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    HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [ Homo sapiens (human) ]

    Gene ID: 3119, updated on 9-Dec-2024

    Summary

    Official Symbol
    HLA-DQB1provided by HGNC
    Official Full Name
    major histocompatibility complex, class II, DQ beta 1provided by HGNC
    Primary source
    HGNC:HGNC:4944
    See related
    Ensembl:ENSG00000179344 MIM:604305; AllianceGenome:HGNC:4944
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    IDDM1; CELIAC1; HLA-DQB
    Summary
    HLA-DQB1 belongs to the HLA class II beta chain paralogs. This class II molecule is a heterodimer consisting of an alpha (DQA) and a beta chain (DQB), both anchored in the membrane. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages). The beta chain is approximately 26-28 kDa and it contains six exons. Exon 1 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. Within the DQ molecule both the alpha chain and the beta chain contain the polymorphisms specifying the peptide binding specificities, resulting in up to four different molecules. Typing for these polymorphisms is routinely done for bone marrow transplantation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]
    Expression
    Broad expression in lung (RPKM 158.2), lymph node (RPKM 135.4) and 19 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HLA-DQB1 in Genome Data Viewer
    Location:
    6p21.32
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32659467..32666657, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (32482491..32489842, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32627244..32634434, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene major histocompatibility complex, class II, DR beta 1 Neighboring gene HLA-DQA1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24360 Neighboring gene major histocompatibility complex, class II, DQ alpha 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:32623606-32624294 Neighboring gene HLA-DQB1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32632197-32632724 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32682862 Neighboring gene MT-CO3 pseudogene 1 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32685380 Neighboring gene uncharacterized LOC102725019

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.
    EBI GWAS Catalog
    A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population.
    EBI GWAS Catalog
    A genome-wide association study of chronic hepatitis B identified novel risk locus in a Japanese population.
    EBI GWAS Catalog
    A genome-wide association study reveals ARL15, a novel non-HLA susceptibility gene for rheumatoid arthritis in North Indians.
    EBI GWAS Catalog
    A genome-wide integrative genomic study localizes genetic factors influencing antibodies against Epstein-Barr virus nuclear antigen 1 (EBNA-1).
    EBI GWAS Catalog
    A genome-wide meta-analysis of nodular sclerosing Hodgkin lymphoma identifies risk loci at 6p21.32.
    EBI GWAS Catalog
    A meta-analysis of genome-wide association studies for serum total IgE in diverse study populations.
    EBI GWAS Catalog
    Genome wide analysis of narcolepsy in China implicates novel immune loci and reveals changes in association prior to versus after the 2009 H1N1 influenza pandemic.
    EBI GWAS Catalog
    Genome-wide association analysis identifies 11 risk variants associated with the asthma with hay fever phenotype.
    EBI GWAS Catalog
    Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
    EBI GWAS Catalog
    Genome-wide association study for serum complement C3 and C4 levels in healthy Chinese subjects.
    EBI GWAS Catalog
    Genome-wide association study identifies susceptibility loci for IgA nephropathy.
    EBI GWAS Catalog
    Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population.
    EBI GWAS Catalog
    Genome-wide association study of follicular lymphoma identifies a risk locus at 6p21.32.
    EBI GWAS Catalog
    Genome-wide association study of HPV seropositivity.
    EBI GWAS Catalog
    Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus.
    EBI GWAS Catalog
    Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
    EBI GWAS Catalog
    Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis.
    EBI GWAS Catalog
    GWAS of follicular lymphoma reveals allelic heterogeneity at 6p21.32 and suggests shared genetic susceptibility with diffuse large B-cell lymphoma.
    EBI GWAS Catalog
    HLA-DQB1*03 confers susceptibility to chronic hepatitis C in Japanese: a genome-wide association study.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog
    Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy.
    EBI GWAS Catalog
    Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization.
    EBI GWAS Catalog
    Multiple common variants for celiac disease influencing immune gene expression.
    EBI GWAS Catalog
    New sequence variants in HLA class II/III region associated with susceptibility to knee osteoarthritis identified by genome-wide association study.
    EBI GWAS Catalog
    Novel associations for hypothyroidism include known autoimmune risk loci.
    EBI GWAS Catalog
    Novel risk loci for rheumatoid arthritis in Han Chinese and congruence with risk variants in Europeans.
    EBI GWAS Catalog
    Oligoclonal band status in Scandinavian multiple sclerosis patients is associated with specific genetic risk alleles.
    EBI GWAS Catalog
    Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants.
    EBI GWAS Catalog
    Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies.
    EBI GWAS Catalog
    Susceptibility to amoxicillin-clavulanate-induced liver injury is influenced by multiple HLA class I and II alleles.
    EBI GWAS Catalog
    Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study.
    EBI GWAS Catalog
    Variants within the immunoregulatory CBLB gene are associated with multiple sclerosis.
    EBI GWAS Catalog
    Variation at HLA-DRB1 is associated with resistance to enteric fever.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Amino acid residues 42-49 in the V1 region of CD4 are involved in the interaction between HIV-1 gp120 and class II major histocompatibility complex molecules PubMed
    env HIV envelope protein gp120 can specifically inhibit CD4-dependent class II MHC-restricted T cell response to Ag PubMed
    Envelope surface glycoprotein gp160, precursor env Processing of HIV-1 gp160 to gp120 and gp41 is necessary for the association of HIV-1 envelope glycoproteins with class II MHC PubMed
    Envelope transmembrane glycoprotein gp41 env Soluble HIV-1 gp41 enhancement effects on MHC class I and II antigen expression can be inhibited by soluble gp41-binding proteins of 45, 49 and 62 kD from human B cells PubMed
    env Soluble HIV-1 gp41 can selectively enhance MHC class I and II expression on human B cells, but does not increase expression of other cell surface antigens such as CD21 and CD54 (ICAM-1) PubMed
    env A 43-amino-acid sequence between amino acids 708 and 750 in the HIV-1 gp41(TM) cytoplasmic tail is required for efficient incorporation of HLA class II proteins into virions PubMed
    Nef nef Expression of patient-derived HIV-1 nef alleles downregulates MHC-II cell surface expression in activated CD4+ T cells PubMed
    nef HIV-1 group N and group O Nef alleles only weakly downregulate CD4, CD28, and class I and II MHC molecules PubMed
    nef HIV-1 Nef expression inhibits MHC II presentation of viral antigens in infected antigen-presenting cells PubMed
    nef Nef-triggered MHCII endocytosis requires Rab5 activity and lyst function, whereas lysosomal trafficking of internalized MHCII molecules requires Rab7 activity PubMed
    Pr55(Gag) gag HIV-1 Gag virus-like particles efficiently activate human monocyte-derived dendritic cells (MDDC) and induce MDDC maturation with an associated increase in the surface expression of CD80, CD86 and MHC classes I and II PubMed
    gag Two peptides of the CA domain of HIV-1 Gag, VDRFYKTLRAEQASQ and DRFYKLTRAEQASQ, are presented on MHC II molecules of dendritic cells and have similar sensitivity for antigen-specific T cells PubMed
    gag HIV-1 Gag virus-like particle-induced monocyte activation is shown by upregulation of molecules involved in antigen presentation (MHC II, CD80, CD86) and cell adhesion (CD54) PubMed
    Tat tat HIV-1 Tat downregulates expression of MHC class II genes in antigen-presenting cells (APC) by inhibiting the transactivator of MHC class II genes, CIITA PubMed
    Vif vif HIV-1 Vif downregulates the expression of major histocompatibility complex, class II, DQ beta 1 (HLA-DQB1) in Vif-expression T cells PubMed
    Vpu vpu HIV-1 Vpu interacts with CD74 and modulates MHC II in HIV-1-infected cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables MHC class II protein complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables MHC class II receptor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables peptide antigen binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables peptide antigen binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in ER to Golgi transport vesicle membrane TAS
    Traceable Author Statement
    more info
     
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
     
    part_of MHC class II protein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of MHC class II protein complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in clathrin-coated endocytic vesicle membrane TAS
    Traceable Author Statement
    more info
     
    located_in endocytic vesicle membrane TAS
    Traceable Author Statement
    more info
     
    is_active_in late endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lumenal side of endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
     
    located_in membrane HDA PubMed 
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in trans-Golgi network membrane TAS
    Traceable Author Statement
    more info
     
    located_in transport vesicle membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    HLA class II histocompatibility antigen, DQ beta 1 chain
    Names
    MHC class II DQ beta chain
    MHC class II HLA-DQ beta glycoprotein
    MHC class II antigen DQB1
    MHC class II antigen HLA-DQ-beta-1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_029922.1 RefSeqGene

      Range
      5001..12601
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001243961.2NP_001230890.1  HLA class II histocompatibility antigen, DQ beta 1 chain isoform 2 precursor

      See identical proteins and their annotated locations for NP_001230890.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) includes an alternate in-frame exon in the coding region, compared to variant 1. It encodes isoform 2 which is longer than isoform 1. This transcript represents the DQB1*06:02:01:01 allele of the HLA-DQB1 gene, as represented in the assembled chromosome 6 in the primary assembly of the reference genome.
      Source sequence(s)
      AL662789
      Consensus CDS
      CCDS59006.1
      UniProtKB/TrEMBL
      A0A0I9N852, A0A182AUA9, A0A5C0C6F6, A0A7R8ND50, Q5SU54
      Related
      ENSP00000364080.4, ENST00000374943.8
      Conserved Domains (2) summary
      pfam00969
      Location:45117
      MHC_II_beta; Class II histocompatibility antigen, beta domain
      cd21001
      Location:126222
      IgC1_MHC_II_beta_HLA-DQ_I-A; Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and I-A; member of the C1-set of Ig superfamily (IgSF) domains
    2. NM_001243962.1NP_001230891.1  HLA class II histocompatibility antigen, DQ beta 1 chain isoform 1 precursor

      See identical proteins and their annotated locations for NP_001230891.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has the same exon combination as variant 1 but represents the DQB1*02:01:01:01 allele of the HLA-DQB1 gene, as represented in the alternate locus group ALT_REF_LOCI_2 of the reference genome. It encodes isoform 1.
      Source sequence(s)
      AL731683
      UniProtKB/TrEMBL
      A0A0U5IHY9, A0A0U5KKN5, A0A0U5PZE4, A0A0U5Q0N0, A0A0U5Q141, A0A346XQV6, A0A6S6WVL2, A0A6S6WWB2, A0A6S6WWB8, A0A6S6X6D7, A0A6V6XY56, A0A6V6XY77, Q30096, Q5Y7D3, U3Q031
      Conserved Domains (2) summary
      pfam00969
      Location:45117
      MHC_II_beta; Class II histocompatibility antigen, beta domain
      cd21001
      Location:126222
      IgC1_MHC_II_beta_HLA-DQ_I-A; Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and I-A; member of the C1-set of Ig superfamily (IgSF) domains
    3. NM_002123.5NP_002114.3  HLA class II histocompatibility antigen, DQ beta 1 chain isoform 1 precursor

      See identical proteins and their annotated locations for NP_002114.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the predominant transcript and encodes isoform 1. This transcript represents the DQB1*06:02:01:01 allele of the HLA-DQB1 gene, as represented in the assembled chromosome 6 in the primary assembly of the reference genome.
      Source sequence(s)
      AK296613, BF510934, M20432
      Consensus CDS
      CCDS43451.1
      UniProtKB/TrEMBL
      A0A0U5II17, A0A0U5PZ81, A0A0U5Q221, A0A0U5QLX2, A0A146BIB8, A0A182AT06, A0A182AT43, A0A182ATM8, A0A182ATY6, A0A2S0RR36, A0A2S0RR37, A0A2S0RR51, A0A2S0RR52, A0A2S0RR65, A0A2S0RR73, A0A5P8NK23, A0A6S6WXH0, A0A7S7YJM2, A0A891XKH8, Q5Y7D6, U3PXY6, U3PYN4, U3PYN7, U3Q055, U3Q229, U3Q232
      Related
      ENSP00000407332.2, ENST00000434651.7
      Conserved Domains (2) summary
      pfam00969
      Location:45117
      MHC_II_beta; Class II histocompatibility antigen, beta domain
      cd21001
      Location:126222
      IgC1_MHC_II_beta_HLA-DQ_I-A; Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and I-A; member of the C1-set of Ig superfamily (IgSF) domains

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      32659467..32666657 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      4072405..4080005 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      3900293..3907537 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      4076914..4084511 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      3955831..3963184 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      3853369..3860969 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      4056695..4063940 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      32482491..32489842 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)