HLA-DOB

gene
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Summary

HLA-DOB (major histocompatibility complex, class II, DO beta, HGNC:4937) is a protein-coding gene on chromosome 6p21.32, encoding HLA class II histocompatibility antigen, DO beta chain (P13765). Important modulator in the HLA class II restricted antigen presentation pathway by interaction with the HLA-DM molecule in B-cells.

HLA-DOB belongs to the HLA class II beta chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DOA) and a beta chain (DOB), both anchored in the membrane. It is located in intracellular vesicles. DO suppresses peptide loading of MHC class II molecules by inhibiting HLA-DM. Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages). The beta chain is approximately 26-28 kDa and its gene contains 6 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and exon 5 encodes the cytoplasmic tail.

Source: NCBI Gene 3112 — RefSeq curated summary.

At a glance

  • GWAS associations: 28
  • Clinical variants (ClinVar): 6 total
  • MANE Select transcript: NM_002120

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4937
Approved symbolHLA-DOB
Namemajor histocompatibility complex, class II, DO beta
Location6p21.32
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000241106
Ensembl biotypeprotein_coding
OMIM600629
Entrez3112

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000438763, ENST00000447394, ENST00000475235, ENST00000488325, ENST00000648009, ENST00000900286, ENST00000944925

RefSeq mRNA: 1 — MANE Select: NM_002120 NM_002120

CCDS: CCDS4754

Canonical transcript exons

ENST00000426644 — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 96.70.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 2.7222 / max 515.6970, expressed in 144 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
730152.6799137
730160.029712
730170.01276

Top tissues by expression

136 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
lymph nodeUBERON:000002996.70gold quality
spleenUBERON:000210694.35gold quality
vermiform appendixUBERON:000115491.45gold quality
granulocyteCL:000009490.93gold quality
bone marrow cellCL:000209287.49gold quality
bloodUBERON:000017884.78gold quality
lower esophagus mucosaUBERON:003583483.23gold quality
bone marrowUBERON:000237182.51gold quality
tonsilUBERON:000237281.93gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047380.76gold quality
small intestine Peyer’s patchUBERON:000345480.39gold quality
leukocyteCL:000073879.66gold quality
monocyteCL:000057678.49gold quality
small intestineUBERON:000210878.31gold quality
rectumUBERON:000105278.18gold quality
endometriumUBERON:000129578.04gold quality
gall bladderUBERON:000211074.64gold quality
saliva-secreting glandUBERON:000104474.30gold quality
mucosa of transverse colonUBERON:000499174.27gold quality
minor salivary glandUBERON:000183074.24gold quality
duodenumUBERON:000211472.78gold quality
right lungUBERON:000216772.45gold quality
upper lobe of left lungUBERON:000895272.32gold quality
adenohypophysisUBERON:000219671.48gold quality
esophagus mucosaUBERON:000246971.20gold quality
skin of legUBERON:000151170.39gold quality
zone of skinUBERON:000001470.36gold quality
skin of abdomenUBERON:000141670.29gold quality
pituitary glandUBERON:000000769.99gold quality
quadriceps femorisUBERON:000137769.42gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-8142yes68.21
E-ANND-3yes14.34
E-MTAB-6678yes8.67
E-MTAB-8410no0.94

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CIITA, CREB1, POU2F2, RFX1, RFX5, RFXANK, RFXAP

miRNA regulators (miRDB)

64 targeting HLA-DOB, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4533100.0069.482758
HSA-MIR-548N99.9871.944170
HSA-MIR-185-3P99.9567.011743
HSA-MIR-548AB99.9571.313488
HSA-MIR-55999.9572.283609
HSA-MIR-548I99.9471.253481
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548AS-5P99.9471.223482
HSA-MIR-548AU-5P99.9471.243488
HSA-MIR-548AY-5P99.9471.233502
HSA-MIR-548B-5P99.9471.233502
HSA-MIR-548BB-5P99.9471.273509
HSA-MIR-548C-5P99.9471.243488
HSA-MIR-548D-5P99.9471.233502
HSA-MIR-548H-5P99.9471.243488
HSA-MIR-548J-5P99.9471.143489
HSA-MIR-548O-5P99.9471.243488
HSA-MIR-548W99.9471.243488
HSA-MIR-548Y99.9471.283514
HSA-MIR-589-3P99.9169.622088
HSA-MIR-449699.8868.892236
HSA-MIR-449299.8768.253611
HSA-MIR-6857-5P99.8765.32985

Literature-anchored findings (GeneRIF, showing 9)

  • HLA-DOB mutations were analyzed for association with autoimmune diseases and B-cell leukemias. (PMID:12439622)
  • In transgenic mice expressing human HLA-DOA & HLA-DOB from a DC-specific promoter, as DO increased, A(b)-CLIP increased & class II-peptides decreased. DO impaired H-2M function, causing Ag-specific downmodulation of class II Ag processing/presentation. (PMID:15265882)
  • A new DOB allele, DOB*010103, was identified in the Korean population during sequence-based HLA-DOB typing. (PMID:15730525)
  • results show that HLA-DO inhibits HLA-DM function by acting as a substrate mimic, and the findings also limit the possible functional roles for HLA-DO in antigen presentation (PMID:23222639)
  • HLA-DO beta-chain antigens are ubiquitinated by MARCH family E3 ligases 1, 8, and 9. (PMID:23400868)
  • TAP2, HLA-DOA, HLA-DOB, and tapasin loci are novel candidate regions for susceptibility to HCV infection and viral clearance in the Chinese population (PMID:25874709)
  • results indicate that HLA-DOB is co-inherited with DQA2-B2 genes and thus may contribute to HCV and HBV persistence (PMID:28813660)
  • MUC22, HLA-A, and HLA-DOB variants and COVID-19 in resilient super-agers from Brazil. (PMID:36389712)
  • Potential role of SNP rs2071475 in rheumatoid arthritis and inflammatory bowel disease in the East Asian population: a Mendelian randomization study. (PMID:37855981)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusH2-ObENSMUSG00000041538
rattus_norvegicusRT1-DObENSRNOG00000000454

Paralogs (13): B2M (ENSG00000166710), HLA-DQB1 (ENSG00000179344), HLA-DRB1 (ENSG00000196126), HLA-DQA1 (ENSG00000196735), HLA-DRB5 (ENSG00000198502), HLA-DOA (ENSG00000204252), HLA-DMA (ENSG00000204257), HLA-DRA (ENSG00000204287), HLA-DPB1 (ENSG00000223865), HLA-DPA1 (ENSG00000231389), HLA-DQB2 (ENSG00000232629), HLA-DQA2 (ENSG00000237541), HLA-DMB (ENSG00000242574)

Protein

Protein identifiers

HLA class II histocompatibility antigen, DO beta chainP13765 (reviewed: P13765)

Alternative names: MHC class II antigen DOB

All UniProt accessions (4): E9PI00, P13765, H0Y4X4, Q5QNS2

UniProt curated annotations — full annotation on UniProt →

Function. Important modulator in the HLA class II restricted antigen presentation pathway by interaction with the HLA-DM molecule in B-cells. Modifies peptide exchange activity of HLA-DM.

Subunit / interactions. Heterodimer of an alpha chain (DOA) and a beta chain (DOB). Forms a heterotetrameric complex with an HLA-DM molecule during intracellular transport in endosomal/lysosomal compartments in B-cells.

Subcellular location. Endosome membrane. Lysosome membrane.

Polymorphism. The following alleles of DOB are known: DOB01:01, DOB01:02, DOB01:03 and DOB01:04. The sequence shown is that of DOB*01:01.

Similarity. Belongs to the MHC class II family.

RefSeq proteins (1): NP_002111* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000353MHC_II_b_NDomain
IPR003006Ig/MHC_CSConserved_site
IPR003597Ig_C1-setDomain
IPR007110Ig-like_domDomain
IPR011162MHC_I/II-like_Ag-recogHomologous_superfamily
IPR013783Ig-like_foldHomologous_superfamily
IPR014745MHC_II_a/b_NHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR050160MHC/ImmunoglobulinFamily

Pfam: PF00969, PF07654

UniProt features (36 total): strand 12, helix 5, sequence variant 4, turn 3, region of interest 3, disulfide bond 2, topological domain 2, signal peptide 1, chain 1, transmembrane region 1, domain 1, glycosylation site 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
4I0PX-RAY DIFFRACTION3.2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P13765-F187.440.71

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (2): 41–105, 143–199

Glycosylation sites (1): 45

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-2132295MHC class II antigen presentation

MSigDB gene sets: 274 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_OR_POLYSACCHARIDE_ANTIGEN_VIA_MHC_CLASS_II, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOCC_VACUOLAR_MEMBRANE, GOBP_REGULATION_OF_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN, GOBP_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN, MODULE_143, GOBP_POSITIVE_REGULATION_OF_CELL_ADHESION, GOBP_CELL_CELL_ADHESION, KEGG_VIRAL_MYOCARDITIS, GOBP_REGULATION_OF_IMMUNE_RESPONSE, KEGG_TYPE_I_DIABETES_MELLITUS, GOBP_REGULATION_OF_ANTIGEN_PROCESSING_AND_PRESENTATION, GOBP_ANTIGEN_PROCESSING_AND_PRESENTATION, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5

GO Biological Process (10): adaptive immune response (GO:0002250), peptide antigen assembly with MHC class II protein complex (GO:0002503), negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587), antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886), positive regulation of immune response (GO:0050778), positive regulation of T cell activation (GO:0050870), immune system process (GO:0002376), antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002504), immune response (GO:0006955), antigen processing and presentation (GO:0019882)

GO Molecular Function (3): MHC class II protein complex binding (GO:0023026), MHC class II receptor activity (GO:0032395), peptide antigen binding (GO:0042605)

GO Cellular Component (7): lysosome (GO:0005764), lysosomal membrane (GO:0005765), late endosome membrane (GO:0031902), MHC class II protein complex (GO:0042613), endosome (GO:0005768), endosome membrane (GO:0010008), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Adaptive Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
antigen processing and presentation of peptide antigen via MHC class II3
immune response2
immune system process2
MHC class II protein complex assembly1
peptide antigen assembly with MHC protein complex1
negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II1
negative regulation of antigen processing and presentation of peptide antigen1
regulation of antigen processing and presentation of peptide antigen via MHC class II1
antigen processing and presentation of exogenous peptide antigen1
positive regulation of immune system process1
positive regulation of response to stimulus1
regulation of immune response1
T cell activation1
regulation of T cell activation1
positive regulation of lymphocyte activation1
positive regulation of leukocyte cell-cell adhesion1
biological_process1
antigen processing and presentation1
response to stimulus1
MHC protein complex binding1
transmembrane signaling receptor activity1
MHC class II protein binding1
immune receptor activity1
antigen binding1
peptide binding1
lytic vacuole1
lysosome1
lytic vacuole membrane1
late endosome1
endosome membrane1
MHC protein complex1
endomembrane system1
cytoplasmic vesicle1
endosome1
cytoplasmic vesicle membrane1
bounding membrane of organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

1572 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HLA-DOBPSMB9P28065839
HLA-DOBHLA-DMAP28067835
HLA-DOBPSMB8P28062832
HLA-DOBHLA-BP01889549
HLA-DOBHLA-DQA2P01906527
HLA-DOBHLA-CP04222501
HLA-DOBHLA-DOAP06340486
HLA-DOBTAP1Q03518476
HLA-DOBTNFP01375473
HLA-DOBHLA-DMBP28068465
HLA-DOBRING1Q06587460
HLA-DOBLILRB1Q8NHL6436
HLA-DOBPBX2P40425429
HLA-DOBBRD2P25440426
HLA-DOBHLA-DRAP01903426

IntAct

7 interactions, top by confidence:

ABTypeScore
HLA-DMAHLA-DOApsi-mi:“MI:0915”(physical association)0.590
HLA-DMAHLA-DOApsi-mi:“MI:0407”(direct interaction)0.590
HLA-DMAHLA-DOApsi-mi:“MI:0914”(association)0.590
HLA-DOAHLA-DOBpsi-mi:“MI:0407”(direct interaction)0.440
CDKN2AHLA-DOBpsi-mi:“MI:0915”(physical association)0.370
SLC22A14CLGNpsi-mi:“MI:0914”(association)0.350

BioGRID (4): HLA-DOB (Two-hybrid), HLA-DOB (Affinity Capture-Western), HLA-DOB (Affinity Capture-Western), HLA-DOB (Affinity Capture-MS)

ESM2 similar proteins: C1ITJ8, O19477, O35799, P01901, P01902, P01920, P01921, P04440, P05538, P06339, P06341, P06342, P06343, P06344, P06345, P06346, P13765, P14428, P14429, P14432, P14483, P15464, P15979, P15982, P15983, P16391, P18467, P18469, P18470, P23068, P25311, P29826, P60018, P70387, Q29980, Q29983, Q2KN22, Q30201, Q5RD09, Q63678

Diamond homologs: C1ITJ8, O19477, O35799, P01888, P01889, P01893, P01894, P01895, P01896, P01897, P01898, P01899, P01900, P01901, P01902, P03991, P04223, P04439, P06126, P06140, P06339, P10321, P13747, P13748, P13749, P13750, P13751, P13752, P13753, P13765, P14426, P14427, P14428, P14429, P14430, P14431, P14432, P15464, P15978, P15979

SIGNOR signaling

3 interactions.

AEffectBMechanism
CIITA“up-regulates quantity by expression”HLA-DOB“transcriptional regulation”
RFX1“up-regulates quantity by expression”HLA-DOB“transcriptional regulation”
“RFX complex”“up-regulates quantity by expression”HLA-DOB“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

6 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance0
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1142 predictions. Top by Δscore:

VariantEffectΔscore
6:32814318:A:ACdonor_gain1.0000
6:32814319:C:CCdonor_gain1.0000
6:32814319:CTCCA:Cdonor_gain1.0000
6:32814602:C:CCacceptor_gain1.0000
6:32816855:TCTTA:Tdonor_loss1.0000
6:32816856:CTTA:Cdonor_loss1.0000
6:32816856:CTTAC:Cdonor_loss1.0000
6:32816857:TTACC:Tdonor_loss1.0000
6:32816858:TA:Tdonor_loss1.0000
6:32816858:TAC:Tdonor_loss1.0000
6:32816859:A:Cdonor_loss1.0000
6:32816859:ACC:Adonor_loss1.0000
6:32816860:C:Gdonor_loss1.0000
6:32816948:CCATT:Cacceptor_gain1.0000
6:32816949:CATT:Cacceptor_gain1.0000
6:32816949:CATTC:Cacceptor_gain1.0000
6:32816951:TT:Tacceptor_gain1.0000
6:32816953:C:CCacceptor_gain1.0000
6:32814318:ACT:Adonor_gain0.9900
6:32814319:CT:Cdonor_gain0.9900
6:32814319:CTC:Cdonor_gain0.9900
6:32814344:G:Cdonor_gain0.9900
6:32814437:T:TAdonor_gain0.9900
6:32814598:TGCA:Tacceptor_gain0.9900
6:32814599:GCA:Gacceptor_gain0.9900
6:32814600:CA:Cacceptor_gain0.9900
6:32814600:CAC:Cacceptor_gain0.9900
6:32815039:CTCA:Cdonor_loss0.9900
6:32815040:TCA:Tdonor_loss0.9900
6:32815041:CA:Cdonor_loss0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000128687 (6:32813181 T>A), RS1000928748 (6:32817209 G>A), RS1001263464 (6:32813110 G>A,C), RS1001337250 (6:32813385 C>G,T), RS1001411351 (6:32812377 G>A), RS1002209984 (6:32818667 G>A), RS1002985913 (6:32814583 A>G), RS1004645921 (6:32812331 G>C), RS1004715638 (6:32813051 A>T), RS1005390150 (6:32815815 A>G), RS1005751947 (6:32817152 A>G), RS1005914119 (6:32816468 G>A), RS1006495814 (6:32814897 G>A,C), RS1006792093 (6:32814503 T>C), RS1007072196 (6:32817294 T>C)

Disease associations

OMIM: gene MIM:600629 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

28 associations (top):

StudyTraitp-value
GCST001455_2Kawasaki disease5.000000e-11
GCST001785_9Crohn’s disease9.000000e-59
GCST004521_126Autism spectrum disorder or schizophrenia2.000000e-10
GCST004521_170Autism spectrum disorder or schizophrenia4.000000e-14
GCST004521_296Autism spectrum disorder or schizophrenia6.000000e-18
GCST004521_81Autism spectrum disorder or schizophrenia1.000000e-14
GCST004748_116Lung cancer1.000000e-11
GCST004749_11Lung cancer in ever smokers1.000000e-10
GCST004750_63Squamous cell lung carcinoma2.000000e-10
GCST005541_24Sarcoidosis (Lofgren’s syndrome vs non-Lofgren’s syndrome)4.000000e-11
GCST006575_22Takayasu arteritis2.000000e-10
GCST006867_50Type 2 diabetes7.000000e-11
GCST007201_152Schizophrenia4.000000e-12
GCST007564_33Asthma or allergic disease (pleiotropy)8.000000e-35
GCST008916_16Asthma3.000000e-17
GCST008916_27Asthma5.000000e-31
GCST008916_90Asthma4.000000e-15
GCST008921_2Asthma and major depressive disorder3.000000e-13
GCST010979_15Kawasaki disease7.000000e-13
GCST011940_11Bullous pemphigoid7.000000e-06
GCST012227_798Hip circumference adjusted for BMI2.000000e-10
GCST012228_259Waist-hip index3.000000e-14
GCST012230_444Waist-to-hip ratio adjusted for BMI1.000000e-15
GCST012231_216A body shape index1.000000e-08
GCST90002388_83Lymphocyte count1.000000e-11
GCST90020024_1108A body shape index1.000000e-09
GCST90020024_1112A body shape index3.000000e-09
GCST90020028_1278Hip circumference adjusted for BMI9.000000e-09

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0008039BMI-adjusted hip circumference
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0007789BMI-adjusted waist circumference
EFO:0004587lymphocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2071554HLA-DOB0.000

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression, decreases methylation2
Nickelincreases expression2
TL8-506affects cotreatment, increases expression1
Meropenemaffects expression1
Aldehydesincreases expression1
Benzalkonium Compoundsaffects response to substance1
Hydralazineaffects cotreatment, increases expression1
Poly I-Cincreases expression, affects cotreatment1
Tobacco Smoke Pollutionincreases expression1
Trimethoprimaffects expression1
Valproic Acidaffects cotreatment, increases expression1
Mifepristonedecreases expression1
Antirheumatic Agentsdecreases expression1
Okadaic Acidincreases expression1

Cellosaurus cell lines

2 cell lines: 2 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_C5VJLG2 DO-KO-1Transformed cell lineMale
CVCL_C5VKLG2 DO-KO-2Transformed cell lineMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.