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COVID-19 research

Gene: TAPBP

Green List (high 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

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