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

Gene ID: 3119, updated on 7-Aug-2022

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
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Genomic context

See HLA-DQB1 in Genome Data Viewer
Location:
6p21.32
Exon count:
6
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32659467..32666657, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (32482491..32489842, complement)
105.20220307 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 uncharacterized LOC124901301 Neighboring gene major histocompatibility complex, class II, DQ alpha 1 Neighboring gene HLA-DQB1 antisense RNA 1 Neighboring gene MT-CO3 pseudogene 1 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

Associated conditions

Description Tests
Celiac disease, susceptibility to, 1
MedGen: C1859310 OMIM: 212750 GeneReviews: Celiac Disease
not available
Inherited Creutzfeldt-Jakob disease
MedGen: C0751254 OMIM: 123400 GeneReviews: Genetic Prion Disease
Compare labs
Multiple sclerosis, susceptibility to
MedGen: C1868685 OMIM: 126200 GeneReviews: Not available
Compare labs

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

Homology

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
PubMed 
enables MHC class II receptor activity NAS
Non-traceable Author Statement
more info
PubMed 
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
PubMed 
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
 
located_in endosome membrane IEA
Inferred from Electronic Annotation
more info
 
located_in integral component of lumenal side of endoplasmic reticulum membrane TAS
Traceable Author Statement
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
    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/Swiss-Prot
    P01920
    UniProtKB/TrEMBL
    Q5Y7D3
    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/Swiss-Prot
    P01920
    UniProtKB/TrEMBL
    Q5Y7A9, Q5Y7D6
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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)