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

Summary

Official Symbol: HLA-DQA2provided by HGNC
Official Full Name: major histocompatibility complex, class II, DQ alpha 2provided by HGNC
Primary source: HGNC:HGNC:4943
See related: Ensembl:ENSG00000237541 MIM:613503; AllianceGenome:HGNC:4943
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; HLA-DCA; HLA-DXA; HLADQA2; DC-alpha; DX-ALPHA
Summary: 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]
Expression: Broad expression in lymph node (RPKM 32.9), spleen (RPKM 26.8) and 20 other tissues See more
Orthologs: all
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Genomic context

Location:: 6p21.32

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (32741391..32747198)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (32564117..32569925)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (32709168..32714975)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Association of GWAS-supported noncoding area loci rs404860, rs3117098, and rs7775228 with asthma in Chinese Zhuang population.
Title: Association of GWAS-supported noncoding area loci rs404860, rs3117098, and rs7775228 with asthma in Chinese Zhuang population.
HLA-DQB1/HLA-DQA2 rs9275328 may play a part in influencing the systemic lupus erythematosis susceptibility in Malays and Chinese in Malaysia.
Title: HLA variants rs9271366 and rs9275328 are associated with systemic lupus erythematosus susceptibility in Malays and Chinese.
HLA-DQA2 and HLA-DQB2 genes are expressed in human Langerhans cells and encode a new HLA class II molecule.
Title: HLA-DQA2 and HLA-DQB2 genes are specifically expressed in human Langerhans cells and encode a new HLA class II molecule.
Parkinson's disease-associated SNP4 is correlated (r2=0.95) with variants that are associated with HLA-DQA2 expression.
Title: Evidence for more than one Parkinson's disease-associated variant within the HLA region.
Results indicate that two SNPs rs9468925 in HLA-C/HLA-B and rs2858881 in HLA-DQA2 were repeatedly selected in all models, suggesting that multiple loci outside PSOR1 locus were associated with psoriasis.
Title: Psoriasis regression analysis of MHC loci identifies shared genetic variants with vitiligo.
a significant single nucleotide polymorphism , rs3998159, between HLA-DQB1 and HLA-DQA2 was identified in patients with asthma
Title: Genome-wide association study of asthma identifies RAD50-IL13 and HLA-DR/DQ regions.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Genome-wide association study identifies new HLA class II haplotypes strongly protective against narcolepsy.
Observational study of gene-disease association. (HuGE Navigator)
Title: Examination of genetic polymorphisms in newborns for signatures of sex-specific prenatal selection.

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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 identifies 2 susceptibility Loci for Crohn's disease in a Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study of plasma total IgE concentrations in the Framingham Heart Study. 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
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 meta-analysis of genome-wide association studies for serum total IgE in diverse study populations. 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 study identifies new HLA class II haplotypes strongly protective against narcolepsy. 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 in alopecia areata implicates both innate and adaptive immunity. 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 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-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide pathway analysis of genome-wide association studies on systemic lupus erythematosus and rheumatoid arthritis. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. 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
Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases. EBI GWAS Catalog EBI GWAS CatalogPubMed
Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies. 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	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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:480660

RH79899 (e-PCR)
- UniSTS:90069

RH46692 (e-PCR)
- UniSTS:32245

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 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
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 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 2 chain

Names: 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 I antigen; 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)

NM_020056.5 → NP_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)

AL672104

Consensus CDS

CCDS4753.1

UniProtKB/Swiss-Prot

A2BF37, B0V0E7, O19789, P01906, Q5SQ94, Q5SR04

UniProtKB/TrEMBL

A0A140TA34, A0A1U9X7S6, A0A1U9X7T6, A0A1U9X7T9, Q76NI6

Related

ENSP00000364076.3, ENST00000374940.4

Conserved Domains (2) summary

cd05767
Location:112 → 205

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

pfam00993
Location:29 → 109

MHC_II_alpha; Class II histocompatibility antigen, alpha domain