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

Gene ID: 3117, updated on 11-Jun-2021

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
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
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
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Genomic context

See HLA-DQA1 in Genome Data Viewer
Location:
6p21.32
Exon count:
6
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (32637406..32654846)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32605183..32611461)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA, U1 small nuclear 152, pseudogene Neighboring gene major histocompatibility complex, class II, DR beta 1 Neighboring gene uncharacterized LOC107986589 Neighboring gene HLA-DQB1 antisense RNA 1 Neighboring gene major histocompatibility complex, class II, DQ beta 1 Neighboring gene MT-CO3 pseudogene 1

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
A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.
GeneReviews: Not available
A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21.
GeneReviews: Not available
A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population.
GeneReviews: Not available
A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren's syndrome at 7q11.23.
GeneReviews: Not available
A genome-wide association study of host genetic determinants of the antibody response to Anthrax Vaccine Adsorbed.
GeneReviews: Not available
A genome-wide association study of rheumatoid arthritis without antibodies against citrullinated peptides.
GeneReviews: Not available
A genome-wide association study reveals ARL15, a novel non-HLA susceptibility gene for rheumatoid arthritis in North Indians.
GeneReviews: Not available
Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency.
GeneReviews: Not available
Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX.
GeneReviews: Not available
Celiac disease 1
MedGen: C1859310 OMIM: 212750 GeneReviews: Celiac Disease
not available
Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis.
GeneReviews: Not available
Common variants on chromosome 6p22.1 are associated with schizophrenia.
GeneReviews: Not available
Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
GeneReviews: Not available
Genome-wide association analysis of Vogt-Koyanagi-Harada syndrome identifies two new susceptibility loci at 1p31.2 and 10q21.3.
GeneReviews: Not available
Genome-wide association study identifies a novel susceptibility locus at 6p21.3 among familial CLL.
GeneReviews: Not available
Genome-wide association study identifies susceptibility loci for IgA nephropathy.
GeneReviews: Not available
Genome-wide association study identifies variants associated with autoimmune hepatitis type 1.
GeneReviews: Not available
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
GeneReviews: Not available
Genome-wide association study of clinical dimensions of schizophrenia: polygenic effect on disorganized symptoms.
GeneReviews: Not available
Genome-wide association study of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations.
GeneReviews: Not available
Genome-wide association study of hepatitis C virus- and cryoglobulin-related vasculitis.
GeneReviews: Not available
Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility.
GeneReviews: Not available
Genome-wide association study of susceptibility loci for cervical cancer.
GeneReviews: Not available
Genome-wide association study of ulcerative colitis in Koreans suggests extensive overlapping of genetic susceptibility with Caucasians.
GeneReviews: Not available
GWAS identifies novel susceptibility loci on 6p21.32 and 21q21.3 for hepatocellular carcinoma in chronic hepatitis B virus carriers.
GeneReviews: Not available
HLA-DQ strikes again: genome-wide association study further confirms HLA-DQ in the diagnosis of asthma among adults.
GeneReviews: Not available
HLA-DQB1*03 confers susceptibility to chronic hepatitis C in Japanese: a genome-wide association study.
GeneReviews: Not available
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
GeneReviews: Not available
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
GeneReviews: Not available
Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy.
GeneReviews: Not available
Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease.
GeneReviews: Not available
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
GeneReviews: Not available
Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization.
GeneReviews: Not available
Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci.
GeneReviews: Not available
Multiple common variants for celiac disease influencing immune gene expression.
GeneReviews: Not available
Novel associations for hypothyroidism include known autoimmune risk loci.
GeneReviews: Not available
Oligoclonal band status in Scandinavian multiple sclerosis patients is associated with specific genetic risk alleles.
GeneReviews: Not available
Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy.
GeneReviews: Not available
Single-nucleotide polymorphisms in HLA- and non-HLA genes associated with the development of antibodies to interferon-β therapy in multiple sclerosis patients.
GeneReviews: Not available
Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies.
GeneReviews: Not available
Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study.
GeneReviews: Not available
Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo.
GeneReviews: Not available

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ27088, FLJ27328, MGC149527

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 

General protein information

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
truncated MHC class II antigen

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

  1. NG_032876.1 RefSeqGene

    Range
    5001..11266
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002122.5NP_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/Swiss-Prot
    P01909
    UniProtKB/TrEMBL
    A0A173ADG5, Q8MH44
    Related
    ENSP00000339398.5, ENST00000343139.11
    Conserved Domains (2) summary
    pfam00993
    Location:29109
    MHC_II_alpha; Class II histocompatibility antigen, alpha domain
    cd21008
    Location:111205
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    32637406..32654846
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715079.4XP_006715142.1  HLA class II histocompatibility antigen, DQ alpha 1 chain isoform X1

    Related
    ENSP00000437302.1, ENST00000496318.5
    Conserved Domains (2) summary
    cd05767
    Location:112205
    IgC_MHC_II_alpha; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    pfam00993
    Location:30108
    MHC_II_alpha; Class II histocompatibility antigen, alpha domain

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    4055465..4061785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

    Range
    3881325..3887518
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

    Range
    4055723..4061916
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

    Range
    3938468..3944695
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

    Range
    3836434..3842754
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    4039337..4045564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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