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

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: all
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Genomic context

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_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HLA-DQA1*01:03 and DQB1*06:01 are risk factors for severe COVID-19 pneumonia.
Title: HLA-DQA1*01:03 and DQB1*06:01 are risk factors for severe COVID-19 pneumonia.
The protective association of HLA-C*12:02 and HLA-DQB1*06:01 with severe acute hepatitis of unknown origin in the Japanese population.
Title: The protective association of HLA-C*12:02 and HLA-DQB1*06:01 with severe acute hepatitis of unknown origin in the Japanese population.
HLA-DQB1 Allele Polymorphism Associated with Oral Submucous Fibrosis in Hunan, China.
Title: HLA-DQB1 Allele Polymorphism Associated with Oral Submucous Fibrosis in Hunan, China.
Genome-Wide Association Study Identifies IFIH1 and HLA-DQB1*05:02 Loci Associated With Anti-NMDAR Encephalitis.
Title: Genome-Wide Association Study Identifies IFIH1 and HLA-DQB1*05:02 Loci Associated With Anti-NMDAR Encephalitis.
The protective association of HLA-B *52:01, HLA-C *12:02, and DQB1 *06:01 alleles with severe acute hepatitis of unknown origin in Japanese children.
Title: The protective association of HLA-B∗52:01, HLA-C∗12:02, and DQB1∗06:01 alleles with severe acute hepatitis of unknown origin in Japanese children.
A Celiac Gene HLA-DQB1 *02:01 Is Associated with Linear IgA Bullous Dermatosis in the Chinese Population.
Title: A Celiac Gene HLA-DQB1∗02:01 Is Associated with Linear IgA Bullous Dermatosis in the Chinese Population.
HLA-C*07:01 and HLA-DQB1*02:01 protect against white matter hyperintensities and deterioration of cognitive function: A population-based cohort study.
Title: HLA-C*07:01 and HLA-DQB1*02:01 protect against white matter hyperintensities and deterioration of cognitive function: A population-based cohort study.
Epigenome-wide methylation haplotype association analysis identified HLA-DRB1, HLA-DRB5 and HLA-DQB1 as risk factors for rheumatoid arthritis.
Title: Epigenome-wide methylation haplotype association analysis identified HLA-DRB1, HLA-DRB5 and HLA-DQB1 as risk factors for rheumatoid arthritis.
Association between Human Leukocyte Antigen (HLA) DQB1*06 and HLA DQB1*03 and adverse outcomes in a group of critically ill patients with COVID-19 in Tunisia: a cross-sectional study.
Title: Association between Human Leukocyte Antigen (HLA) DQB1*06 and HLA DQB1*03 and adverse outcomes in a group of critically ill patients with COVID-19 in Tunisia: a cross-sectional study.
Role of HLA-DQB1 alleles in the risk, signs and symptoms, and severity of celiac disease in a Venezuelan population.
Title: Role of HLA-DQB1 alleles in the risk, signs and symptoms, and severity of celiac disease in a Venezuelan population.

Submit: New GeneRIF Correction See all GeneRIFs (566)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-K02405 (e-PCR)
- UniSTS:64780

D6S2202 (e-PCR)
- UniSTS:44624

RH36565 (e-PCR)
- UniSTS:79192

RH46706 (e-PCR)
- UniSTS:863

D6S1841 (e-PCR)
- UniSTS:55662

D6S2447 (e-PCR)
- UniSTS:480411

RH69385 (e-PCR)
- UniSTS:15520

HLA-DQB1_3386 (e-PCR)
- UniSTS:462246

RH80803 (e-PCR)
- UniSTS:85674

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

Process	Evidence Code	Pubs
involved_in T cell receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
involved_in antigen processing and presentation of exogenous peptide antigen via MHC class II	IBA Inferred from Biological aspect of Ancestor more info
involved_in antigen processing and presentation of exogenous peptide antigen via MHC class II	IDA Inferred from Direct Assay more info	PubMed
involved_in humoral immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in immune response	NAS Non-traceable Author Statement more info	PubMed
involved_in peptide antigen assembly with MHC class II protein complex	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of T cell activation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of immune response	IBA Inferred from Biological aspect of Ancestor more info

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 more info	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

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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)

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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

NG_029922.1 RefSeqGene

Range

5001..12601

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001243961.2 → NP_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:45 → 117

MHC_II_beta; Class II histocompatibility antigen, beta domain

cd21001
Location:126 → 222

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
NM_001243962.1 → NP_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:45 → 117

MHC_II_beta; Class II histocompatibility antigen, beta domain

cd21001
Location:126 → 222

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
NM_002123.5 → NP_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:45 → 117

MHC_II_beta; Class II histocompatibility antigen, beta domain

cd21001
Location:126 → 222

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