TAPBP
Basic information
Region (hg38): 6:33299694-33314284
Links
Phenotypes
GenCC
Source:
- MHC class I deficiency (Limited), mode of inheritance: AR
- MHC class I deficiency (Supportive), mode of inheritance: AR
- MHC class I deficiency (Limited), mode of inheritance: AR
- MHC class I deficiency (Moderate), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
MHC class I deficiency 3 | AR | Allergy/Immunology/Infectious | Although the described individual did not have the same types of infections as other individuals with TAP deficiency, antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial | Allergy/Immunology/Infectious | 10074495; 12149238 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAPBP gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 66 | 72 | ||||
missense | 135 | 11 | 148 | |||
nonsense | 5 | |||||
start loss | 1 | |||||
frameshift | 9 | |||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 3 | 5 | 1 | 9 | ||
non coding | 13 | 18 | ||||
Total | 0 | 0 | 154 | 90 | 13 |
Variants in TAPBP
This is a list of pathogenic ClinVar variants found in the TAPBP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TAPBP | protein_coding | protein_coding | ENST00000426633 | 7 | 14694 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
6.60e-9 | 0.440 | 125637 | 1 | 110 | 125748 | 0.000441 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.764 | 258 | 295 | 0.875 | 0.0000154 | 3156 |
Missense in Polyphen | 81 | 97.312 | 0.83237 | 1081 | ||
Synonymous | 0.977 | 113 | 127 | 0.890 | 0.00000677 | 1144 |
Loss of Function | 0.949 | 15 | 19.5 | 0.768 | 0.00000105 | 182 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00116 | 0.00115 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.0000522 | 0.0000462 |
European (Non-Finnish) | 0.000605 | 0.000580 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.000262 | 0.000261 |
Other | 0.000332 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the association of MHC class I with transporter associated with antigen processing (TAP) and in the assembly of MHC class I with peptide (peptide loading). {ECO:0000269|PubMed:10636848}.;
- Disease
- DISEASE: Bare lymphocyte syndrome 1 (BLS1) [MIM:604571]: A HLA class I deficiency. Contrary to bare lymphocyte syndromes type 2 and type 3, which are characterized by early-onset severe combined immunodeficiency, class I antigen deficiencies are not accompanied by particular pathologic manifestations during the first years of life. Systemic infections have not been described. Chronic bacterial infections, often beginning in the first decade of life, are restricted to the respiratory tract. {ECO:0000269|PubMed:12149238}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Antigen processing and presentation - Homo sapiens (human);Immune System;Adaptive Immune System;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;ER-Phagosome pathway;Antigen Presentation: Folding, assembly and peptide loading of class I MHC
(Consensus)
Intolerance Scores
- loftool
- 0.977
- rvis_EVS
- 0.13
- rvis_percentile_EVS
- 63.49
Haploinsufficiency Scores
- pHI
- 0.0691
- hipred
- N
- hipred_score
- 0.257
- ghis
- 0.536
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.992
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tapbp
- Phenotype
- immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- MHC class Ib protein complex assembly;antigen processing and presentation of peptide antigen via MHC class I;antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;immune response;regulation of gene expression;antigen processing and presentation of endogenous peptide antigen via MHC class I;amide transport;peptide antigen stabilization;regulation of protein complex stability;protein-containing complex assembly;vesicle fusion with endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane
- Cellular component
- Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;phagocytic vesicle membrane;endoplasmic reticulum-Golgi intermediate compartment membrane;MHC class I peptide loading complex;integral component of lumenal side of endoplasmic reticulum membrane
- Molecular function
- protein binding;peptide antigen-transporting ATPase activity;MHC class I protein binding;peptide antigen binding;TAP1 binding;TAP2 binding;unfolded protein binding;TAP complex binding