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LILRB4 leukocyte immunoglobulin like receptor B4 [ Homo sapiens (human) ]

Gene ID: 11006, updated on 9-Apr-2019

Summary

Official Symbol
LILRB4provided by HGNC
Official Full Name
leukocyte immunoglobulin like receptor B4provided by HGNC
Primary source
HGNC:HGNC:6608
See related
Ensembl:ENSG00000186818 MIM:604821
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
ILT3; LIR5; CD85K; ILT-3; LIR-5
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. The receptor can also function in antigen capture and presentation. 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
Broad expression in appendix (RPKM 9.2), lymph node (RPKM 8.1) and 17 other tissues See more
Orthologs

Genomic context

See LILRB4 in Genome Data Viewer
Location:
19q13.42
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (54662524..54670359)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (55174271..55181810)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene microRNA 8061 Neighboring gene vomeronasal 1 receptor 105 pseudogene Neighboring gene uncharacterized LOC102724290 Neighboring gene leukocyte immunoglobulin-like receptor pseudogene 1

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations
NHGRI GWA Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog

Pathways from BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystem (from REACTOME)
    Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystemA number of receptors and cell adhesion molecules play a key role in modifying the response of cells of lymphoid origin (such as B-, T- and NK cells) to self and tumor antigens, as well as to pathoge...
  • Osteoclast differentiation, organism-specific biosystem (from KEGG)
    Osteoclast differentiation, organism-specific biosystemThe osteoclasts, multinucleared cells originating from the hematopoietic monocyte-macrophage lineage, are responsible for bone resorption. Osteoclastogenesis is mainly regulated by signaling pathways...
  • Osteoclast differentiation, conserved biosystem (from KEGG)
    Osteoclast differentiation, conserved biosystemThe osteoclasts, multinucleared cells originating from the hematopoietic monocyte-macrophage lineage, are responsible for bone resorption. Osteoclastogenesis is mainly regulated by signaling pathways...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
antigen binding TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor activity TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
extracellular exosome HDA PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
leukocyte immunoglobulin-like receptor subfamily B member 4
Names
CD85 antigen-like family member K
immunoglobulin-like transcript 3
leucocyte Ig-like receptor B4
leukocyte immunoglobulin-like receptor 5
leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4
monocyte inhibitory receptor HM18

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.

mRNA and Protein(s)

  1. NM_001278426.3NP_001265355.2  leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001265355.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AC243962, AF025532, BU175229
    Consensus CDS
    CCDS12902.1
    UniProtKB/Swiss-Prot
    Q8NHJ6
    Related
    ENSP00000375616.1, ENST00000391736.5
    Conserved Domains (3) summary
    cd05751
    Location:27118
    Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins
    smart00410
    Location:130198
    IG_like; Immunoglobulin like
    cl11960
    Location:123217
    Ig; Immunoglobulin domain
  2. NM_001278427.3NP_001265356.2  leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AC243962, AF025532, AF283988, BU175229
    Consensus CDS
    CCDS42618.1
    UniProtKB/Swiss-Prot
    Q8NHJ6
    UniProtKB/TrEMBL
    A0A0A0MSZ8
    Related
    ENSP00000408995.2, ENST00000430952.6
    Conserved Domains (3) summary
    cd05751
    Location:27118
    Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins
    smart00410
    Location:130198
    IG_like; Immunoglobulin like
    cl11960
    Location:123217
    Ig; Immunoglobulin domain
  3. NM_001278428.3NP_001265357.2  leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses two alternate in-frame splice sites in the central and 3' coding region, compared to variant 1. The encoded isoform (3) is the same length, compared to isoform 1.
    Source sequence(s)
    AC243962, AF025532, AK292082, BU175229
    UniProtKB/Swiss-Prot
    Q8NHJ6
    Conserved Domains (3) summary
    cd05751
    Location:27118
    Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins
    smart00410
    Location:130198
    IG_like; Immunoglobulin like
    cl11960
    Location:123217
    Ig; Immunoglobulin domain
  4. NM_001278429.3NP_001265358.2  leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 4

    See identical proteins and their annotated locations for NP_001265358.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame exon in the 5' coding region, uses an alternate in-frame splice site in the central coding region, and initiates translation at an upstream start codon, compared to variant 1. The encoded isoform (4) is longer and contains a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC243962, AK292082, AK314783, BC026309, BU175229
    UniProtKB/Swiss-Prot
    Q8NHJ6
    Conserved Domains (2) summary
    cd05751
    Location:56147
    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:152246
    Ig; Immunoglobulin domain
  5. NM_001278430.3NP_001265359.2  leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 5 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks several exons, and its 3'-terminal exon extends past a splice site that is used in variant 1. The encoded isoform (5) has a shorter and distinct C-terminus, compared to isoform 1. Isoform 5 lacks the transmembrane domain found in isoform 1 and is suspected to be soluble (PMID: 19658091).
    Source sequence(s)
    AF025532, BU175229, EU915607
    UniProtKB/Swiss-Prot
    Q8NHJ6
    Conserved Domains (3) summary
    cd05751
    Location:27118
    Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins
    smart00410
    Location:130198
    IG_like; Immunoglobulin like
    cl11960
    Location:123217
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    54662524..54670359
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017026215.1XP_016881704.1  leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X1

    Related
    ENSP00000375613.3, ENST00000391733.7
  2. XM_017026216.1XP_016881705.1  leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X2

  3. XM_024451331.1XP_024307099.1  leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X3

    Related
    ENSP00000401962.1, ENST00000434286.1
    Conserved Domains (2) summary
    cd05751
    Location:68159
    Ig1_LILR_KIR_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILRs), Natural killer inhibitory receptors (KIRs) and similar domains
    cl11960
    Location:164258
    Ig; Immunoglobulin domain
  4. XM_017026217.1XP_016881706.1  leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X4

    Related
    ENSP00000375614.3, ENST00000391734.7

RNA

  1. XR_002958246.1 RNA Sequence

Reference GRCh38.p12 ALT_REF_LOCI_1

Genomic

  1. NW_003571054.1 Reference GRCh38.p12 ALT_REF_LOCI_1

    Range
    569210..576762
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_7

Genomic

  1. NW_003571060.1 Reference GRCh38.p12 ALT_REF_LOCI_7

    Range
    567701..575241
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_8

Genomic

  1. NW_003571061.2 Reference GRCh38.p12 ALT_REF_LOCI_8

    Range
    389310..396863
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_9

Genomic

  1. NT_187693.1 Reference GRCh38.p12 ALT_REF_LOCI_9

    Range
    645385..652924
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001081438.1: Suppressed sequence

    Description
    NM_001081438.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
  2. NM_006847.3: Suppressed sequence

    Description
    NM_006847.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
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