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    LILRB3 leukocyte immunoglobulin like receptor B3 [ Homo sapiens (human) ]

    Gene ID: 11025, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LILRB3provided by HGNC
    Official Full Name
    leukocyte immunoglobulin like receptor B3provided by HGNC
    Primary source
    HGNC:HGNC:6607
    See related
    Ensembl:ENSG00000204577 MIM:604820; AllianceGenome:HGNC:6607
    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
    HL9; ILT5; LIR3; PIRB; CD85A; ILT-5; LIR-3; PIR-B; LILRA6
    Summary
    This gene is a member of the leukocyte immunoglobulin-like receptor (LIR) family, which is found in a gene cluster at chromosomal region 19q13.4. The encoded protein belongs to the subfamily B class of LIR receptors which contain two or four extracellular immunoglobulin domains, a transmembrane domain, and two to four cytoplasmic immunoreceptor tyrosine-based inhibitory motifs (ITIMs). The receptor is expressed on immune cells where it binds to MHC class I molecules on antigen-presenting cells and transduces a negative signal that inhibits stimulation of an immune response. It is thought to control inflammatory responses and cytotoxicity to help focus the immune response and limit autoreactivity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in appendix (RPKM 14.3), bone marrow (RPKM 8.1) and 7 other tissues See more
    Orthologs
    all
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    Genomic context

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    See LILRB3 in Genome Data Viewer
    Location:
    19q13.42
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (54216278..54223007, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57296666..57303395, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (54720147..54746631, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene membrane bound O-acyltransferase domain containing 7 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:54692762-54693444 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:54693445-54694126 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:54695049-54695250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54696095-54696610 Neighboring gene tRNA splicing endonuclease subunit 34 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54704113-54704783 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54709694-54710202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54710710-54711217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54711218-54711724 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:54711820-54712003 Neighboring gene ribosomal protein S9 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:54712450-54712625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54720754-54721590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54721591-54722426 Neighboring gene uncharacterized LOC124904768 Neighboring gene uncharacterized LOC107985279 Neighboring gene LSM14A, SCD6 homolog A (S. cerevisiae) pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54735962-54736715 Neighboring gene leukocyte immunoglobulin like receptor A6

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. LilrB3 is a putative cell surface receptor of APOE4. Zhou J, et al. Cell Res, 2023 Feb. PMID 36588123, Free PMC Article
    2. LILRB3 supports acute myeloid leukemia development and regulates T-cell antitumor immune responses through the TRAF2-cFLIP-NF-κB signaling axis. Wu G, et al. Nat Cancer, 2021 Nov. PMID 35122056, Free PMC Article
    3. Epithelial cells remove precancerous cells by cell competition via MHC class I-LILRB3 interaction. Ayukawa S, et al. Nat Immunol, 2021 Nov. PMID 34686865
    4. LILRB3 (ILT5) is a myeloid cell checkpoint that elicits profound immunomodulation. Yeboah M, et al. JCI Insight, 2020 Sep 1. PMID 32870822, Free PMC Article
    5. The Orphan Immune Receptor LILRB3 Modulates Fc Receptor-Mediated Functions of Neutrophils. Zhao Y, et al. J Immunol, 2020 Feb 15. PMID 31915259, Free PMC Article

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of the hybrid gene LILRB5-3 by long-read sequencing and implication of its novel signaling function.
      Title: Identification of the hybrid gene LILRB5-3 by long-read sequencing and implication of its novel signaling function.
    2. Distinct frequency patterns of LILRB3 and LILRA6 allelic variants in Europeans.
      Title: Distinct frequency patterns of LILRB3 and LILRA6 allelic variants in Europeans.
    3. LilrB3 is a putative cell surface receptor of APOE4.
      Title: LilrB3 is a putative cell surface receptor of APOE4.
    4. LILRB3 supports acute myeloid leukemia development and regulates T-cell antitumor immune responses through the TRAF2-cFLIP-NF-kappaB signaling axis.
      Title: LILRB3 supports acute myeloid leukemia development and regulates T-cell antitumor immune responses through the TRAF2-cFLIP-NF-κB signaling axis.
    5. Epithelial cells remove precancerous cells by cell competition via MHC class I-LILRB3 interaction.
      Title: Epithelial cells remove precancerous cells by cell competition via MHC class I-LILRB3 interaction.
    6. KLRD1, FOSL2 and LILRB3 as potential biomarkers for plaques progression in acute myocardial infarction and stable coronary artery disease.
      Title: KLRD1, FOSL2 and LILRB3 as potential biomarkers for plaques progression in acute myocardial infarction and stable coronary artery disease.
    7. Characterization of LILRB3 and LILRA6 allelic variants in the Japanese population.
      Title: Characterization of LILRB3 and LILRA6 allelic variants in the Japanese population.
    8. LILRB3 (ILT5) is a myeloid cell checkpoint that elicits profound immunomodulation.
      Title: LILRB3 (ILT5) is a myeloid cell checkpoint that elicits profound immunomodulation.
    9. The Orphan Immune Receptor LILRB3 Modulates Fc Receptor-Mediated Functions of Neutrophils.
      Title: The Orphan Immune Receptor LILRB3 Modulates Fc Receptor-Mediated Functions of Neutrophils.
    10. Together, this study identified ILT5 as an immunosuppressive regulator during sepsis, which may provide potential therapeutic strategy for sepsis.
      Title: Immunoglobulin-Like Transcript 5 Inhibits Macrophage-Mediated Bacterial Killing and Antigen Presentation During Sepsis.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC138403

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables amyloid-beta binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables inhibitory MHC class I receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables signaling receptor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables transmembrane signaling receptor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell surface receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cytokine-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in defense response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in immune response-regulating signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of osteoclast differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in secretory granule membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    leukocyte immunoglobulin-like receptor subfamily B member 3
    Names
    CD85 antigen-like family member A
    immunoglobulin-like transcript 5
    leucocyte Ig-like receptor B3
    leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6
    leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3
    monocyte inhibitory receptor HL9

    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_001081450.3 → NP_001074919.2  leukocyte immunoglobulin-like receptor subfamily B member 3 isoform 1 precursor

      Status: REVIEWED

      Source sequence(s)
      AF009633, AF009635, BC028153, CA434108, DA620532
      Consensus CDS
      CCDS46175.1
      UniProtKB/TrEMBL
      F8W6G6
      Related
      ENSP00000245620.9, ENST00000245620.13
      Conserved Domains (2) summary
      cd05751
      Location:27 → 118
      Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins
      cl11960
      Location:123 → 217
      Ig; Immunoglobulin domain

    2. NM_001320960.2 → NP_001307889.1  leukocyte immunoglobulin-like receptor subfamily B member 3 isoform 3 precursor

      Status: REVIEWED

      Source sequence(s)
      AC245052, AF009633, AF009637, BC028153, CA434108, DA843308
      UniProtKB/TrEMBL
      A0A0G2JMM1
      Related
      ENSP00000345184.6, ENST00000346401.10
      Conserved Domains (2) summary
      cd05751
      Location:27 → 118
      Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins
      cl11960
      Location:123 → 217
      Ig; Immunoglobulin domain

    3. NM_006864.4 → NP_006855.3  leukocyte immunoglobulin-like receptor subfamily B member 3 isoform 2 precursor

      See identical proteins and their annotated locations for NP_006855.3

      Status: REVIEWED

      Source sequence(s)
      AF009633, BC028153, CA434108, DA620532
      Consensus CDS
      CCDS33105.1
      UniProtKB/TrEMBL
      C9JWL8, F8W6G6
      Related
      ENSP00000388199.2, ENST00000445347.2
      Conserved Domains (2) summary
      cd05751
      Location:27 → 118
      Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins
      cl11960
      Location:123 → 217
      Ig; Immunoglobulin domain

    RNA

    1. NR_135493.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC245052, AF009640, BC028153, CA434108, DA843308

    2. NR_135494.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC245052, AF009643, BC028153, CA434108, DA843308

    3. NR_135495.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AF009633, BC028153, CA434108, DA843308

    4. NR_135496.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC245052, AF009633, BC028153, CA434108, DA843308
      Related
      ENST00000414379.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      54216278..54223007 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438108.1 → XP_047294064.1  leukocyte immunoglobulin-like receptor subfamily B member 3 isoform X1

      UniProtKB/TrEMBL
      F8W6G6

    2. XM_011526381.3 → XP_011524683.1  leukocyte immunoglobulin-like receptor subfamily B member 3 isoform X3

      UniProtKB/TrEMBL
      A0A0G2JMM1
      Conserved Domains (2) summary
      cd05751
      Location:27 → 118
      Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins
      cl11960
      Location:123 → 217
      Ig; Immunoglobulin domain

    3. XM_011526382.3 → XP_011524684.1  leukocyte immunoglobulin-like receptor subfamily B member 3 isoform X4

      UniProtKB/TrEMBL
      A0A0G2JMM1
      Conserved Domains (2) summary
      cd05751
      Location:27 → 118
      Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins
      cl11960
      Location:123 → 217
      Ig; Immunoglobulin domain

    4. XM_047438109.1 → XP_047294065.1  leukocyte immunoglobulin-like receptor subfamily B member 3 isoform X2

      UniProtKB/TrEMBL
      A0A0G2JMM1

    5. XM_047438110.1 → XP_047294066.1  leukocyte immunoglobulin-like receptor subfamily B member 3 isoform X5

      UniProtKB/TrEMBL
      A0A0G2JN08

    6. XM_047438111.1 → XP_047294067.1  leukocyte immunoglobulin-like receptor subfamily B member 3 isoform X6

      UniProtKB/TrEMBL
      A0A0G2JN08

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      57296666..57303395 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319653.1 → XP_054175628.1  leukocyte immunoglobulin-like receptor subfamily B member 3 isoform X3

      UniProtKB/TrEMBL
      A0A0G2JMM1

    2. XM_054319654.1 → XP_054175629.1  leukocyte immunoglobulin-like receptor subfamily B member 3 isoform X4

      UniProtKB/TrEMBL
      A0A0G2JMM1

    3. XM_054319652.1 → XP_054175627.1  leukocyte immunoglobulin-like receptor subfamily B member 3 isoform X2

      UniProtKB/TrEMBL
      A0A0G2JMM1

    RNA

    1. XR_008485077.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75022.3 GenPept UniProtKB/Swiss-Prot:O75022

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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