HLA-DQA1 major histocompatibility complex, class II, DQ alpha 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HLA-DQA1provided by HGNC
Official Full Name: major histocompatibility complex, class II, DQ alpha 1provided by HGNC
Primary source: HGNC:HGNC:4942
See related: Ensembl:ENSG00000196735 MIM:146880; AllianceGenome:HGNC:4942
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: DQA1; DQ-A1; CELIAC1; HLA-DQA; HLA-DQB1; HLA-DQA1*
Summary: HLA-DQA1 belongs to the HLA class II alpha chain paralogues. The 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 alpha chain is approximately 33-35 kDa. It is encoded by 5 exons; exon 1 encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, and exon 4 encodes the transmembrane domain and 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. [provided by RefSeq, Jul 2008]
Expression: Broad expression in lung (RPKM 134.8), lymph node (RPKM 101.5) and 18 other tissues See more
Orthologs: mouse 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 (32637406..32655272)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (32466412..32472812)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (32605183..32611461)

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 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.
Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma.
Title: Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma.
A web-based genome-wide association study reveals the susceptibility loci of common adverse events following COVID-19 vaccination in the Japanese population.
Title: A web-based genome-wide association study reveals the susceptibility loci of common adverse events following COVID-19 vaccination in the Japanese population.
Association Study Identified HLA-DQA1 as a Novel Genetic Risk of Systemic Lupus Erythematosus-Associated Pulmonary Arterial Hypertension.
Title: Association Study Identified HLA-DQA1 as a Novel Genetic Risk of Systemic Lupus Erythematosus-Associated Pulmonary Arterial Hypertension.
HLA-DQA1*05 and upstream variants of PPARGC1B are associated with infliximab persistence in Japanese Crohn's disease patients.
Title: HLA-DQA1*05 and upstream variants of PPARGC1B are associated with infliximab persistence in Japanese Crohn's disease patients.
Candidate Genes for IgA Nephropathy in Pediatric Patients: Exome-Wide Association Study.
Title: Candidate Genes for IgA Nephropathy in Pediatric Patients: Exome-Wide Association Study.
Identification of mutation gene prognostic biomarker in multiple myeloma through gene panel exome sequencing and transcriptome analysis in Chinese population.
Title: Identification of mutation gene prognostic biomarker in multiple myeloma through gene panel exome sequencing and transcriptome analysis in Chinese population.
Multi-population genome-wide association study implicates immune and non-immune factors in pediatric steroid-sensitive nephrotic syndrome.
Title: Multi-population genome-wide association study implicates immune and non-immune factors in pediatric steroid-sensitive nephrotic syndrome.
Characterization of the novel HLA-DQA1*05:05:14 allele by sequencing-based typing.
Title: Characterization of the novel HLA-DQA1*05:05:14 allele by sequencing-based typing.
Characterization of the novel HLA-DQA1*02:01:14 allele by sequencing-based typing.
Title: Characterization of the novel HLA-DQA1*02:01:14 allele by sequencing-based typing.

Submit: New GeneRIF Correction See all GeneRIFs (284)

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

Associated conditions

Description	Tests
Celiac disease, susceptibility to, 1 MedGen: C1859310 OMIM: 212750 GeneReviews: Celiac Disease	not available

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 for celiac disease identifies risk variants in the region harboring IL2 and IL21. 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 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 host genetic determinants of the antibody response to Anthrax Vaccine Adsorbed. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study of rheumatoid arthritis without antibodies against citrullinated peptides. 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
Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency. EBI GWAS Catalog EBI GWAS CatalogPubMed
Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants on chromosome 6p22.1 are associated with schizophrenia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis of Vogt-Koyanagi-Harada syndrome identifies two new susceptibility loci at 1p31.2 and 10q21.3. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies a novel susceptibility locus at 6p21.3 among familial CLL. 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 variants associated with autoimmune hepatitis type 1. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of clinical dimensions of schizophrenia: polygenic effect on disorganized symptoms. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of hepatitis C virus- and cryoglobulin-related vasculitis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of susceptibility loci for cervical cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of ulcerative colitis in Koreans suggests extensive overlapping of genetic susceptibility with Caucasians. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS identifies novel susceptibility loci on 6p21.32 and 21q21.3 for hepatocellular carcinoma in chronic hepatitis B virus carriers. EBI GWAS Catalog EBI GWAS CatalogPubMed
HLA-DQ strikes again: genome-wide association study further confirms HLA-DQ in the diagnosis of asthma among adults. 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
Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. 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
Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Multiple common variants for celiac disease influencing immune gene expression. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel associations for hypothyroidism include known autoimmune risk loci. 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
Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy. EBI GWAS Catalog EBI GWAS CatalogPubMed
Single-nucleotide polymorphisms in HLA- and non-HLA genes associated with the development of antibodies to interferon-&#x003b2; therapy in multiple sclerosis patients. EBI GWAS Catalog EBI GWAS CatalogPubMed
Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies. 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
Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo. 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 upregulates the expression of major histocompatibility complex, class II, DQ alpha 1 (HLA-DQA1) in human primary T cells	PubMed
	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

G43562 (e-PCR)
- UniSTS:95013

G28524 (e-PCR)
- UniSTS:6197

RH78929 (e-PCR)
- UniSTS:85056

PMC204479P1 (e-PCR)
- UniSTS:271940

RH76581 (e-PCR)
- UniSTS:93029

D5S498 (e-PCR), detects polymorphism
- UniSTS:35727

SHGC-152784 (e-PCR)
- UniSTS:177603

D6S2446 (e-PCR)
- UniSTS:256718

RH79899 (e-PCR)
- UniSTS:90069

D6S1666 (e-PCR)
- UniSTS:38121

D6S291 (e-PCR), detects polymorphism
- UniSTS:36598

D6S1666 (e-PCR)
- UniSTS:464376

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 MHC class II receptor activity	TAS 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 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 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 plasma 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 alpha 1 chain

Names: DC-1 alpha chain; DC-alpha; HLA class II histocompatibility antigen DQ alpha chain; HLA-DCA; MHC HLA-DQ alpha; MHC class II DQ alpha chain; MHC class II DQA1; MHC class II HLA-DQ-alpha-1; MHC class II antigen DQA1; MHC class II protein

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_032876.1 RefSeqGene

Range

5001..11279

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_002122.5 → NP_002113.2 HLA class II histocompatibility antigen, DQ alpha 1 chain precursor

See identical proteins and their annotated locations for NP_002113.2

Status: REVIEWED

Source sequence(s)

AF533896, AK130811, AL662789, BU617246, M20431

Consensus CDS

CCDS4752.1

UniProtKB/TrEMBL

A0A173ADG5, A0A4P8DL21, A0A4P8JAG8, A0A5B9RAZ7, A0A5P8NFP0, A0A649ZU79, A0A649ZV55, A0A7D3QX10, A0A7H0TJC5, A0A8F2Q4A3, A0A8F5FT89, G4XQK2, G4XQK3, I7KE75

Related

ENSP00000339398.5, ENST00000343139.11

Conserved Domains (2) summary

pfam00993
Location:29 → 109

MHC_II_alpha; Class II histocompatibility antigen, alpha domain

cd21008
Location:111 → 205

IgC1_MHC_II_alpha_HLA-DQ; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and related proteins; 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

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

32637406..32655272

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006715079.5 → XP_006715142.1 HLA class II histocompatibility antigen, DQ alpha 1 chain isoform X1

UniProtKB/TrEMBL

E9PMV2

Related

ENSP00000437302.1, ENST00000496318.5

Conserved Domains (2) summary

cd05767
Location:112 → 205

IgC_MHC_II_alpha; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain

pfam00993
Location:30 → 108

MHC_II_alpha; Class II histocompatibility antigen, alpha domain