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

    Gene ID: 3106, updated on 5-Jan-2020

    Summary

    Official Symbol
    HLA-Bprovided by HGNC
    Official Full Name
    major histocompatibility complex, class I, Bprovided by HGNC
    Primary source
    HGNC:HGNC:4932
    See related
    Ensembl:ENSG00000234745 MIM:142830
    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
    AS; HLAB; B-4901
    Summary
    HLA-B 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. 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, exon 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. Hundreds of HLA-B alleles have been described. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in spleen (RPKM 583.7), lung (RPKM 569.7) and 24 other tissues See more
    Orthologs

    Genomic context

    See HLA-B in Genome Data Viewer
    Location:
    6p21.33
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    109.20191205 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (31353875..31357179, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31321649..31324989, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene WASP family member 5, pseudogene Neighboring gene uncharacterized LOC112267902 Neighboring gene long intergenic non-protein coding RNA 2571 Neighboring gene microRNA 6891 Neighboring gene dihydrofolate reductase pseudogene 2 Neighboring gene RNA, U6 small nuclear 283, pseudogene

    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
    Abacavir hypersensitivity
    MedGen: C1840547 GeneReviews: Not available
    Compare labs
    Allopurinol response
    MedGen: CN160494 GeneReviews: Not available
    Compare labs
    Ankylosing spondylitis
    MedGen: C1862852 OMIM: 106300 GeneReviews: Not available
    Compare labs
    Carbamazepine hypersensitivity
    MedGen: C3277286 GeneReviews: Not available
    Compare labs
    Carbamazepine response
    MedGen: CN077964 GeneReviews: Not available
    Compare labs
    Susceptibility to severe cutaneous adverse reaction
    MedGen: C1840548 OMIM: 608579 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    A genome-wide association study identifies two new risk loci for Graves' disease.
    NHGRI GWA Catalog
    A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci.
    NHGRI GWA Catalog
    A genome-wide association study of rheumatoid arthritis without antibodies against citrullinated peptides.
    NHGRI GWA Catalog
    A genome-wide integrative genomic study localizes genetic factors influencing antibodies against Epstein-Barr virus nuclear antigen 1 (EBNA-1).
    NHGRI GWA Catalog
    Ankylosing spondylitis
    Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls.
    NHGRI GWA Catalog
    Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles.
    NHGRI GWA Catalog
    Common genetic variation and the control of HIV-1 in humans.
    NHGRI GWA Catalog
    Genetic variation in the HLA region is associated with susceptibility to herpes zoster.
    NHGRI GWA Catalog
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    NHGRI GWA Catalog
    Genome-wide association study for vitiligo identifies susceptibility loci at 6q27 and the MHC.
    NHGRI GWA Catalog
    Genome-wide association study identified the human leukocyte antigen region as a novel locus for plasma beta-2 microglobulin.
    NHGRI GWA Catalog
    Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma.
    NHGRI GWA Catalog
    Genome-wide association study in Chinese identifies novel loci for blood pressure and hypertension.
    NHGRI GWA Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    NHGRI GWA Catalog
    Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci.
    NHGRI GWA Catalog
    HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin.
    NHGRI GWA Catalog
    Host determinants of HIV-1 control in African Americans.
    NHGRI GWA Catalog
    Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility.
    NHGRI GWA Catalog
    Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci.
    NHGRI GWA Catalog
    Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization.
    NHGRI GWA Catalog
    Meta-analysis of genome-wide association studies in african americans provides insights into the genetic architecture of type 2 diabetes.
    NHGRI GWA Catalog
    Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.
    NHGRI GWA Catalog
    Multiple loci are associated with white blood cell phenotypes.
    NHGRI GWA Catalog
    New gene functions in megakaryopoiesis and platelet formation.
    NHGRI GWA Catalog
    Novel associations for hypothyroidism include known autoimmune risk loci.
    NHGRI GWA Catalog
    Quantitative trait loci for CD4:CD8 lymphocyte ratio are associated with risk of type 1 diabetes and HIV-1 immune control.
    NHGRI GWA Catalog
    The major genetic determinants of HIV-1 control affect HLA class I peptide presentation.
    NHGRI GWA Catalog

    HIV-1 interactions

    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

    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-A*02 and HLA-B*07 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
    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 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 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 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 B*07, HLA B*35, HLA B*58, HLA A*02 and HLA A*03 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 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 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-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 Different levels of the modulation of MHC-1 are induced by different Nef proteins derived from HIV-1 infected adults and children 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 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 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 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-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 A methionine residue at amino acid 20 in the alpha-helix domain is required for the ability of HIV-1 Nef to downregulate MHC-I expression but not for the downregulation of CD4 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 In promonocytic cells, Nef/Hck recruits the ZAP-70 homolog Syk to downregulate MHC-I PubMed
    nef Amino acid residue Y320 in the MHC-I cytoplasmic domain and residues E62-65 and P78 in HIV-1 Nef are required for interaction with the mu subunit of AP-1 PubMed
    nef MHC-I is found in the Rab7(+) vesicles and is targeted for degradation via the activity of the Nef-interacting protein, beta-COP PubMed
    nef HIV-1 group N or O Nef alleles only weakly downregulate CD4, CD28, and class I and II MHC molecules PubMed
    nef Two distinct regions of HIV-1 Nef modulate MHC-I expression on cell surface: an N-terminal alpha-helix (residues 17-26) and a proline-rich motif (residues 75-78) 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 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-specific CTL clones are suppressed to kill primary CD4(+) T cells infected with a Nef-positive HIV-1 strain (NL-432) but efficiently lysed CD4(+) T cells infected with a nef-mutant NL-M20A 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 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 HIV-1 Nef-mediated cellular phenotypes, including MHC-1 and CD4 downregulation, are differentially expressed as a function of intracellular Nef concentrations 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 Downregulation of MHC-I by 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
    Pr55(Gag) gag HIV-1 Gag is affected by HLA-B27-mediated peptide presentation PubMed
    gag HLA-B-restricted epitopes contribute to a broad Gag-specific CD8+ response that is associated with relative suppression of viremia PubMed
    gag HLA-B subjects are associated with HIV-1 disease progression with HIV-1 Gag sequence diversity 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 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 Specific HIV-1 residues in Vpr, Gag, and Rev and HLA alleles (particularly B and C) confer susceptibility to the CTL response in HIV-1 infected patients PubMed
    gag Targeting HIV-1 Gag into the defective ribosomal product pathway enhances MHC class I antigen presentation and CD8+ T cell activation PubMed
    Rev rev Specific HIV-1 residues in Vpr, Gag, and Rev and HLA alleles (particularly B and C) confer susceptibility to the CTL response in HIV-1 infected patients 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 Specific HIV-1 residues in Vpr, Gag, and Rev and HLA alleles (particularly B and C) confer susceptibility to the CTL response in HIV-1 infected patients 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 B*07, HLA B*58, HLA A*02 and HLA A*03 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 B*07, HLA B*58, HLA A*02 and HLA A*03 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

    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

    • FLJ26645, FLJ26659, FLJ52207, FLJ53569, FLJ99386, MGC111087

    General protein information

    Preferred Names
    major histocompatibility complex, class I, B
    Names
    HLA class I antigen HLA-B
    HLA class I histocompatibility antigen, B alpha chain
    MHC HLA-B cell surface glycoprotein
    MHC HLA-B transmembrane glycoprotein
    MHC class 1 antigen
    MHC class I antigen HLA-B alpha chain
    MHC class I antigen HLA-B heavy chain
    MHC class I antigen SHCHA
    MHC class I molecule
    leukocyte antigen class I-B

    NCBI Reference Sequences (RefSeq)

    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_023187.1 RefSeqGene

      Range
      5034..8338
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_005514.8NP_005505.2  major histocompatibility complex, class I, B precursor

      See identical proteins and their annotated locations for NP_005505.2

      Status: REVIEWED

      Source sequence(s)
      AW273181, DC345094, U29057
      Consensus CDS
      CCDS34394.1
      UniProtKB/Swiss-Prot
      P01889
      UniProtKB/TrEMBL
      E5FQ95
      Related
      ENSP00000399168.2, ENST00000412585.7
      Conserved Domains (3) summary
      cd07698
      Location:207299
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam06623
      Location:346362
      MHC_I_C; MHC_I C-terminus
      pfam00129
      Location:26203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

    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
      31353875..31357179 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p13 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

      Range
      2834235..2837538 complement
      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
      2662487..2665791 complement
      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
      2695847..2699160 complement
      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
      2609572..2612876 complement
      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
      2656113..2659417 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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