed from gene: TAPBP

6 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

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

29 Mar 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

TAPBP was added to Primary immunodeficiency disorders panel. Sources: GOSH PID 20171202

29 Mar 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

TAPBP was created by Louise Daugherty