HLA-DMB belongs to the HLA class II beta chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DMA) and a beta (DMB) chain, both anchored in the membrane. It is located in intracellular vesicles. DM plays a central role in the peptide loading of MHC class II molecules by helping to release the CLIP (class II-associated invariant chain peptide) molecu... See more...

Aliases for HLA-DMB Gene

Aliases for HLA-DMB Gene

  • Major Histocompatibility Complex, Class II, DM Beta 2 3 5
  • RING7 2 3 4
  • HLA Class II Histocompatibility Antigen, DM Beta Chain 3 4
  • Really Interesting New Gene 7 Protein 3 4
  • MHC Class II Antigen DMB 3 4
  • D6S221E 2 3
  • Class II Histocompatibility Antigen, M Beta Chain 3
  • MHC Class II Antigen HLA-DM Beta Chain 3
  • MHC Class II HLA-DMB 3
  • HLA-DMB 5
  • DMB 4

External Ids for HLA-DMB Gene

Previous GeneCards Identifiers for HLA-DMB Gene

  • GC06M032899
  • GC06M032673
  • GC06M032949
  • GC06M033010
  • GC06Mf32973
  • GC06M032903
  • GC06M032644

Summaries for HLA-DMB Gene

Entrez Gene Summary for HLA-DMB Gene

  • HLA-DMB belongs to the HLA class II beta chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DMA) and a beta (DMB) chain, both anchored in the membrane. It is located in intracellular vesicles. DM plays a central role in the peptide loading of MHC class II molecules by helping to release the CLIP (class II-associated invariant chain peptide) molecule from the peptide binding site. 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. [provided by RefSeq, Jul 2008]

GeneCards Summary for HLA-DMB Gene

HLA-DMB (Major Histocompatibility Complex, Class II, DM Beta) is a Protein Coding gene. Diseases associated with HLA-DMB include Rheumatoid Arthritis and Type 1 Diabetes Mellitus. Among its related pathways are Rheumatoid arthritis and Allograft rejection. Gene Ontology (GO) annotations related to this gene include MHC class II protein complex binding. An important paralog of this gene is ENSG00000248993.

UniProtKB/Swiss-Prot Summary for HLA-DMB Gene

  • Plays a critical role in catalyzing the release of class II-associated invariant chain peptide (CLIP) from newly synthesized MHC class II molecules and freeing the peptide binding site for acquisition of antigenic peptides. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO.

Gene Wiki entry for HLA-DMB Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HLA-DMB Gene

Genomics for HLA-DMB Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HLA-DMB Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HLA-DMB on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HLA-DMB

Top Transcription factor binding sites by QIAGEN in the HLA-DMB gene promoter:
  • AML1a
  • C/EBPalpha
  • GCNF
  • GCNF-1
  • GCNF-2
  • MyoD
  • SRY
  • TBP
  • TFIID

Genomic Locations for HLA-DMB Gene

Latest Assembly
chr6:32,934,629-32,941,028
(GRCh38/hg38)
Size:
6,400 bases
Orientation:
Minus strand

Previous Assembly
chr6:32,902,413-32,908,805
(GRCh37/hg19 by Entrez Gene)
Size:
6,393 bases
Orientation:
Minus strand

chr6:32,902,406-32,908,847
(GRCh37/hg19 by Ensembl)
Size:
6,442 bases
Orientation:
Minus strand

Alternative Locations (GRCh38/hg38)

  • chr6(ALT_REF_LOCI_1):4,239,481-4,245,873 (-)
  • chr6(ALT_REF_LOCI_2):4,346,831-4,353,223 (-)
  • chr6(ALT_REF_LOCI_3):4,178,165-4,184,557 (-)
  • chr6(ALT_REF_LOCI_4):4,354,004-4,360,396 (-)
  • chr6(ALT_REF_LOCI_5):4,233,679-4,240,071 (-)
  • chr6(ALT_REF_LOCI_6):4,128,944-4,135,335 (-)
  • chr6(ALT_REF_LOCI_7):4,333,869-4,340,261 (-)

Genomic View for HLA-DMB Gene

Genes around HLA-DMB on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HLA-DMB Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HLA-DMB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for HLA-DMB Gene

  • Protein details for HLA-DMB Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P28068-DMB_HUMAN
    Recommended name:
    HLA class II histocompatibility antigen, DM beta chain
    Protein Accession:
    P28068
    Secondary Accessions:
    • O77936
    • Q13012
    • Q29751
    • Q58ZE2
    • Q5SNZ8
    • Q5STC4
    • Q9XRX2

    Protein attributes for HLA-DMB Gene

    Size:
    263 amino acids
    Molecular mass:
    28943 Da
    Quaternary structure:
    • Heterodimer of an alpha chain (DMA) and a beta chain (DMB) (PubMed:16547258, PubMed:9768757). Interacts with MHCII; this interaction mediates rapid selection of high-affinity peptides in a pH-dependent manner, with an optimum at pH 5.5 (PubMed:23260142).

    Three dimensional structures from OCA and Proteopedia for HLA-DMB Gene

neXtProt entry for HLA-DMB Gene

Post-translational modifications for HLA-DMB Gene

  • Glycosylation at Asn110
  • Modification sites at PhosphoSitePlus

Other Protein References for HLA-DMB Gene

No data available for DME Specific Peptides for HLA-DMB Gene

Domains & Families for HLA-DMB Gene

Gene Families for HLA-DMB Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for HLA-DMB Gene

InterPro:
Blocks:
  • Immunoglobulin C-type
  • Class II histocompatibility antigen, beta chain, beta-1 domain

Suggested Antigen Peptide Sequences for HLA-DMB Gene

GenScript: Design optimal peptide antigens:
  • Major histocompatibility complex, class II, DM beta (A2AAT1_HUMAN)
  • Major histocompatibility complex, class II, DM beta (A2AAT2_HUMAN)
  • Major histocompatibility complex, class II, DM beta (A2AAT6_HUMAN)
  • Major histocompatibility complex, class II, DM beta (A2ABH7_HUMAN)
  • Major histocompatibility complex, class II, DM beta (A2ABI3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P28068

UniProtKB/Swiss-Prot:

DMB_HUMAN :
  • The YXXZ (Tyr-Xaa-Xaa-Zaa, where Zaa is a hydrophobic residue) motif mediates the targeting to the lysosomal compartments.
  • Belongs to the MHC class II family.
Domain:
  • The YXXZ (Tyr-Xaa-Xaa-Zaa, where Zaa is a hydrophobic residue) motif mediates the targeting to the lysosomal compartments.
Family:
  • Belongs to the MHC class II family.
genes like me logo Genes that share domains with HLA-DMB: view

Function for HLA-DMB Gene

Molecular function for HLA-DMB Gene

UniProtKB/Swiss-Prot Function:
Plays a critical role in catalyzing the release of class II-associated invariant chain peptide (CLIP) from newly synthesized MHC class II molecules and freeing the peptide binding site for acquisition of antigenic peptides. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO.
GENATLAS Biochemistry:
HLA-DM,beta chain,class II related,expressed in B cell lysosomes,same as RING7

Phenotypes From GWAS Catalog for HLA-DMB Gene

Gene Ontology (GO) - Molecular Function for HLA-DMB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21131964
GO:0023026 MHC class II protein complex binding IDA 9075930
genes like me logo Genes that share ontologies with HLA-DMB: view
genes like me logo Genes that share phenotypes with HLA-DMB: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HLA-DMB

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for HLA-DMB Gene

Localization for HLA-DMB Gene

Subcellular locations from UniProtKB/Swiss-Prot for HLA-DMB Gene

Late endosome membrane. Single-pass type I membrane protein. Lysosome membrane. Single-pass type I membrane protein. Note=Localizes to late endocytic compartment. Associates with lysosome membranes.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HLA-DMB gene
Compartment Confidence
plasma membrane 5
endosome 4
lysosome 4
extracellular 3
endoplasmic reticulum 2
cytoskeleton 1
mitochondrion 1
nucleus 1
cytosol 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HLA-DMB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane TAS --
GO:0005768 endosome IEA --
GO:0010008 endosome membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with HLA-DMB: view

Pathways & Interactions for HLA-DMB Gene

PathCards logo

SuperPathways for HLA-DMB Gene

SuperPathway Contained pathways
1 Allograft rejection
.44
.39
.38
2 Th17 cell differentiation
.36
3 ICos-ICosL Pathway in T-Helper Cell
.66
.66
.31
4 TCR Signaling (Qiagen)
.68
.68
.54
5 Immune response NFAT in immune response
.56
.56
.52
genes like me logo Genes that share pathways with HLA-DMB: view

Pathways by source for HLA-DMB Gene

6 GeneGo (Thomson Reuters) pathways for HLA-DMB Gene
  • G-protein signaling N-RAS regulation pathway
  • Immune response Antigen presentation by MHC class II
  • Immune response ICOS pathway in T-helper cell
  • Immune response IL-22 signaling pathway
  • Immune response NFAT in immune response
12 Qiagen pathways for HLA-DMB Gene
  • Calcium Mediated T-Cell Apoptosis
  • CD28 Signaling in T-Helper Cell
  • CDC42 Pathway
  • CTL Mediated Apoptosis
  • CTLA4 Signaling

SIGNOR curated interactions for HLA-DMB Gene

Is activated by:

Gene Ontology (GO) - Biological Process for HLA-DMB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0002399 MHC class II protein complex assembly IMP 8139689
GO:0002503 peptide antigen assembly with MHC class II protein complex IDA 7606781
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II IEA --
genes like me logo Genes that share ontologies with HLA-DMB: view

Drugs & Compounds for HLA-DMB Gene

(1) Additional Compounds for HLA-DMB Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HLA-DMB: view

Transcripts for HLA-DMB Gene

mRNA/cDNA for HLA-DMB Gene

1 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HLA-DMB

Alternative Splicing Database (ASD) splice patterns (SP) for HLA-DMB Gene

No ASD Table

Relevant External Links for HLA-DMB Gene

GeneLoc Exon Structure for
HLA-DMB

Expression for HLA-DMB Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HLA-DMB Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HLA-DMB Gene

This gene is overexpressed in Spleen (x5.9).

Protein differential expression in normal tissues from HIPED for HLA-DMB Gene

This gene is overexpressed in Blymphocyte (25.1) and Lymph node (11.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for HLA-DMB Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HLA-DMB

SOURCE GeneReport for Unigene cluster for HLA-DMB Gene:

Hs.351279

Evidence on tissue expression from TISSUES for HLA-DMB Gene

  • Blood(4.6)
  • Bone marrow(4.3)
  • Spleen(3)
  • Lymph node(2.5)
  • Lung(2.4)
genes like me logo Genes that share expression patterns with HLA-DMB: view

Primer products for research

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HLA-DMB Gene

Orthologs for HLA-DMB Gene

This gene was present in the common ancestor of chordates.

Orthologs for HLA-DMB Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PATR-DMB 29 30
  • 99.11 (n)
OneToMany
Dog
(Canis familiaris)
Mammalia DLA-DMB 29
  • 82.45 (n)
-- 30
  • 78 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia BOLA-DMB 29
  • 79.89 (n)
HLA-DMB 30
  • 74 (a)
OneToMany
Mouse
(Mus musculus)
Mammalia H2-DMb2 29 16 30
  • 79.08 (n)
ManyToMany
H2-DMb1 16 30
  • 72 (a)
ManyToMany
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 61 (a)
OneToMany
Chicken
(Gallus gallus)
Aves BMA2 29
  • 54.18 (n)
-- 30
  • 29 (a)
ManyToMany
-- 30
  • 28 (a)
ManyToMany
BLB1 30
  • 25 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 26 (a)
ManyToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100495183 29
  • 47.12 (n)
Zebrafish
(Danio rerio)
Actinopterygii si:zfos-2070c2.3 30
  • 33 (a)
ManyToMany
mhc2dbb 30
  • 25 (a)
ManyToMany
si:busm1-228j01.4 30
  • 23 (a)
ManyToMany
wu:fd58b11 30
  • 22 (a)
ManyToMany
mhc2dab 30
  • 22 (a)
ManyToMany
si:busm1-194e12.12 30
  • 21 (a)
ManyToMany
si:busm1-104n07.3 30
  • 20 (a)
ManyToMany
si:dkey-33b17.3 30 30
  • 19 (a)
ManyToMany
si:busm1-228j01.6 30
  • 19 (a)
ManyToMany
Species where no ortholog for HLA-DMB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for HLA-DMB Gene

ENSEMBL:
Gene Tree for HLA-DMB (if available)
TreeFam:
Gene Tree for HLA-DMB (if available)
Alliance of Genome Resources:
Additional Orthologs for HLA-DMB

Paralogs for HLA-DMB Gene

genes like me logo Genes that share paralogs with HLA-DMB: view

Variants for HLA-DMB Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for HLA-DMB Gene

DMB_HUMAN-P28068
The following alleles of DMB are known: DMB*01:01, DMB*01:02, DMB*01:03, DMB*01:04 (DMB3.4), DMB*01:05, DMB*01:06, and DMB*01:07. The sequence shown is that of DMB*01:01.

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HLA-DMB Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs1042337 -- p.Ile197Thr
rs17583782 -- p.Thr28Ala
rs17617321 -- p.Ser71Asn
rs17617333 -- p.Asp49Val
rs2071555 -- p.Ala162Glup.Ala162Val

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for HLA-DMB Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for HLA-DMB Gene

Variant ID Type Subtype PubMed ID
esv2759417 CNV gain 17122850
esv33619 CNV gain 17666407
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1119076 CNV deletion 24896259
nsv1161376 CNV duplication 26073780
nsv483081 CNV loss 15286789
nsv819732 CNV loss 19587683
nsv830633 CNV loss 17160897

Variation tolerance for HLA-DMB Gene

Residual Variation Intolerance Score: 77.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.57; 56.04% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HLA-DMB Gene

Human Gene Mutation Database (HGMD)
HLA-DMB
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HLA-DMB
Leiden Open Variation Database (LOVD)
HLA-DMB

SNP Genotyping and Copy Number Assays for research

Disorders for HLA-DMB Gene

MalaCards: The human disease database

(4) MalaCards diseases for HLA-DMB Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HLA-DMB

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with HLA-DMB: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HLA-DMB Gene

Publications for HLA-DMB Gene

  1. HLA-DM polymorphism and risk of trichloroethylene induced medicamentosa-like dermatitis. (PMID: 18348411) Yue F … Chen XM (Biomedical and environmental sciences : BES 2007) 3 22 40
  2. Association of HLA-DM polymorphism with the production of antiphospholipid antibodies. (PMID: 15547089) Sanchez ML … Khamashta MA (Annals of the rheumatic diseases 2004) 3 22 40
  3. Association of TAP and HLA-DM genes with psoriasis in Koreans. (PMID: 12648225) Pyo CW … Kim TG (The Journal of investigative dermatology 2003) 3 22 40
  4. Polymorphisms of TAP, LMP and HLA-DM genes in the Chinese. (PMID: 11775239) Zhu X … Wang F (Chinese medical journal 2000) 3 22 40
  5. A new human HLA class II-related locus, DM. (PMID: 1922365) Kelly AP … Trowsdale J (Nature 1991) 2 3 4

Products for HLA-DMB Gene

Sources for HLA-DMB Gene