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HLA-DQA2 major histocompatibility complex, class II, DQ alpha 2 [ Homo sapiens (human) ]

Gene ID: 3118, updated on 11-Jun-2021


Official Symbol
HLA-DQA2provided by HGNC
Official Full Name
major histocompatibility complex, class II, DQ alpha 2provided by HGNC
Primary source
See related
Ensembl:ENSG00000237541 MIM:613503
Gene type
protein coding
RefSeq status
Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
This gene belongs to the HLA class II alpha chain family. The encoded protein forms a heterodimer with a class II beta chain. It is located in intracellular vesicles and plays a central role in the peptide loading of MHC class II molecules by helping to release the CLIP molecule from the peptide binding site. Class II molecules are expressed in antigen presenting cells (B lymphocytes, dendritic cells, macrophages) and are used to present antigenic peptides on the cell surface to be recognized by CD4 T-cells. [provided by RefSeq, Jun 2010]
Broad expression in lymph node (RPKM 32.9), spleen (RPKM 26.8) and 20 other tissues See more
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Genomic context

See HLA-DQA2 in Genome Data Viewer
Exon count:
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (32741391..32747198)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32709168..32714975)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene MT-CO3 pseudogene 1 Neighboring gene uncharacterized LOC102725019 Neighboring gene microRNA 3135b Neighboring gene major histocompatibility complex, class II, DQ beta 2

Genomic regions, transcripts, and products


  • 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


GeneRIFs: Gene References Into Functions

What's a GeneRIF?


Associated conditions

Description Tests
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 of plasma total IgE concentrations in the Framingham Heart Study.
GeneReviews: Not available
A genome-wide association study on chronic HBV infection and its clinical progression in male Han-Taiwanese.
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
A meta-analysis of genome-wide association studies for serum total IgE in diverse study populations.
GeneReviews: Not available
Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
GeneReviews: Not available
Genome-wide association study identifies new HLA class II haplotypes strongly protective against narcolepsy.
GeneReviews: Not available
Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population.
GeneReviews: Not available
Genome-wide association study in alopecia areata implicates both innate and adaptive immunity.
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 joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
GeneReviews: Not available
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
GeneReviews: Not available
Genome-wide pathway analysis of genome-wide association studies on systemic lupus erythematosus and rheumatoid arthritis.
GeneReviews: Not available
GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region.
GeneReviews: Not available
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
GeneReviews: Not available
New sequence variants in HLA class II/III region associated with susceptibility to knee osteoarthritis identified by genome-wide association study.
GeneReviews: Not available
Novel associations for hypothyroidism include known autoimmune risk loci.
GeneReviews: Not available
Novel risk loci for rheumatoid arthritis in Han Chinese and congruence with risk variants in Europeans.
GeneReviews: Not available
Oligoclonal band status in Scandinavian multiple sclerosis patients is associated with specific genetic risk alleles.
GeneReviews: Not available
Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases.
GeneReviews: Not available
Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies.
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 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
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
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

Pathways from PubChem


Products Interactant Other Gene Complex Source Pubs Description

General gene information



Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables MHC class II receptor activity NAS
Non-traceable Author Statement
more info
enables protein binding IPI
Inferred from Physical Interaction
more info

General protein information

Preferred Names
HLA class II histocompatibility antigen, DQ alpha 2 chain
DC-1 alpha chain
DX alpha chain
HLA class II histocompatibility antigen, DQ alpha 1 chain
HLA class II histocompatibility antigen, DQ(6) alpha chain
MHC class II DQA1
MHC class II DQA2
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.

mRNA and Protein(s)

  1. NM_020056.5NP_064440.1  HLA class II histocompatibility antigen, DQ alpha 2 chain precursor

    See identical proteins and their annotated locations for NP_064440.1

    Status: REVIEWED

    Source sequence(s)
    Consensus CDS
    ENSP00000364076.3, ENST00000374940.4
    Conserved Domains (2) summary
    IgC_MHC_II_alpha; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    MHC_II_alpha; Class II histocompatibility antigen, alpha domain

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


  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_1


  1. NT_167244.2 Reference GRCh38.p13 ALT_REF_LOCI_1

    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_2


  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_3


  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_4


  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_5


  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_6


  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_7


  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    GenBank, FASTA, Sequence Viewer (Graphics)
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