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

Gene ID: 11025, updated on 14-Nov-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 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?
  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 Variation Viewer (GRCh37.p13)

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

  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

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

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

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

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

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

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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