HLA-DPB1 major histocompatibility complex, class II, DP beta 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HLA-DPB1provided by HGNC
Official Full Name: major histocompatibility complex, class II, DP beta 1provided by HGNC
Primary source: HGNC:HGNC:4940
See related: Ensembl:ENSG00000223865 MIM:142858; AllianceGenome:HGNC:4940
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: DPB1; HLA-DP; HLA-DPB; HLA-DP1B
Summary: HLA-DPB belongs to the HLA class II beta chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DPA) and a beta chain (DPB), 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 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. Within the DP molecule both the alpha chain and the beta chain contain the polymorphisms specifying the peptide binding specificities, resulting in up to 4 different molecules. [provided by RefSeq, Jul 2008]
Expression: Broad expression in spleen (RPKM 88.0), lymph node (RPKM 85.6) and 22 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_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (33075990..33089696)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (32897341..32911047)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (33043767..33057473)

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:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HLA sequencing identifies novel associations and suggests clinical relevance of DPB1*04:01 in ANCA-associated Granulomatosis with polyangiitis.
Title: HLA sequencing identifies novel associations and suggests clinical relevance of DPB1*04:01 in ANCA-associated Granulomatosis with polyangiitis.
The novel HLA-DPB1 allele, HLA-DPB1*1344:01, first identified in Korean individuals by next-generation sequencing.
Title: The novel HLA-DPB1 allele, HLA-DPB1*1344:01, first identified in Korean individuals by next-generation sequencing.
Characterization of the novel HLA-DPB1*11:01:06 allele by sequencing-based typing.
Title: Characterization of the novel HLA-DPB1*11:01:06 allele by sequencing-based typing.
Characterization of the novel HLA-DPB1*1348:01 allele by sequencing-based typing.
Title: Characterization of the novel HLA-DPB1*1348:01 allele by sequencing-based typing.
Influence of HLA Class II Alleles and DRB1-DQB1 Haplotypes on Rheumatoid Arthritis Susceptibility and Autoantibody Status in the Chinese Han Population.
Title: Influence of HLA Class II Alleles and DRB1-DQB1 Haplotypes on Rheumatoid Arthritis Susceptibility and Autoantibody Status in the Chinese Han Population.
Integrated transcriptomic and regulatory network analyses uncovers the role of let-7b-5p, SPIB, and HLA-DPB1 in sepsis.
Title: Integrated transcriptomic and regulatory network analyses uncovers the role of let-7b-5p, SPIB, and HLA-DPB1 in sepsis.
Association of HLA-DPB1, NLRP10, OVOL1, and ABCC11 with the axillary microbiome in a Japanese population.
Title: Association of HLA-DPB1, NLRP10, OVOL1, and ABCC11 with the axillary microbiome in a Japanese population.
DNA Methylation Patterns in the HLA-DPB1 and PDCD1LG2 Gene Regions in Patients with Autoimmune Thyroiditis from Different Water Iodine Areas.
Title: DNA Methylation Patterns in the HLA-DPB1 and PDCD1LG2 Gene Regions in Patients with Autoimmune Thyroiditis from Different Water Iodine Areas.
Predicting HLA-DPB1 permissive probabilities through a DPB1 prediction service towards the optimization of HCT donor selection.
Title: Predicting HLA-DPB1 permissive probabilities through a DPB1 prediction service towards the optimization of HCT donor selection.
Association of HLA-DPA1, HLA-DPB1, and HLA-DQB1 Alleles With the Long-Term and Booster Immune Responses of Young Adults Vaccinated Against the Hepatitis B Virus as Neonates.
Title: Association of HLA-DPA1, HLA-DPB1, and HLA-DQB1 Alleles With the Long-Term and Booster Immune Responses of Young Adults Vaccinated Against the Hepatitis B Virus as Neonates.

Submit: New GeneRIF Correction See all GeneRIFs (193)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study identified new variants associated with the risk of chronic hepatitis B. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study identifies two new risk loci for Graves' disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sj&#x000c3;&#x000b6;gren's syndrome at 7q11.23. 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 of hepatitis B vaccine response in an Indonesian population reveals multiple independent risk variants in the HLA region. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study on chronic HBV infection and its clinical progression in male Han-Taiwanese. EBI GWAS Catalog EBI GWAS CatalogPubMed
Association of granulomatosis with polyangiitis (Wegener's) with HLA-DPB1*04 and SEMA6A gene variants: evidence from genome-wide analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study confirming association of HLA-DP with protection against chronic hepatitis B and viral clearance in Japanese and Korean. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies HLA-DP as a susceptibility gene for pediatric asthma in Asian populations. 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 of aspirin-exacerbated respiratory disease in a Korean population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of novel genetic Loci associated with thyroid peroxidase antibodies and clinical thyroid disease. 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

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	HIV envelope protein gp120 can specifically inhibit CD4-dependent class II MHC-restricted T cell response to Ag	PubMed
	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
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 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	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	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
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

RH37399 (e-PCR)
- UniSTS:26369

SHGC-173634 (e-PCR)
- UniSTS:185403

PMC316580P2 (e-PCR)
- UniSTS:273009

D6S1867 (e-PCR)
- UniSTS:2942

HLA-DPB1_3384 (e-PCR)
- UniSTS:462245

STS-M57466 (e-PCR)
- UniSTS:47807

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 peptide antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables peptide antigen binding	IDA Inferred from Direct Assay 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 antigen processing and presentation of exogenous peptide antigen via MHC class II	IMP Inferred from Mutant Phenotype 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 T cell activation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of T cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of type II interferon production	IMP Inferred from Mutant Phenotype 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	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	IMP Inferred from Mutant Phenotype 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 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, DP beta 1 chain

Names: HLA class II histocompatibility antigen, DP(W4) beta chain; HLA-DP histocompatibility type, beta-1 subunit; MHC HLA DPB1; MHC class II HLA-DP-beta-1; MHC class II antigen DPB1

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_033242.1 RefSeqGene

Range

5065..18771

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_002121.6 → NP_002112.3 HLA class II histocompatibility antigen, DP beta 1 chain precursor

See identical proteins and their annotated locations for NP_002112.3

Status: REVIEWED

Source sequence(s)

AL645931, BP213121, M28202

Consensus CDS

CCDS4765.1

UniProtKB/Swiss-Prot

A0PFJ7, A5I886, A8YPB3, B5U8B4, B7VF80, B7VF87, B8ZX68, B8ZYT0, B9W5S8, B9W6F7, B9W6F9, C0MPP5, C0MPQ2, C0MPQ3, C0MPQ5, C0MPQ6, C0MPQ7, C4R9J5, C5IZL1, O00259, O19698, O19700, O19702, O19749, O46884, O77952, O98215, O98216, O98217, O98218, O98219, O98222, O98223, P01916, P04232, P04440, P13763, P79493, P79608, Q0P0L4, Q0ZFN3, Q14279, Q27S71, Q29682, Q29684, Q29698, Q29714, Q29775, Q29776, Q29778, Q29779, Q29781, Q29827, Q29828, Q29879, Q29880, Q29898, Q29977, Q2MGW3, Q30015, Q30031, Q30032, Q30033, Q30034, Q30050, Q30051, Q30052, Q30053, Q30054, Q30055, Q30174, Q4GY31, Q4JHD8, Q5ENE0, Q5ENE1, Q5ENW3, Q5EP46, Q5EP47, Q5EP49, Q5EP51, Q5EP52, Q5EP53, Q5EP56, Q5I4H8, Q5I4H9, Q5ISH4, Q5ISH5, Q5SQ73, Q5STP2, Q5YLA6, Q6IVX1, Q6LBX2, Q6LBX3, Q6LBX4, Q6LBX5, Q6LBX6, Q6LBX7, Q6PWX6, Q6TAS4, Q714U1, Q714U2, Q7YQ10, Q860Z7, Q8HWL7, Q8HWT5, Q8SNC4, Q95HC1, Q95IT7, Q95IT8, Q9BD13, Q9GIM2, Q9GIM4, Q9GIX6, Q9GJ41, Q9MY67, Q9TNT7, Q9TQE2, Q9XS11, Q9XS12

UniProtKB/TrEMBL

A0A0D6K9C3, A0A1C3PI18, A0A1C3PI48, A0A1N7SYF5, A0A1N7SYF8, A0A1N7SYH1, A0A1Y6MTB1, A0A1Y6MTI7, A0A1Y6MV69, A0A212PCE6, A0A212PCF7, A0A212PCG9, A0A380T930, A0A6B9V331, A0A6S6UMJ7, A0A6S6XMQ2, A0A6S6XSN5, A0A6S6XW01, A0A7D9BF82, A0A7D9FDH2, A0A7D9FFZ3, A0A977TMG3, I4EC15, I4EC17

Related

ENSP00000408146.2, ENST00000418931.7

Conserved Domains (2) summary

pfam00969
Location:42 → 114

MHC_II_beta; Class II histocompatibility antigen, beta domain

cd21003
Location:121 → 216

IgC1_MHC_II_beta_HLA-DP; Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DP; member of the C1-set of Ig superfamily (IgSF) domains

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

33075990..33089696

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

4380652..4394348

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054328495.1 → XP_054184470.1 HLA class II histocompatibility antigen, DP beta 1 chain isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

4487841..4501470

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

Range

4319521..4333219

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

Range

4495687..4509399

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330579.1 → XP_054186554.1 HLA class II histocompatibility antigen, DP beta 1 chain isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

Range

4375037..4388733

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330807.1 → XP_054186782.1 HLA class II histocompatibility antigen, DP beta 1 chain isoform X3

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

Range

4270622..4284330

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054331054.1 → XP_054187029.1 HLA class II histocompatibility antigen, DP beta 1 chain isoform X5
XM_054331053.1 → XP_054187028.1 HLA class II histocompatibility antigen, DP beta 1 chain isoform X4