HLA-A major histocompatibility complex, class I, A [Homo sapiens (human)] - Gene

Summary

Official Symbol: HLA-Aprovided by HGNC
Official Full Name: major histocompatibility complex, class I, Aprovided by HGNC
Primary source: HGNC:HGNC:4931
See related: Ensembl:ENSG00000206503 MIM:142800; AllianceGenome:HGNC:4931
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: HLAA
Summary: HLA-A belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. Class I molecules play a central role in the immune system by presenting peptides derived from the endoplasmic reticulum lumen so that they can be recognized by cytotoxic T cells. They are expressed in nearly all cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon 1 encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domains, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exons 6 and 7 encode the cytoplasmic tail. Polymorphisms within exon 2 and exon 3 are responsible for the peptide binding specificity of each class one molecule. Typing for these polymorphisms is routinely done for bone marrow and kidney transplantation. More than 6000 HLA-A alleles have been described. The HLA system plays an important role in the occurrence and outcome of infectious diseases, including those caused by the malaria parasite, the human immunodeficiency virus (HIV), and the severe acute respiratory syndrome coronavirus (SARS-CoV). The structural spike and the nucleocapsid proteins of the novel coronavirus SARS-CoV-2, which causes coronavirus disease 2019 (COVID-19), are reported to contain multiple Class I epitopes with predicted HLA restrictions. Individual HLA genetic variation may help explain different immune responses to a virus across a population.[provided by RefSeq, Aug 2020]
Annotation information: Note: This gene has been reviewed for its involvement in coronavirus biology, and is involved in immune response or antiviral activity.
Expression: Ubiquitous expression in colon (RPKM 288.9), lung (RPKM 280.7) and 25 other tissues See more
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Genomic context

Location:: 6p22.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (29942532..29945870)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (29806459..29809798)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (29910309..29913647)

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?

Molecular mechanism of specific HLA-A mRNA recognition by the RNA-binding-protein hMEX3B to promote tumor immune escape.
Title: Molecular mechanism of specific HLA-A mRNA recognition by the RNA-binding-protein hMEX3B to promote tumor immune escape.
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.
Contribution of ADD3 and the HLA Genes to Biliary Atresia Risk in Chinese.
Title: Contribution of ADD3 and the HLA Genes to Biliary Atresia Risk in Chinese.
Association of HLA-A*11:01, -A*24:02, and -B*18:01 with Prostate Cancer Risk: A Case-Control Study.
Title: Association of HLA-A*11:01, -A*24:02, and -B*18:01 with Prostate Cancer Risk: A Case-Control Study.
Human Leukocyte Antigen Polymorphism HLA-A*24:02 is Associated with Acute Liver Disease in HBV-Infected Han Chinese Adults.
Title: Human Leukocyte Antigen Polymorphism HLA-A*24:02 is Associated with Acute Liver Disease in HBV-Infected Han Chinese Adults.
HLA-A*02:06 allele may be susceptible to myelodysplastic syndrome in Zhejiang Han population, China.
Title: HLA-A*02:06 allele may be susceptible to myelodysplastic syndrome in Zhejiang Han population, China.
Frequency changes in HLA-I alleles: A marker to guide immunotherapy in lung adenocarcinoma patients and its relationship with tumor mutational burden and PD-L1 expression.
Title: Frequency changes in HLA-I alleles: A marker to guide immunotherapy in lung adenocarcinoma patients and its relationship with tumor mutational burden and PD-L1 expression.
The impact of HLA polymorphism on herpesvirus infection and disease.
Title: The impact of HLA polymorphism on herpesvirus infection and disease.
Characterization of the novel HLA-A*33 allele, HLA-A*33:03:55 in a Chinese individual.
Title: Characterization of the novel HLA-A*33 allele, HLA-A*33:03:55 in a Chinese individual.
Description of two new HLA alleles, HLA-A*26:01:70 and HLA-A*26:01:74 in Chinese individuals.
Title: Description of two new HLA alleles, HLA-A*26:01:70 and HLA-A*26:01:74 in Chinese individuals.

Submit: New GeneRIF Correction See all GeneRIFs (569)

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
Carbamazepine response MedGen: CN077964 GeneReviews: Not available	Compare labs
Susceptibility to severe cutaneous adverse reaction MedGen: C1840548 OMIM: 608579 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci. 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 scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common genetic variation and the control of HIV-1 in humans. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study for serum complement C3 and C4 levels in healthy Chinese subjects. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identified the human leukocyte antigen region as a novel locus for plasma beta-2 microglobulin. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study reveals multiple nasopharyngeal carcinoma-associated loci within the HLA region at chromosome 6p21.3. EBI GWAS Catalog EBI GWAS CatalogPubMed
HLA-A*3101 and carbamazepine-induced hypersensitivity reactions in Europeans. EBI GWAS Catalog EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. EBI GWAS Catalog EBI GWAS CatalogPubMed
Susceptibility to amoxicillin-clavulanate-induced liver injury is influenced by multiple HLA class I and II alleles. 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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Replication interactions

Interaction	Pubs
Capsid expressing (p24+) cells from pleural fluid of HIV-1/TB coinfected patients or in vitro infected PBMC (NL4-3 or NLAD8) downregulate HLA-A/B/C and BST2 (Tetherin) concomitantly with CD4 downregulation	PubMed
HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of HLA-A	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Asp	asp	Two ASP peptide sequences, ASP-YL9 (89YLYNSLLQL97) and ASP-TL10 (79TPNGSIFTTL88), show high binding affinity to HLA-A02 and HLA-B07 molecules, respectively	PubMed
	asp	Antisense reading frame-derived cryptic epitopes from the gag, pol, and nef genes are inhibited by the predicted HLA-I alleles, and presented by HIV-1-infected CD8+ T-cells	PubMed
	asp	Antisense reading frame-derived cryptic epitopes from the env gene are inhibited by the HLA-I alleles in CD8+ T-cells	PubMed
Envelope surface glycoprotein gp120	env	Conformational changes in HIV-1 gp120, including an enhanced expression of the V3 loop of gp120 and of epitopes that are exposed upon CD4 binding, are consistent with the formation of a multimolecular complex between HLA class I and gp120/160	PubMed
	env	Treatment of CD4+ T cells with HIV-1 gp120 significantly increases CD4 association with CD3, CD45RA, CD45RB, CD59, CD38, CD26 and HLA class I, and decreases that with CD45RC	PubMed
Envelope surface glycoprotein gp160, precursor	env	HIV-1 gp160-derived peptide p18 presented by H-2Dd class I major histocompatibility complex molecules is processed by angiotensin-1 converting enzyme (ACE) prior to T cell stimulation by the peptide p18	PubMed
	env	Epitope Env37-46 from HIV-1 gp160 binds strongly to HLA-A3 molecules and forms very stable complexes	PubMed
Envelope transmembrane glycoprotein gp41	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
	env	HIV-1 gp41 selectively enhances MHC class I, ICAM-1, IFN-alpha, IFN-beta, and IFN-omega expression in H9 cells	PubMed
Nef	nef	HIV-1 (SF2) Nef downregulates MHC-I (HLA-A/B/C); downregulation is dependent upon a proline-rich SH3 binding domain in Nef	PubMed
	nef	HIV-1 NL4-3 and SK68 Nef downregulates HLA-A (HLA-A*02), which is dependent upon amino acids M20 and S88	PubMed
	nef	HIV-1 NL4-3 and subtype B Nef downregulates HLA-A more than HLA-B, which discerned by amino acid 202 in Nef	PubMed
	nef	HIV-1 NL4-3 Nef downregulates HLA-A/B/C, which moderately requires the CPG-motif in Nef	PubMed
	nef	A methionine residue at amino acid 20 in the alpha-helix domain of HIV-1 Nef is required for the ability of Nef to downregulate MHC-I expression but not for the downregulation of CD4	PubMed
	nef	HIV-1 Nef downregulates the expression of MHC-I at the surface of lymphoid, monocytic and epithelial cells, causing MHC-I molecules to be rapidly internalized, accumulated in endosomal vesicles and degraded	PubMed
	nef	HIV-1 Nef interacts with HLA-A (MHC1) and this interaction occurs partially within RAB5+ early endosomes	PubMed
	nef	HIV-1 Nef downregulates cell (CEMT4) surface expression of HLA-A	PubMed
	nef	Expression of HIV-1 Nef in human T cells inhibits HLA-A2 transport to the cell surface	PubMed
	nef	In promonocytic cells, Nef/Hck recruits the ZAP-70 homolog Syk to downregulate MHC-I	PubMed
	nef	Nef/Hck complex recruits and phosphorylates the tyrosine kinase ZAP-70, which binds class I PI3K to trigger MHC-I downregulation in primary CD4+ T cells	PubMed
	nef	HIV-1 Nef-mediated downregulation of MHC-I requires Nef motif EEEE(65)-dependent binding to the sorting protein PACS-2, which targets Nef to the paranuclear region and enables Nef PXXP(75) to bind and activate a trans-Golgi network localized Src kinase	PubMed
	nef	Dominant active ARF1 (Q71L) potently stabilizes interactions among AP-1 mu1, HIV-1 Nef, and HLA-A2 and that the formation of a static complex sequesters necessary trafficking components	PubMed
	nef	Knocking down either AP-1 gamma, AP-1 mu1, or clathrin strongly inhibits Nef-induced downregulation of HLA-A2	PubMed
	nef	beta-COP as a cellular cofactor is required for HIV-1 Nef-mediated HLA-A2, CD4, and CD8 downregulation	PubMed
	nef	HIV-1 Nef clones from acute controllers display a lesser ability to downregulate CD4 and HLA class I from the cell surface, and a reduced ability to enhance virion infectivity compared to those from acute progressors	PubMed
	nef	HIV-1 Nef clones obtained from chronic patients infected with HIV-1 subtypes A, B, C or D show a functional hierarchy of subtype B > A/D > C for Nef-mediated HLA class I downregulation	PubMed
	nef	HLA supertypes such as HLA B07, HLA B58, HLA A02 and HLA A03 are most successful in restricting the amino acid positions of epitope dense regions of HIV-1 Nef, CA, and MA with low entropy and hydrophobic property	PubMed
	nef	Protective HLA alleles have a true preference for HIV-1 Gag protein, while non-protective HLA alleles preferentially interact with HIV-1 Nef	PubMed
	nef	HIV-1 Nef clones, isolated from plasma of elite controllers (EC) and chronic progressors (CP), show significantly lower HLA class I downregulation activity in EC than that in CP	PubMed
	nef	Interaction of HIV-1 Nef with the mu subunit of AP adaptor complexes requires the recognition of tyrosine-based sorting signals, which likely facilitates the connection between MHC I and the clathrin-dependent sorting machinery during MHC I downregulation	PubMed
	nef	Four glutamic acids from position 62 to 65 in the SH3 domain of HIV-1 Nef bind to the cytoplasmic tail at position 320Y of MHC-I, and are required for the Nef-mediated downregulation of MHC-I from the cell surface	PubMed
	nef	HIV-1 selectively downregulates HLA-A and HLA-B but does not significantly affect HLA-C or HLA-E, which allows HIV-infected cells to avoid NK cell-mediated lysis; this effect is likely mediated by the HIV-1 Nef protein	PubMed
	nef	The N-terminal alpha helix (17-26), polyproline (72-78), acidic (62-65), and oligomerization (123) domains of HIV-1 Nef are required for Nef-mediated disruption of the transport of HLA-A2 to the cell surface and for Nef to coprecipitate with HLA-A2	PubMed
	nef	The ability of HIV-1 Nef to disrupt MHC-I trafficking and inhibit antigen presentation is regulated by the expression of the mu1 subunit of adaptor protein (AP) AP-1A, a cellular protein complex implicated in TGN to endolysosomal pathways	PubMed
	nef	Different levels of MHC-I modulation are induced by different HIV-1 Nef proteins derived from HIV-1 infected adults and children	PubMed
	nef	The HIV-1 Nef highly conserved valine-glycine-phenylalanine amino acid triplet (VGF) motif, which links the acidic cluster and the proline-rich motif, is important for downregulation of CXCR4 and MHC-I	PubMed
	nef	HLA-A2 molecules with HLA-A cytoplasmic domains are more downregulated by HIV-1 Nef than those with HLA-B domains. There is no downregulation of HLA-A2 with HLA-C cytoplasmic domains by Nef	PubMed
	nef	Asp327 and Tyr320 of MHC-I, Asp123 of Nef, and Arg225, Arg393, Lys396, Arg211, and Arg246 of mu 1 are involved in a crucial three-way electrostatic network, which results in the Nef-MHC-I CD-mu 1 complex formation	PubMed
	nef	HIV-1 Nef with A84D, Y135F, and G140R mutation impairs to its ability to downregulate MHC-I	PubMed
	nef	Double (W13A/V16R) and triple (W13A/V16R/M20A) substitution mutants of HIV-1 Nef fail to downregulate MHC-I	PubMed
	nef	HIV-1 Nef acidic (Glu62-65) and polyproline domains (Pro75/78) stabilize the interaction between the HLA-A2/Nef fusion protein and AP-1 mu1	PubMed
	nef	Mutating three amino acids (Y320, A324, and D327) in the cytoplasmic tail of HLA-A2 abrogates Nef-induced downregulation of HLA-A2 through a failuer to recruit the mu1 or gamma subunits of AP-1	PubMed
	nef	Knocking down AP-2 enhances Nef activity by causing increased delivery of HLA-A2 to a prelysosomal compartment	PubMed
	nef	MHC-I is found in the Rab7(+) vesicles and targeted for degradation via the activity of the Nef-interacting protein, beta-COP	PubMed
	nef	HIV-1 Nef sequesters HLA-I A2 and colocalizes with CD63 and LAMP1 markers in late endosomes and lysosomes	PubMed
	nef	ARF6(T27N/Q67L) and RAB11(Q67L) mutants induce significant reversal of HLA-I A2 downregulation by HIV-1 Nef through redistributing HLA-I A2 from the perinuclear vesicles to the peripheral punctate vesicles at the plasma membrane	PubMed
	nef	HIV-1 Nef-induced downregulation of MHC-I expression and MHC-I targeting to the trans-Golgi network (TGN) require the binding of Nef to PACS-1, a molecule that controls the TGN localization of the cellular protein furin	PubMed
	nef	HIV-1 Nef downregulates expression of MHC-I by blocking transport of MHC-I molecules to the cell surface through a mechanism that requires phosphoinositide 3-kinase (PI 3-kinase) activity	PubMed
	nef	Two distinct regions of HIV-1 Nef modulate MHC-I cell surface expression: an N-terminal alpha-helix (residues 17-26) and a proline-rich motif (residues 75-78)	PubMed
	nef	The HIV-1 Nef 73-82 epitope binds strongly to HLA-A3 molecules and forms very stable complexes	PubMed
	nef	Mutation of amino acid P78 in HIV-1 Nef affects downregulation of MHC-I molecules from the cell surface, but does not interfere with Nef binding to Src homology 3 (SH3) domains	PubMed
	nef	HIV-1 Nef induces drastic and moderate downregulation of CD4 and MHC-I in resting CD4(+) T lymphocytes, respectively, but markedly upregulates cell surface levels of the MHC-II invariant chain CD74	PubMed
	nef	HIV-1 Nef has been observed to downregulate HLA-A2 on immature dendritic cells from two donors	PubMed
	nef	HIV-1 Nef-mediated downregulation of HLA class I suppresses the cytolytic activity of HIV-1-specific cytotoxic T-lymphocyte (CTL) clones	PubMed
	nef	Macrophage-tropic HIV-1 Nef downregulates expression of HLA-A2 on the surface of productively infected macrophages; point mutations in Nef at prolines P74 or P80 abrogate the downregulation of HLA-A2	PubMed
	nef	HIV-1 Nef downregulates MHC-I in Jurkat cells in a concentration-dependent manner	PubMed
	nef	HIV-1 Nef downregulates human MHC-I more efficiently than murine MHC-I molecules in HeLa cells, and Nef does not function efficiently in murine endothelial cells	PubMed
	nef	HIV-1 Nef alleles derived from perinatally infected children efficiently downregulate both CD4 and MHC-I in HeLa-CD4+ 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 disrupts antigen presentation by binding to MHC-I (HLA-A2) hypophosphorylated cytoplasmic tails in the endoplasmic reticulum; this Nef-MHC-I complex migrates normally into the Golgi apparatus but subsequently fails to arrive at the cell surface	PubMed
	nef	PxxP motifs in HIV-1 Nef induce the accumulation of CCR5 in a perinuclear compartment where both molecules co-localize with MHC-1	PubMed
	nef	The HIV-1 Nef mutant NefAAAA, which cannot interact with the endosomal sorting protein PACS-1, increases the number of cells containing long and stable tubules, which allows the internalization of MHC-1 into the tubules from the cell surface	PubMed
	nef	Downregulation of MHC-I by HIV-1 Nef decreases the incorporation of MHC-I molecules into virions, but does not decrease virion infectivity	PubMed
	nef	Downregulation of major histocompatibility class I on human dendritic cells by HIV-1 Nef impairs antigen presentation to HIV-specific CD8+ T lymphocytes	PubMed
	nef	A dominant-negative mutant protein derived from Hck, (composed of the N-terminal region, SH2, and SH3 domains) interacts with HIV-1 Nef and inhibits Nef-induced downregulation of MHC class I	PubMed
	nef	Deletion of the 19 N-terminal amino acids including the myristoylation signal from HIV-1 Nef inhibits both MHC-I and CD4 downregulation while preserving most CTL, T-helper and B-cell epitopes	PubMed
Pol	gag-pol	The HIV-1 Pol 325-333 epitope binds strongly to HLA-A3 molecules and forms very stable complexes	PubMed
Pr55(Gag)	gag	HIV-1 p6 Gag mutation affects HLA-A antigen presentation; p6 mutation of Glu residues to Alas impairs Gag processing & virus release and enhances Gag-membrane association with increased polyubiquitation & entry of Gag into the MHC-1 presentation pathway	PubMed
	gag	Protective HLA alleles have a true preference for HIV-1 Gag protein, while non-protective HLA alleles preferentially interact with HIV-1 Nef	PubMed
	gag	The S40F mutation in HIV-1 p6 enhances MHC-I antigen presentation of Gag	PubMed
	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	The PTAP L-domains in the p6 domain of HIV-1 Gag regulates ubiquitination of Gag which controls MHC-I presentation and gag processing in the DRiP pathway.	PubMed
	gag	The degree of HIV-1 Nef-mediated HLA-A2 downregulation strongly influences recognition of virus-infected cells by the Gag-specific CD8+ cytotoxic T lymphocyte clone	PubMed
	gag	Targeting HIV-1 Gag into the defective ribosomal product pathway enhances MHC class I antigen presentation and CD8+ T cell activation	PubMed
	gag	The HIV-1 Gag 20-28 epitope binds strongly to HLA-A3 molecules and forms very stable complexes	PubMed
Tat	tat	Four mutations (C27S, K51T, R55L, and G79A) on HIV-1 Tat result in the loss of the deleterious effects of Tat on the expression of MHC I, IL-2, and CD25 genes compared with wild-type Tat in Jurkat cells	PubMed
	tat	HIV-1 Tat upregulates MHC class I in monocyte-derived dendritic cells and CD8(+) T cells, thereby driving T cell-mediated immune responses	PubMed
	tat	HIV-1 Tat represses the MHC class I gene promoter by binding to and repressing TAFII250, a component of the general transcription factor TFIID, suggesting a mechanism for HIV-1 to downregulate MHC class I expression and avoid immune surveillance	PubMed
Vpr	vpr	A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies upregulation of HLA-A (A-68 alpha chain) expression by HIV-1 Vpr in Vpr transduced macrophages	PubMed
Vpu	vpu	Using antibodies specific to MHC class I A, B, and C molecules (clone W6/32), HIV-1 Vpu protein has been shown to downregulate the expression of MHC class I molecules on the surface of HIV-1 infected cells	PubMed
	vpu	HLA class I-associated immune responses have minor effects on Vpu variability, suggesting that Vpu conformation and function are preserved through many possible combinations of primary and secondary polymorphisms	PubMed
capsid	gag	HLA supertypes such as HLA B07, HLA B58, HLA A02 and HLA A03 are most successful in restricting the amino acid positions of epitope dense regions of HIV-1 Nef, CA, and MA with low entropy and hydrophobic property	PubMed
matrix	gag	HLA supertypes such as HLA B07, HLA B58, HLA A02 and HLA A03 are most successful in restricting the amino acid positions of epitope dense regions of HIV-1 Nef, CA, and MA with low entropy and hydrophobic property	PubMed
p6	gag	The S40F mutation in HIV-1 p6 enhances MHC-I antigen presentation of Gag	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

RH66830 (e-PCR)
- UniSTS:58376

D6S1105E (e-PCR)
- UniSTS:10277

RH80801 (e-PCR)
- UniSTS:84049

WI-12714 (e-PCR)
- UniSTS:75114

PMC316580P5 (e-PCR)
- UniSTS:273012

SHGC-172558 (e-PCR)
- UniSTS:184455

SHGC-172574 (e-PCR)
- UniSTS:184457

PMC165225P1 (e-PCR)
- UniSTS:271533

RH80274 (e-PCR)
- UniSTS:87469

RH70531 (e-PCR)
- UniSTS:75451

PMC155279P1 (e-PCR)
- UniSTS:271336

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables CD8 receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
enables T cell receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables TAP binding	IDA Inferred from Direct Assay more info	PubMed
enables TAP complex binding	IDA Inferred from Direct Assay more info	PubMed
enables beta-2-microglobulin binding	IC Inferred by Curator more info	PubMed
enables beta-2-microglobulin binding	IDA Inferred from Direct Assay more info	PubMed
enables beta-2-microglobulin binding	IMP Inferred from Mutant Phenotype more info	PubMed
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 peptide antigen binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in CD8-positive, alpha-beta T cell activation	IDA Inferred from Direct Assay more info	PubMed
involved_in T cell mediated cytotoxicity	IDA Inferred from Direct Assay more info	PubMed
involved_in T cell mediated cytotoxicity directed against tumor cell target	IDA Inferred from Direct Assay more info	PubMed
involved_in T cell receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in antibacterial humoral response	IDA Inferred from Direct Assay more info	PubMed
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class I	IDA Inferred from Direct Assay more info	PubMed
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent	IBA Inferred from Biological aspect of Ancestor more info
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent	IDA Inferred from Direct Assay more info	PubMed
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class Ib	IBA Inferred from Biological aspect of Ancestor more info
involved_in antigen processing and presentation of exogenous peptide antigen via MHC class I	IDA Inferred from Direct Assay more info	PubMed
involved_in defense response to Gram-positive bacterium	IDA Inferred from Direct Assay more info	PubMed
involved_in detection of bacterium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in immune response	NAS Non-traceable Author Statement more info	PubMed
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in peptide antigen assembly with MHC class I protein complex	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of CD8-positive, alpha-beta T cell activation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of CD8-positive, alpha-beta T cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of T cell cytokine production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of T cell mediated cytotoxicity	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of T cell mediated cytotoxicity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of memory T cell activation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of type II interferon production	IDA Inferred from Direct Assay more info	PubMed
NOT involved_in protection from natural killer cell mediated cytotoxicity	IDA Inferred from Direct Assay more info	PubMed
involved_in protection from natural killer cell mediated cytotoxicity	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in ER to Golgi transport vesicle membrane	TAS Traceable Author Statement more info
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi medial cisterna	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi membrane	TAS Traceable Author Statement more info
part_of MHC class I peptide loading complex	IDA Inferred from Direct Assay more info	PubMed
part_of MHC class I protein complex	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome membrane	TAS Traceable Author Statement more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum exit site	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular exosome	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in lumenal side of endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
located_in phagocytic vesicle membrane	TAS Traceable Author Statement more info
located_in plasma membrane	IDA Inferred from Direct Assay 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 recycling endosome membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: HLA class I histocompatibility antigen, A alpha chain

Names: HLA class I histocompatibility antigen, A-1 alpha chain; MHC class I antigen HLA-A heavy chain; leukocyte antigen class I-A

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_029217.3 RefSeqGene

Range

5002..8340

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mRNA and Protein(s)

NM_001242758.1 → NP_001229687.1 HLA class I histocompatibility antigen, A alpha chain isoform A*01:01:01:01 precursor

See identical proteins and their annotated locations for NP_001229687.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) represents the A*01:01:01:01 allele of the HLA-A gene, as found in the alternate locus group ALT_REF_LOCI_2 of the reference genome and in the RefSeqGene NG_029217.

Source sequence(s)

AL645935

UniProtKB/TrEMBL

A0A0S2IIT2, A0A0S4XR33, A0A0U5PXL2, A0A0U5PXM5, A0A1G4HPU6, A0A1V0EFF3, A0A1V0EFG6, A0A1W1B5T2, A0A2H4UK40, A0A2S1B6V5, A0A2U3QLL2, A0A493QP44, A0A4P2SR70, A0A5A4LLE3, A0A5A4LTS8, A0A5H2UF95, A0A5H2UIF3, A0A6B7HGN3, A0A6B7HGQ4, A0A6B9KNP2, A0A7L4X795, A0A7R9PSZ4, A0A7S9C280, A0A858LGC0, C5IWX4, Q5SUL5

Conserved Domains (3) summary

pfam00129
Location:25 → 203

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

pfam06623
Location:337 → 362

MHC_I_C; MHC_I C-terminus

cd21026
Location:204 → 299

IgC1_MHC_Ia_HLA-B; Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) B and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains
NM_002116.8 → NP_002107.3 HLA class I histocompatibility antigen, A alpha chain isoform A*03:01:01:01 precursor

See identical proteins and their annotated locations for NP_002107.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the A*03:01:0:01 allele of the HLA-A gene, as found in the primary assembly of the reference genome.

Source sequence(s)

AK313119, BE875389, U32184

Consensus CDS

CCDS34373.1

UniProtKB/Swiss-Prot

B1PKZ3, O02939, O02954, O02955, O02963, O19509, O19546, O19598, O19605, O19606, O19619, O19647, O19673, O19687, O19695, O19756, O19794, O19795, O43906, O43907, O46874, O62921, O62924, O77937, O77938, O77964, O78073, O78171, O98009, O98010, O98011, O98137, P01891, P01892, P04439, P05534, P06338, P10313, P10314, P10315, P10316, P13746, P16188, P16189, P16190, P18462, P30443, P30444, P30445, P30446, P30447, P30448, P30449, P30450, P30451, P30452, P30453, P30454, P30455, P30456, P30457, P30458, P30459, P30512, P30514, P79505, P79562, P79563, Q09160, Q29680, Q29747, Q29835, Q29837, Q29838, Q29899, Q29908, Q29909, Q29910, Q30208, Q31623, Q5S3G1, Q65A82, Q8MHM1, Q8MHN9, Q95352, Q95355, Q95362, Q95377, Q95380, Q95IZ5, Q9BCN0, Q9BD15, Q9BD19, Q9GJE6, Q9GJE7, Q9GJE8, Q9MW42, Q9MY89, Q9MYA3, Q9MYA5, Q9MYC4, Q9MYE6, Q9MYE9, Q9MYG4, Q9MYG5, Q9MYI5, Q9TP25, Q9TPQ3, Q9TPR8, Q9TPX8, Q9TPX9, Q9TPY0, Q9TQ24, Q9TQE8, Q9TQE9, Q9TQF1, Q9TQF5, Q9TQF8, Q9TQF9, Q9TQG0, Q9TQG5, Q9TQG7, Q9TQH5, Q9TQI3, Q9TQK5, Q9TQM6, Q9TQN5, Q9TQP5, Q9TQP6, Q9TQP7, Q9UIN1, Q9UIN2, Q9UIP7, Q9UQU3, Q9UQU6, Q9UQU7

UniProtKB/TrEMBL

A0A0S4XQY1, A0A0S4XRI5, A0A345F0V2, A0A346MPT9, A0A3G4R8Q7, A0A3S6RF59, A0A3S6RFA8, A0A3S6RFH9, A0A3S6RHP3, A0A4V0NP52, A0A5A4LJA0, A0A678ZN67, A0A678ZZD8, A0A678ZZE9, A0A6B7FU34, A0A6C1HWE5, A0A6C1HWN0, A0A7L4X7E9, A0A7R8ND24, A0A7U3K2B1, A0A858B925, A0A858LHP8, A0A8E4J527, B1PKY1, B2R7U3, I0J2M4

Related

ENSP00000366005.5, ENST00000376809.10

Conserved Domains (3) summary

pfam00129
Location:25 → 203

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

pfam06623
Location:337 → 362

MHC_I_C; MHC_I C-terminus

cd21026
Location:204 → 299

IgC1_MHC_Ia_HLA-B; Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) B and similar proteins; 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

29942532..29945870

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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

1200217..1203632

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Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

1421892..1425307

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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

1198085..1201438

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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

1197074..1200428

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

Range

1286642..1289974

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_041680767.1 → XP_041536701.1 HLA class I histocompatibility antigen, A alpha chain isoform X1

UniProtKB/TrEMBL

A0A140T9I0, A0A7L4X7A9, O78126, Q53Z42

Conserved Domains (3) summary

pfam00129
Location:22 → 200

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

pfam06623
Location:334 → 359

MHC_I_C; MHC_I C-terminus

cd21027
Location:201 → 295

IgC1_MHC_Ia_HLA-A; Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) A; member of the C1-set of Ig superfamily (IgSF) domains
XM_041680768.2 → XP_041536702.1 HLA class I histocompatibility antigen, A alpha chain isoform X2

UniProtKB/TrEMBL

A0A9L9PYF9

Conserved Domains (1) summary

smart00407
Location:219 → 290

IGc1; Immunoglobulin C-Type