MHC class I deficiency

disease
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Also known as Bare lymphocyte syndrome type 1BLS type 1immunodeficiency by defective expression of HLA class 1immunodeficiency by defective expression of HLA class type 1

Summary

MHC class I deficiency (MONDO:0011476) is a disease caused by variants in TAP1 and TAP2, with 7 cohort genes. The dominant Reactome pathway is ER-Phagosome pathway (5 cohort genes).

At a glance

  • Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
  • Causal genes: TAP1 (GenCC Definitive), TAP2 (GenCC Strong)
  • Cohort genes: 7
  • ClinVar variants: 1,223

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Cases/families30WorldwideValidated
Point prevalence<1 / 1 000 000WorldwideValidated

Identifiers

Disease identifiers

FieldValue
Canonical nameMHC class I deficiency
Mondo IDMONDO:0011476
OMIM604571
Orphanet34592
DOIDDOID:0060009
ICD-11489749747
SNOMED CT725136003
UMLSC1858266
MedGen346868
GARD0009548
Is cancer (heuristic)no

Also known as: Bare lymphocyte syndrome type 1 · BLS type 1 · immunodeficiency by defective expression of HLA class 1 · immunodeficiency by defective expression of HLA class type 1

Data availability: 1,223 ClinVar variants · 11 GenCC gene-disease records · 6 cell lines.

Disease family

An umbrella term covering 3 Mondo subtypes.

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary diseaseimmunodeficiency diseasecombined immunodeficiencyMHC class I deficiency

Related subtypes (32): ataxia telangiectasia, combined immunodeficiency due to ZAP70 deficiency, X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia, combined immunodeficiency due to moesin deficiency, Wiskott-Aldrich syndrome, combined immunodeficiency due to STK4 deficiency, combined immunodeficiency due to MALT1 deficiency, combined immunodeficiency due to OX40 deficiency, combined immunodeficiency due to CD3gamma deficiency, combined immunodeficiency due to CTPS1 deficiency, combined immunodeficiency due to CRAC channel dysfunction, severe combined immunodeficiency, non-SCID combined immunodeficiency, combined immunodeficiency due to RELA haploinsufficiency, combined immunodeficiency due to GINS1 deficiency, combined immunodeficiency syndrome, combined immunodeficiency due to POLE2 deficiency, autosomal recessive combined immunodeficiency due to complete IL6ST deficiency, autosomal recessive combined immunodeficiency due to partial IL6ST deficiency, autosomal dominant combined immunodeficiency due to partial IL6ST deficiency, autosomal recessive combined immunodeficiency due to IL6R deficiency, autosomal dominant combined immunodeficiency due to ERBIN deficiency, combined immunodeficiency due to TBX1 deficiency, RAC2-related combined immunodeficiency-bronchiectasis-cancer-predisposing syndrome, combined immunodeficiency due to dimerization defective IKAROS mutation, late-onset combined immunodeficiency due to ICOSL deficiency, combined immunodeficiency-hypogammaglobulinemia-skeletal anomalies syndrome due to IKBKA deficiency, early-onset combined immunodeficiency with low ig due to dominant negative IKAROS mutation, combined immunodeficiency with low Ig due to BCL10 deficiency, IRF4-related combined immunodeficiency, NFATC1-related combined immunodeficiency, POLD3-related combined immunodeficiency

Subtypes (3): MHC class I deficiency 1, MHC class I deficiency 2, MHC class I deficiency 3

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

600 retrieved; paginated sample, class counts are floors:

294 uncertain significance, 250 likely benign, 20 benign, 19 pathogenic, 8 benign/likely benign, 7 conflicting classifications of pathogenicity, 2 likely pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
2033577NM_001290043.2(TAP2):c.724C>T (p.Gln242Ter)LOC107648851Pathogeniccriteria provided, single submitter
2136377NM_001290043.2(TAP2):c.658C>T (p.Arg220Ter)LOC107648851Pathogeniccriteria provided, single submitter
1074323NM_000593.6(TAP1):c.1866_1879del (p.His622fs)TAP1Pathogeniccriteria provided, single submitter
13732NM_000593.6(TAP1):c.599-1G>ATAP1Pathogenicno assertion criteria provided
1455001NM_000593.6(TAP1):c.1005del (p.Pro336fs)TAP1Pathogeniccriteria provided, single submitter
2054486NC_000006.12:g.32853728dupTAP1Pathogeniccriteria provided, single submitter
2096743NM_000593.6(TAP1):c.335T>A (p.Leu112Ter)TAP1Pathogeniccriteria provided, single submitter
2419034NM_000593.6(TAP1):c.934C>T (p.Arg312Ter)TAP1Pathogeniccriteria provided, single submitter
2572421NM_000593.6(TAP1):c.884del (p.Leu295fs)TAP1Pathogeniccriteria provided, single submitter
2705098NM_000593.6(TAP1):c.1217_1218del (p.Val406fs)TAP1Pathogeniccriteria provided, single submitter
13728NM_001290043.2(TAP2):c.979del (p.Arg327fs)TAP2Pathogenicno assertion criteria provided
1443971NM_001290043.2(TAP2):c.1260del (p.Ser421fs)TAP2Pathogeniccriteria provided, single submitter
1452277NM_001290043.2(TAP2):c.824del (p.Leu275fs)TAP2Pathogeniccriteria provided, single submitter
1456619NM_001290043.2(TAP2):c.373del (p.Gln125fs)TAP2Pathogeniccriteria provided, single submitter
1459385NM_001290043.2(TAP2):c.1101G>A (p.Trp367Ter)TAP2Pathogeniccriteria provided, single submitter
1928904NM_001290043.2(TAP2):c.1837C>T (p.Gln613Ter)TAP2Pathogeniccriteria provided, single submitter
1996596NM_001290043.2(TAP2):c.1606C>T (p.Gln536Ter)TAP2Pathogeniccriteria provided, single submitter
2075917NM_001290043.2(TAP2):c.224del (p.Leu75fs)TAP2Pathogeniccriteria provided, single submitter
2164746NM_001290043.2(TAP2):c.815del (p.Leu272fs)TAP2Pathogeniccriteria provided, single submitter
1480495NM_001290043.2(TAP2):c.494-2A>GLOC107648851Likely pathogeniccriteria provided, single submitter
2501118NM_001290043.2(TAP2):c.814_815delinsC (p.Leu272fs)TAP2Likely pathogeniccriteria provided, single submitter
1060163NM_000593.6(TAP1):c.746A>G (p.Tyr249Cys)TAP1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1339543NM_000593.6(TAP1):c.1937G>A (p.Gly646Asp)TAP1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1386307NM_000593.6(TAP1):c.362C>T (p.Ala121Val)TAP1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1032425NM_001290043.2(TAP2):c.1345C>T (p.Arg449Ter)TAP2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1470803NM_001290043.2(TAP2):c.1742A>G (p.Gln581Arg)TAP2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1906410NM_001290043.2(TAP2):c.166A>G (p.Arg56Gly)TAP2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2174842NM_001290043.2(TAP2):c.1190A>G (p.Gln397Arg)TAP2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1004055NM_001290043.2(TAP2):c.524G>A (p.Arg175His)LOC107648851Uncertain significancecriteria provided, single submitter
1023763NM_001290043.2(TAP2):c.515A>T (p.Tyr172Phe)LOC107648851Uncertain significancecriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 20 · Orphanet: 6 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
TAP1DefinitiveAutosomal recessiveMHC class I deficiency6
TAP2StrongAutosomal recessiveMHC class I deficiency4
TAPBPModerateAutosomal recessiveMHC class I deficiency 14
B2MSupportiveAutosomal recessiveMHC class I deficiency6

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
TAPBPOrphanet:34592Immunodeficiency by defective expression of MHC class I
TAP1Orphanet:34592Immunodeficiency by defective expression of MHC class I
TAP2Orphanet:34592Immunodeficiency by defective expression of MHC class I
B2MOrphanet:314652Variant ABeta2M amyloidosis
B2MOrphanet:34592Immunodeficiency by defective expression of MHC class I
PSMB8Orphanet:324977Proteasome-associated autoinflammatory syndrome

Cohort genes → proteins

7 cohort genes, 6 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence7

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
TAPBPHGNC:11566ENSG00000231925O15533Tapasingencc,clinvar
TAP1HGNC:43ENSG00000168394Q03518Antigen peptide transporter 1gencc,clinvar
TAP2HGNC:44ENSG00000204267Q03519Antigen peptide transporter 2gencc,clinvar
B2MHGNC:914ENSG00000166710P61769Beta-2-microglobulingencc
PSMB8-AS1HGNC:39758ENSG00000204261PSMB8 antisense RNA 1clinvar
B3GALT4HGNC:919ENSG00000235863O96024Beta-1,3-galactosyltransferase 4clinvar
PSMB8HGNC:9545ENSG00000204264P28062Proteasome subunit beta type-8clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
TAPBPTapasinInvolved 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).
TAP1Antigen peptide transporter 1ABC transporter associated with antigen processing.
TAP2Antigen peptide transporter 2ABC transporter associated with antigen processing.
B2MBeta-2-microglobulinComponent of the class I major histocompatibility complex (MHC).
B3GALT4Beta-1,3-galactosyltransferase 4Involved in GM1/GD1B/GA1 ganglioside biosynthesis.
PSMB8Proteasome subunit beta type-8The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH.

Protein-family classification

Druggable: 5 · Difficult: 0 · Unknown: 2 · Druggable fraction: 0.71

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Transporter222.2×0.013
Antibody/Immunoglobulin28.3×0.044
Enzyme (other)11.7×0.609
Other/Unknown20.5×0.968

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
TAPBPAntibody/ImmunoglobulinyesIg_C1-set, Ig-like_dom, Tapasin
TAP1Transporteryes7.4.2.14ABC_transporter-like_ATP-bd, AAA+_ATPase, ABC1_TM_dom
TAP2Transporteryes7.4.2.14ABC_transporter-like_ATP-bd, AAA+_ATPase, Tap2/ABCB3
B2MAntibody/ImmunoglobulinyesIg/MHC_CS, Ig_C1-set, Ig-like_dom
PSMB8-AS1Other/Unknownno
B3GALT4Enzyme (other)yes2.4.1.62Glyco_trans_31
PSMB8Other/UnknownnoPept_T1A_subB, Proteasome_sua/b, Proteasome_bsu_CS

Expression context

Cohort genes with no expression data: 0.

5 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)7
unknown0

Top tissues across cohort

TissueCohort genes
granulocyte6
monocyte3
leukocyte3
lymph node2
vermiform appendix2
blood1
bone marrow cell1
lower esophagus mucosa1
mucosa of transverse colon1
spleen1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
TAPBP133ubiquitousmarkerbone marrow cell, granulocyte, blood
TAP1134ubiquitousmarkergranulocyte, vermiform appendix, lymph node
TAP2134ubiquitousyesvermiform appendix, lymph node, monocyte
B2M134ubiquitousmarkergranulocyte, monocyte, leukocyte
PSMB8-AS1132ubiquitousmarkergranulocyte, leukocyte, monocyte
B3GALT4170ubiquitousyeslower esophagus mucosa, mucosa of transverse colon, granulocyte
PSMB8132ubiquitousmarkergranulocyte, leukocyte, spleen

Protein interactions among cohort

Intra-cohort edges: 7.

Hub genes (top 10 by interactor count)

SymbolInteractor count
PSMB83,188
TAPBP2,253
TAP12,139
TAP21,507
B3GALT4831
B2M415
PSMB8-AS10

Intra-cohort edges

ABSources
B2MTAP2intact
PSMB8TAP1intact, string_interaction
PSMB8TAP2intact, string_interaction
PSMB8TAPBPstring_interaction
TAP1TAP2biogrid_interaction, intact, string_interaction
TAP1TAPBPbiogrid_interaction, intact, string_interaction
TAP2TAPBPbiogrid_interaction, intact, string_interaction

Structural data

PDB: 5 · AlphaFold-only: 1 · No structure: 1

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
B2MP617691,226
TAP1Q0351822
PSMB8P2806222
TAP2Q0351921
TAPBPO155338

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
B3GALT4O9602484.89

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 44. Enrichment computed across 7 evidence-associated genes (6 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
ER-Phagosome pathway5108.1×6e-09TAPBP, TAP1, TAP2, B2M, PSMB8
Antigen Presentation: Folding, assembly and peptide loading of class I MHC4262.5×1e-08TAPBP, TAP1, TAP2, B2M
Antigen processing-Cross presentation3158.6×8e-06TAP1, TAP2, B2M
Class I MHC mediated antigen processing & presentation335.0×6e-04TAP1, TAP2, B2M
Adaptive Immune System314.9×0.006TAP1, TAP2, B2M
Modulation by Mtb of host immune system1271.9×0.025B2M
Nef mediated downregulation of MHC class I complex cell surface expression1190.3×0.025B2M
Blood group systems biosynthesis1190.3×0.025B3GALT4
Infection with Mycobacterium tuberculosis1190.3×0.025B2M
Endosomal/Vacuolar pathway1173.0×0.025B2M
Lewis blood group biosynthesis1112.0×0.029B3GALT4
Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters1105.7×0.029B2M
The role of Nef in HIV-1 replication and disease pathogenesis1105.7×0.029B2M
Glycosphingolipid biosynthesis1100.2×0.029B3GALT4
Antigen processing: Ub, ATP-independent proteasomal degradation195.2×0.029PSMB8
Immune System36.5×0.029TAP1, TAP2, B2M
DAP12 interactions179.3×0.032B2M
DAP12 signaling161.4×0.039B2M
Host Interactions of HIV factors156.0×0.039B2M
Bacterial Infection Pathways156.0×0.039B2M
Glycosphingolipid metabolism150.1×0.041B3GALT4
Cross-presentation of soluble exogenous antigens (endosomes)142.3×0.047PSMB8
Proteasome assembly134.0×0.056PSMB8
Sphingolipid metabolism128.0×0.065B3GALT4
Interferon alpha/beta signaling125.4×0.068PSMB8
Interferon gamma signaling120.9×0.072B2M
Metabolism of carbohydrates and carbohydrate derivatives120.0×0.072B3GALT4
Interferon Signaling120.0×0.072B2M
HIV Infection119.8×0.072B2M
SARS-CoV-2-host interactions119.8×0.072B2M

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
antigen processing and presentation of endogenous peptide antigen via MHC class I41404.3×2e-11TAPBP, TAP1, TAP2, B2M
antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent22808.7×2e-06TAP2, B2M
cytosol to endoplasmic reticulum transport22808.7×2e-06TAP1, TAP2
peptide antigen assembly with MHC class I protein complex2936.2×2e-05TAPBP, B2M
response to molecule of bacterial origin2702.2×3e-05TAP2, B2M
T cell mediated cytotoxicity2374.5×1e-04TAP2, B2M
positive regulation of T cell mediated cytotoxicity2170.2×4e-04TAP2, B2M
MHC class Ib protein complex assembly12808.7×0.002TAPBP
antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent12808.7×0.002TAP2
negative regulation of iron ion transport12808.7×0.002B2M
peptide antigen stabilization12808.7×0.002TAPBP
transmembrane transport256.2×0.002TAP1, TAP2
antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent11404.3×0.002TAP2
regulation of iron ion transport11404.3×0.002B2M
cellular response to iron(III) ion11404.3×0.002B2M
negative regulation of forebrain neuron differentiation11404.3×0.002B2M
peptide antigen transport1936.2×0.004TAP2
antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent1702.2×0.004TAPBP
peptide transport1702.2×0.004TAP1
regulation of erythrocyte differentiation1468.1×0.006B2M
cellular response to iron ion1401.2×0.007B2M
cellular response to nicotine1351.1×0.007B2M
negative regulation of receptor-mediated endocytosis1312.1×0.008B2M
transferrin transport1255.3×0.009B2M
positive regulation of T cell cytokine production1216.1×0.010B2M
positive regulation of cellular senescence1216.1×0.010B2M
ganglioside biosynthetic process1187.2×0.011B3GALT4
peptide antigen assembly with MHC class II protein complex1175.5×0.011B2M
regulation of protein complex stability1175.5×0.011TAPBP
positive regulation of receptor-mediated endocytosis1133.8×0.013B2M

Therapeutics

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 1 · Phased (≥1): 1 · Undrugged: 6

Druggability breadth: 4 of 7 evidence-associated genes (57%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
PSMB8BORTEZOMIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
PSMB874
TAPBP00
TAP100
TAP200
B2M00
PSMB8-AS100
B3GALT400

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
BORTEZOMIB4PSMB8
CARFILZOMIB4PSMB8
IXAZOMIB3PSMB8
MARIZOMIB3PSMB8
OPROZOMIB2PSMB8
DELANZOMIB2PSMB8
ZETOMIPZOMIB2PSMB8

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 3.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
PSMB8262Binding:250, ADMET:9, Functional:3
B2M5Binding:5
TAP14Binding:4
TAP23Binding:3

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
TAP17.4.2.14, 7.4.2.5ABC-type antigen peptide transporter, bacterial ABC-type protein transporter
TAP27.4.2.14, 7.4.2.5ABC-type antigen peptide transporter, bacterial ABC-type protein transporter
B3GALT42.4.1.62ganglioside galactosyltransferase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
PSMB8262

Pharmacogenomics

Cohort genes with a PharmGKB record: 6; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

7 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

CompoundMax phaseCohort target (bioactivity)
BORTEZOMIB4PSMB8
CARFILZOMIB4PSMB8
IXAZOMIB3PSMB8
MARIZOMIB3PSMB8
OPROZOMIB2PSMB8
DELANZOMIB2PSMB8
ZETOMIPZOMIB2PSMB8

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1PSMB8
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug4TAPBP, TAP1, TAP2, B2M
DDruggable family + AlphaFold only, no drug1B3GALT4
EDifficult family or no structure, no drug1PSMB8-AS1

Undrugged target profiles

6 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
TAP14PSMB8
TAP23PSMB8
TAPBP0
B2M5
PSMB8-AS10
B3GALT40

Clinical trials & evidence

Clinical trials

Clinical trials: 0.