Primary immunodeficiency or monogenic inflammatory bowel disease

Gene: TAPBP

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

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

• 12149238

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.