TAPBP

TAP binding protein, the group of C1-set domain containing

Basic information

Region (hg38): 6:33299694-33314284

Links

ENSG00000231925NCBI:6892OMIM:601962HGNC:11566Uniprot:O15533AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
MHC class I deficiency 3ARAllergy/Immunology/InfectiousAlthough 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 beneficialAllergy/Immunology/Infectious10074495; 12149238

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TAPBP gene.

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
clinvar
6
clinvar
72
missense
135
clinvar
11
clinvar
2
clinvar
148
nonsense
5
clinvar
5
start loss
1
clinvar
1
frameshift
9
clinvar
9
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
2
clinvar
2
splice region
3
5
1
9
non coding
13
clinvar
5
clinvar
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.

Position Type Phenotype Significance ClinVar
6-33301762-A-C MHC class I deficiency Uncertain significance (Jan 30, 2020)2436954
6-33301775-G-T MHC class I deficiency Likely benign (Dec 11, 2023)1105304
6-33302502-TTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCCGCCCTCCTCAGCCTCCCAAAGTGCTAGGATTACAGGCGTGAACCAACGCACCTGGCCAAGACTGTAATTTCTTTTTCTTTTTTTTTTGTTGTTGAGACGAAGTTTTCCTTTTGTCACCCAGGCTGGAGTGCAATGGTGTGATCTCAGCTCACTGCAACCTCTGCCTCCCAGGTTCAAGCGATTCTCCTGCCCCAGTCTCCCGAGTAGCTGGGATTACAGGTGCCGTCACATCTGGCTAATTTTTTGTATTTTTAGTAGAGATGGGGTTTCATCATGTTGGCTAAGCTGGTCTTGAACTCCTGACCTCAGGTGATCCTCCCGCCTCGGCCTCCCAAAGTGCAGGGATTACAGGCATGAGCCATCGCACCCGGCCTGTAATTTCTTATATTGTTTACATGTTGCAATAATATTTTGGATGTACAGGTTGAGCATCGCCGATCCAAAACTCTAAAATCTGAAATGTTCCAAAACCTGAAATTTTTTTAGTGCCAACATGATGCCACAAGTGGAAAATCCCACAGCTGCCCTCATGTGATGGGTCACATATATTATTAAAAATATTGTGGTCGGGTGCAGCGGTTCACACCTGTAATCCCAACGCTTTGGGAGGCCAAGGCAGCGGGCGGATCACCTGAGGTCGGGAGTTCGAGACCAGCCTGACCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCAGGCGTGGTGGTGGGTGCCTGTAATCCCAACTACTCGGGAGGCTAAGGCAGGAGAATCGCTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCGCACCATTGCACCCCAGCCTGGGCGACAGAGACTCTGTCTCAAAAAAAAAGAGAAGGAAAAAAATCTTCAGGCCATGTGTATAAGGTGTATAGGAAACATAAATGATTTCTGTGTTTAGATTTGGGTCTGATCCCAAAGATATTAAATATATGCAAATATTCCAAAGTCTGAAAAAATCCAACATCCAAAAACACTTCTGACCCAAGCATTTCAGATAAGGGACCAGAATTATTAGATTAAATAAGGTATATTATTAAGTTAATTTTACCTGTTTCTGCTTATTTTTTTAATGTGAGTACTAGAGTATTTAAATTTACATATGTGGCTTGCATTATCTTTCTATTGGACAGCACTGCCTAAGTAACTTTTTAAAATCCCTACACCCAAGGAAACATATAGATTAAGTAGCATGCTCAAAGAGTCCTACAGTTAGGATATAGTGCCAGGTTTTAACCCAGATCAGTGTGAATTCCAAGCCTAGGTTCTGCCTACCACACCAGCAGCCTCCCTCCATGGGTTTTGAGATAGGATGAGGAGATAAAGTGACAAGGGAAAGATACAGAGAGGTGGAGCACTGTACCTTCTTTGAATCCTTGCAGGTGGACAGGTAGACAGCTGTGGGGAAAGATTGAGAAGGGATGGGATGCTGGAGTGGTAGAGGTGGAGGGCAGAGGGATGGGTGTCAGGCTCTTGGGAGTAGGTGGGGAAAGTCCACCAACCTCAGGTCATGGTCAGGGTAGGGCTGACACTTACCAGCCCAGCCCAGTGCCTTGAAGAGCCCAAGCAGAAGAAAGGCAGACAGGAAAAGGCCTACGCTGTCCTCAAGGGAGGGCCCTGAAAGACCTGGCAGGCAGAAGGGGTGAGAGTGAGCTCCTGTCTTCCTGGGTGCTGGCTCAGATTCCGCAGAGCTCCCAGCTCTTACCTGCTACCTCCAGGGTGACCTCAGCGCTGCGCCCCGAGGCAGGCAGGCTGGGATGGTGAATTCGACAGGCATAGCGTGCCCCATGCTGCTCAGTGGTGACTGGGGGCGGCTGCAAGTGCCCAGAGAGGCTGACAGAGCCATCGGAATGGTGGCGCAGGGCCGAGAGCCACCTCTGCCCCTCGGCCTTCTGAGAGCGGCCCCCTGGGCCACCCCGGAGTTCCCACTCCACCTCCAGGCCCCCAGAAGGGTAGAAGTGGGACACAAGGCAGAGCAATTCCGGGGGTGCCTCCCCTGGGGCGGCCCGTGCAAGGGTTGCTGGCATCAGGGACACTTTGGGGGGTTCTGGGGAAAGAGGACGAAATGAGCATAGGGAAATCAGTCCATACTGTCCTCCCTAAGAGACCCTCAGTTTGCCTGCTGGCTTCCTCAGAACTAAAGAAGGTTAGGTTTCTTCTCCTGAAATAGGGAACCCACTGTCTCTCCATTGGTGCGTCACAGAAATACCCATGTCAAAGCCCCTCAAATTTCCAGGAAACTTCTAGCCTCCCATTACCCCTCTAACTCCCAGGAACCTCTTTCTATCTCTACTTACTTGCCCAGGCACCCTCTTATCCATCATCCCTCCCCCTATTACGGTCCCCACAATCCAGTGCCCACCCTCTACCCCTGGAGACCTCTGTCCCCCAACTCACTGTACACAGCAAGCTCCAGGGTGACCTGTCCTTGCAGGTATGGCAGGTGTATGGTGGCCAGATAGGTGCCCTCCTGAAAGGGTTGAACTGTAGGCAGCCAGAAGGTCCCATTTCCGGTCCATGGGCCCCATGGCTCATCATCATCCCAAGCAGCAAATGCCACGGCCCCTTCTTGGGCTGCTGGCATCTGGCCATTCAGCCCAGGAGTTGCAGCCAGGAGCAGATGTCCCTTACCCAGGTGCTGGCGTCGCCACTCTAGCCCAAAGGGAGGGGGACCCGGAGCCAGAGATGAGGCGGCCTCGGAGGTGGGGGGCATGTAGGCAAAGCTCAAGTCCAGCAGAGCATCTTGTCCCAGTCTCACTCGAGGGGCAGGGGTGTGGGTGAGGACAGTCAGTACCACTGAGGAAGACAGGGAGATGAGGGGTTGGGAGGGGCATGAGGGAGAGAAAGAAGGAGAAAAAAATAGAGAAATGCAGTTATTGGGGAGGGCTAAACTGCAGTTTACCCACCCCTCAGAGGACACCTTTTCTGATACTCACCATTTCCTAGCCCTCCCTGCAAACTCCTTTTGCTCTGCGACTGGGTGGCACCTAGTGTGGCTGAGGGTGAGCAGAGAGGTCTAGGGGTGGTGAGTAGGGGCAATGAGGGGGTATGGCCTTTGAAGCCTACTCTGAACACATAGCACACTCTAGCTCGGGGGACTGCAGAATCCGAGGCCACTTCTGACACAACCTGAACCACTCTATCTCCAAGCACCACCCTTGAGGAACCAGGCCTTTCTTGATTACAGGCGAAGACAATGATTGAGCCATGACTGTCAGTCTTGTGGTGCTGTACAGAATATTTACTGACTCTAGAAGGTTCCAGCTCTAGCCTAGACCTGAGCACAGACCTCTATGCTCTACTGAAGCAGTACAGTGCAGTGGCTAAGTGCCTGGAGCCTGGCTGACCGGGTTCAAATCCCCTCTGCAGCTTATTTATATGGCCTTGGGCCACTTCCTTTTTCCATGGCTCAGCTTCCTAATCTCTAAAATTAAAAGTTGATGATAATAATAGTACCTACTTCATGAGGTTGTTGTGATGGTTAAATCATTAATACCTCTTGCTACTCAAGTCTATTCAGTTCCCAATTTTAGATAACAGAGACACCTACCCATGAAGGGTGCTTACAACACTGTCTGGAACACAGTAAGTCTACACGTGTTTGCTATAGTTACACCTAACTTAGCATACCCCAAGTCAACAGCATCTCTGCAACATTCCCCACCCTGCTCCAATGCCCATCTTCCCTGTCTTTGATGAATGATCACCAAGCCCGCCAGACACTAAAAGCAAACCCTTGGAGTTACTCAGACTCATTTATTCATTCAGCAACTATTGAGCACTGAAGATGTTCAAGGTATCCTGGTAGAAGACAGAATGGTGAACAAGACAAGCAGTCCCTGCTCTCAAATTGCCTATAGTCCAATGACAGACAAGCAAATTGTCAAAAATAATGTGCTATGTGCTATCCCCACCAGGACCTAACAGATCTCACATCTGTTTCCAATTTAGGTTCTCATCAATGTACGTTTAGACAATTACAACAGCCCTCCTGTCTGGTCTCCCTATTCTCAGTCTCTCCTTCAACTCCTTCTTCACACTGTAGCCAAACAAAGTGACTACAAGTCTGATCCCATCACCTACCTGTTTAAAAATCCCAAATATGGGCCAGACGCAGTGGTTCATGCCTATAATCCCAGCACTTTGGGAGGACGAGGCGGGTGGATCACCTGAGTTCGGGAGTTTGAAACCAGCCTGACCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAATTAGCCTGGTGTGGTGGCACATGCCTGTAATCCCAGCTACTCGGGAGACCGAGGCAGTAGAATTGCTTGAACCCGGGAAGCAGAGGTTGCGGTGAGCCGAGATTGTGCCATTGCACTCCAGCCTGGGCAATAAGAGGGAAACCCCGTTTCAAAAAAAAAAAAAAAAATCCCAAATACGGCCAGGCGTGGTGGCTCACACCTGTAATCCCAACACTTTGGTAGCCTGAGGCGGGTGGATTACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGCAAAACCCTGTCTCTACTAAAAATACAAAAATTAGCCAGGTGTGGGGGCAGGCACCTGTAGTCCTAGCTACTTGGGAGGCTGAGGCAGAAGAATCACTTGAACCTGGGAGGTAGAGGTTGCCGTAAGCTGAAATCATGCCACTACACTCCAGCCTGGGCAACAGAGTGAGACTCCGTCTCAAAACTAAATAAATAAATAAAATAAAAATCCCAAATACCTAGGAAGTCAGCTGATAAAGGCATAGGCTGAAGCTATATGGCCTGGGTTCAATTTCTAGCCCTGCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTGAGATAGAGTTTTGCTCGTCACCTAGGCTAGAGTATAGTGGTGTGATCTTGGCTCACTGCAACCTCTGCCTCCCAGGTTCAAGTGAGTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCGTCCACAACCGTGCCCAGCTAATTTTTGTATTTTTGGTAGAGATGGGGTTTCACCATGTTGCCCAGGCTGGTCTTGAACTCCCGACCTCAGGTGATCCACCTGCTTTGGTCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCACGCCTGGCCTCTAGCTCTGCTTCTTACACACTGTGTGTCCTTGGGCAAATTATTTAACTGGTTTGTGTCCTATATTTATCCATATGCAATACAGGGATAATATTAAAACCTACAACCTATGGTTGTTGAGAGGAATAAGTGAGATTATGCATATAAAGTGCTTAGAACAGGGCCTGGCATATAGAAAATACTTGATAAATGTTAGCTGTTACTATTTTCATTACCTTCATCACTATCATGGACTTGCTGGTTAACTTGGAAAAATCATTTAACCTGTATTTTCCTCACTAGTCCAAAGATCTGACCTTTGCCTATCTTTTAAAAGAATCAAGTAAAATAACAGGCTTTTTCCGGGCATGGTGGCTAACACATGTAATCCCAGCACTTTGGGAGGCTGAGGCGAGTGGATTACCTGAGGTCAGGAGTTCGAGAGCAGCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAAAAAAAAAAAAAAAAATTAGCGGGGCGTGGTTGTGGGTGCCTGTGATCCCATCAACTTGGGAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGCCAAGATCACCCCATTGCACTCCAGCATGGGTGACAAGAGTGAAACTCCGTCTCAAAAAATAAATATGTACATAATAAAAACAGGCTTTTTAGAATAACACGCCCTCCAAAAGAACTTCTGATGGTTCGCTCTCACCTACAGAACAAAGCCCAGCTTTCAAGGTATTTGAACATTCAGCCCCTAACCCACCCTTCCAGGCTTCTCCTGCACCCTACAAACCAGCCACATAGAACCCCTTTCTTGTGCCTAGTAGAAGTGGTCATCATTGGTCATCTCTTTGCTTTGGTCATGAGGTCCCTTCAGTTTACATTGTCTTTCCCATTTTCTCCCAAACATCTATCAAGCTTGTCCAACCTCCAGCCCAGGGACCACATGCAGCCAAGGACGGCTTGGAATACAGCCCGACACAAATTCATAAACTTTCTTAAAACATTATGAGATTTTTTCACATTTTTTTTTTTTAGCTTATCAGCCATCGTTAGTGTTCGTATATTTTATGCATGGCCCAAGACAATTCTTCTCCCAGTGTGGCTCAGGGAAGCCAAAAGATTGGAGACCCCTGATCTAAATACTCCATGTACATGAAGGTCACTTTCACTGCTGTTTCTTCCCAGAAATGTCTAGGTCCTTCAGGTAGAAGTAATCTTTTTCTTCTTGTAATTATTTTTATGTTCTTTTTAATCCTAGCTTCTGAGGCCTATAAGGTTAAACTGTTCTCATCTTCATGGAATTGTTCAGTAGAGTAAAAACAGTATGCAATTTCACTTAGTTTGTCAAAATCCAGAAACATACTTTTGAATTGTTAAAAAAAAAAAAAAAGATCCACAGGCTGGGCACAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCCGGTGGATCACCTGAGGTTGGGAGTTTGAGACCAGACTGGAGAAACCCCGTCTCTACTAAAAATACAGAATTATCCGGGCATGGTGGCACACGCCTGTAATCACAGCTGCTTGGGAAGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGCGGAGGTTGTGGTGAGCCGAGATCATGCCATTGCCCTCCAGACTGGGCAACAAGAGCAAAACTTGATCTCAAAAAAAAAAATCCATAGAATTAATAAACAAAACCTGGCTGGGCAGGGTGGCTCAGACTTGTAATCCCAGTACCTTGGGAGGCTGAGGTGGGAGGATCACTTGAACCCAGCAGTTTGAGACCAGCCTGGGCAACATAGCAAGACCCCATCTCTATTTAAAAGAAAAAATTTAAAAAAATAATAAACAAGACCTAAAGGTTTTACAGTTTAACTCTTTTTTTTTTTTTTTTTTTTTTGGAGACAGGGTCTCACTCTGTCACCCATCAAAGGTGCAATCCTCCCAACACAGCCTCCCGAGTAGCTGGGACCATAGGTACATGCCACGACACCCAACCTTTTTTTTTTTTTTTTTTTTTTTGAGACAGTTTCACGCTTGTTGCCCAGGCTGGAGTGCAGTGGCATGATCTTGGCTCACTGCAACCTCCGCCTCCCAGGTTCAAGCAATTCTCTTGCCTCAGCCTTCCGAGTAGCTGGGATTACAGGCATGCACCACCATGCCTGGCTAA-T MHC class I deficiency 3 Pathogenic (Aug 15, 2002)7606
6-33303976-G-A MHC class I deficiency Likely benign (Aug 16, 2022)1667187
6-33303981-G-A MHC class I deficiency Likely benign (Feb 10, 2022)1607876
6-33303993-T-TG MHC class I deficiency Benign (Jan 31, 2023)2832250
6-33304003-T-C MHC class I deficiency Benign (Jan 29, 2024)1169190
6-33304111-G-T MHC class I deficiency Likely benign (Jun 10, 2023)2995529
6-33304117-C-G MHC class I deficiency Likely benign (Oct 31, 2022)2135236
6-33304120-A-G MHC class I deficiency Likely benign (Aug 01, 2023)1128319
6-33304121-CACTT-C MHC class I deficiency Uncertain significance (Dec 13, 2023)649689
6-33304131-C-T MHC class I deficiency • not specified Uncertain significance (May 14, 2024)1426651
6-33304136-C-G MHC class I deficiency Uncertain significance (Jan 29, 2023)2155960
6-33304144-C-T MHC class I deficiency • TAPBP-related disorder Benign (Jun 03, 2021)730560
6-33304149-A-G MHC class I deficiency Uncertain significance (Jul 21, 2022)1722289
6-33304160-A-G MHC class I deficiency Uncertain significance (Jan 31, 2020)1042974
6-33304170-C-T MHC class I deficiency Uncertain significance (Sep 02, 2021)534708
6-33304176-G-A MHC class I deficiency • TAPBP-related disorder Benign (Jan 31, 2024)466397
6-33304180-A-G MHC class I deficiency Likely benign (Aug 23, 2022)1544466
6-33304189-G-A MHC class I deficiency • TAPBP-related disorder Benign (Jan 29, 2024)466396
6-33304194-C-T MHC class I deficiency Likely benign (Jan 04, 2024)534736
6-33304200-G-A MHC class I deficiency Likely benign (Jan 12, 2024)763120
6-33304201-G-A MHC class I deficiency Likely benign (Jan 19, 2024)2709188
6-33304214-A-T MHC class I deficiency Uncertain significance (Dec 13, 2019)843381
6-33304223-A-T MHC class I deficiency Uncertain significance (Aug 16, 2023)1045689

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TAPBPprotein_codingprotein_codingENST00000426633 714694
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
6.60e-90.44012563711101257480.000441
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7642582950.8750.00001543156
Missense in Polyphen8197.3120.832371081
Synonymous0.9771131270.8900.000006771144
Loss of Function0.9491519.50.7680.00000105182

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001160.00115
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.00005220.0000462
European (Non-Finnish)0.0006050.000580
Middle Eastern0.0001090.000109
South Asian0.0002620.000261
Other0.0003320.000326

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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