LILRB3

gene
On this page

Also known as LIR-3HL9ILT5LIR3CD85aPIRBPIR-B

Summary

LILRB3 (leukocyte immunoglobulin like receptor B3, HGNC:6607) is a protein-coding gene on chromosome 19q13.42, encoding Leukocyte immunoglobulin-like receptor subfamily B member 3 (O75022). May act as receptor for class I MHC antigens.

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.

Source: NCBI Gene 11025 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 127 total
  • MANE Select transcript: NM_006864

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6607
Approved symbolLILRB3
Nameleukocyte immunoglobulin like receptor B3
Location19q13.42
Locus typegene with protein product
StatusApproved
AliasesLIR-3, HL9, ILT5, LIR3, CD85a, PIRB, PIR-B
Ensembl geneENSG00000204577
Ensembl biotypeprotein_coding
OMIM604820
Entrez11025

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 6 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000245620, ENST00000346401, ENST00000391750, ENST00000414379, ENST00000436504, ENST00000445347, ENST00000460208, ENST00000468668, ENST00000469273, ENST00000861602, ENST00000861603

RefSeq mRNA: 3 — MANE Select: NM_006864 NM_001081450, NM_001320960, NM_006864

CCDS: CCDS33105, CCDS46175

Canonical transcript exons

ENST00000445347 — 13 exons

ExonStartEnd
ENSE000015096445421627854217239
ENSE000015940895422294354223007
ENSE000024753895422182854222130
ENSE000025194475422274754222782
ENSE000034624345422227854222562
ENSE000034632755422052854220830
ENSE000034739615422015554220205
ENSE000034850265421876354218838
ENSE000035405005421912954219245
ENSE000035410225421836154218413
ENSE000035768805421864554218682
ENSE000035803715421731954217474
ENSE000036508085422108354221379

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 99.19.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1978 / max 18.2486, expressed in 105 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1826143.6357273
1826150.1978105

Top tissues by expression

133 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
bloodUBERON:000017899.19gold quality
granulocyteCL:000009497.55gold quality
leukocyteCL:000073897.36gold quality
monocyteCL:000057697.35gold quality
spleenUBERON:000210696.86gold quality
upper lobe of left lungUBERON:000895294.08gold quality
vermiform appendixUBERON:000115492.47gold quality
right lungUBERON:000216792.37gold quality
bone marrowUBERON:000237191.29gold quality
bone marrow cellCL:000209289.92gold quality
lungUBERON:000204888.89gold quality
omental fat padUBERON:001041487.75gold quality
right coronary arteryUBERON:000162585.73gold quality
right lobe of liverUBERON:000111485.36gold quality
adipose tissueUBERON:000101384.97gold quality
left adrenal gland cortexUBERON:003582583.90gold quality
right adrenal glandUBERON:000123383.76gold quality
left adrenal glandUBERON:000123483.29gold quality
right adrenal gland cortexUBERON:003582783.26gold quality
subcutaneous adipose tissueUBERON:000219082.87gold quality
left uterine tubeUBERON:000130382.26gold quality
gall bladderUBERON:000211081.70gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099181.68gold quality
descending thoracic aortaUBERON:000234581.58gold quality
liverUBERON:000210781.42gold quality
apex of heartUBERON:000209881.33gold quality
placentaUBERON:000198780.47gold quality
left coronary arteryUBERON:000162680.31gold quality
ascending aortaUBERON:000149680.02gold quality
thoracic aortaUBERON:000151579.93gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes9.56

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): RUNX3, SPI1

miRNA regulators (miRDB)

24 targeting LILRB3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-512-3P99.9767.351049
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-6753-3P99.9366.57637
HSA-MIR-7107-3P99.9366.73627
HSA-MIR-120099.7170.421838
HSA-MIR-120899.7068.281533
HSA-MIR-130399.6569.771662
HSA-MIR-103A-1-5P99.3967.781545
HSA-MIR-103A-2-5P99.3967.721577
HSA-MIR-504-3P99.3067.181745
HSA-MIR-427999.1966.702437
HSA-MIR-807799.1766.67862
HSA-MIR-607199.1667.771780
HSA-MIR-367-5P98.8467.18902
HSA-MIR-382-3P98.8367.101074
HSA-MIR-58198.3967.42835
HSA-MIR-1304-3P98.2966.441207
HSA-MIR-6773-3P98.1765.511213
HSA-MIR-122-5P97.2364.921024
HSA-MIR-4445-5P97.2166.16832
HSA-MIR-570296.6868.21958
HSA-MIR-808196.4267.75738

Literature-anchored findings (GeneRIF, showing 16)

  • Coligation of LIR3 to LIR7 or to FcepsilonRI by means of a second monoclonal antibody significantly inhibited net histamine release, cysLT production, and IL-4 generation. LIR3 is counter-regulatory for both adaptive and innate receptors suggests. (PMID:15242876)
  • Progenitor mast cells expressed cell surface inhibitory LILRB3. Mature cord-blood-derived mast cells had detectable mRNA encoding multiple LILRs, none were expressed on the cell surface. (PMID:17998301)
  • LILRB3 is expressed on cultured osteoclast precursor cells derived from peripheral blood monocytes and plays a regulatory role in the development of osteoclasts. (PMID:18802077)
  • Blockade of LILRB1 and LILRB3 receptors by monoclonal antibodies or short interfering RNA (siRNA) abrogated the specific antigen-presenting properties of dendritic cells, implying an important regulatory role of these molecules. (PMID:20631139)
  • RPS9/LILRB3 (rs11666543) was associated with Takayasu arteritis. (PMID:25604533)
  • Glatiramer Acetate Enhances Myeloid-Derived Suppressor Cell Function via Recognition of Paired Ig-like Receptor B. (PMID:30068593)
  • Together, this study identified ILT5 as an immunosuppressive regulator during sepsis, which may provide potential therapeutic strategy for sepsis. (PMID:31250008)
  • The Orphan Immune Receptor LILRB3 Modulates Fc Receptor-Mediated Functions of Neutrophils. (PMID:31915259)
  • LILRB3 (ILT5) is a myeloid cell checkpoint that elicits profound immunomodulation. (PMID:32870822)
  • Characterization of LILRB3 and LILRA6 allelic variants in the Japanese population. (PMID:33526815)
  • KLRD1, FOSL2 and LILRB3 as potential biomarkers for plaques progression in acute myocardial infarction and stable coronary artery disease. (PMID:34271875)
  • Epithelial cells remove precancerous cells by cell competition via MHC class I-LILRB3 interaction. (PMID:34686865)
  • LILRB3 supports acute myeloid leukemia development and regulates T-cell antitumor immune responses through the TRAF2-cFLIP-NF-kappaB signaling axis. (PMID:35122056)
  • Distinct frequency patterns of LILRB3 and LILRA6 allelic variants in Europeans. (PMID:36449053)
  • LilrB3 is a putative cell surface receptor of APOE4. (PMID:36588123)
  • Identification of the hybrid gene LILRB5-3 by long-read sequencing and implication of its novel signaling function. (PMID:38807600)

Cross-species orthologs

15 orthologs

OrganismSymbolGene ID
mus_musculusLilra6ENSMUSG00000030427
mus_musculusPirbENSMUSG00000058818
mus_musculusLilra5ENSMUSG00000070873
mus_musculusPira12ENSMUSG00000074417
mus_musculusPira13ENSMUSG00000074419
mus_musculusPira1ENSMUSG00000081665
mus_musculusPira2ENSMUSG00000089942
rattus_norvegicusLilra5ENSRNOG00000027808
rattus_norvegicusLilrb3ENSRNOG00000046683
rattus_norvegicusLilrb2ENSRNOG00000054954
rattus_norvegicusLilrc2ENSRNOG00000058087
rattus_norvegicusPirbENSRNOG00000058422
rattus_norvegicusLOC134485274ENSRNOG00000062907
rattus_norvegicusENSRNOG00000067708
rattus_norvegicusENSRNOG00000069029

Paralogs (25): GP6 (ENSG00000088053), LILRB1 (ENSG00000104972), LILRA1 (ENSG00000104974), LILRB5 (ENSG00000105609), A1BG (ENSG00000121410), KIR2DL1 (ENSG00000125498), LILRB2 (ENSG00000131042), IGSF1 (ENSG00000147255), LAIR2 (ENSG00000167618), KIR3DL1 (ENSG00000167633), OSCAR (ENSG00000170909), FCAR (ENSG00000186431), LILRB4 (ENSG00000186818), LILRA5 (ENSG00000187116), KIR2DL4 (ENSG00000189013), VSTM1 (ENSG00000189068), NCR1 (ENSG00000189430), KIR2DS4 (ENSG00000221957), LILRA4 (ENSG00000239961), LILRA2 (ENSG00000239998), KIR3DL2 (ENSG00000240403), KIR3DL3 (ENSG00000242019), KIR2DL3 (ENSG00000243772), LILRA6 (ENSG00000244482), TARM1 (ENSG00000248385)

Protein

Protein identifiers

Leukocyte immunoglobulin-like receptor subfamily B member 3O75022 (reviewed: O75022)

Alternative names: CD85 antigen-like family member A, Immunoglobulin-like transcript 5, Monocyte inhibitory receptor HL9

All UniProt accessions (4): C9JWL8, F8W6G6, F8WD89, O75022

UniProt curated annotations — full annotation on UniProt →

Function. May act as receptor for class I MHC antigens. Becomes activated upon coligation of LILRB3 and immune receptors, such as FCGR2B and the B-cell receptor. Down-regulates antigen-induced B-cell activation by recruiting phosphatases to its immunoreceptor tyrosine-based inhibitor motifs (ITIM).

Subunit / interactions. Interacts with LYN, PTPN6/SHP-1 and PTPN11/SHP-2.

Subcellular location. Cell membrane.

Tissue specificity. Detected in monocytes and B-cells.

Post-translational modifications. Phosphorylated on tyrosine residues by LYN. Phosphorylation at Tyr-595 and Tyr-625 is important for interaction with PTPN6/SHP-1 and PTPN11/SHP-2.

Domain organisation. Contains 3 copies of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2-containing phosphatases, including PTPN6/SHP-1, resulting in the dephosphorylation of the downstream protein kinases SYK and BTK.

Miscellaneous. Belongs to the leukocyte receptor cluster (LRC) present on 19q13.4.

Isoforms (3)

UniProt IDNamesCanonical?
O75022-11yes
O75022-22
O75022-33

RefSeq proteins (3): NP_001074919, NP_001307889, NP_006855* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR007110Ig-like_domDomain
IPR013151Immunoglobulin_domDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR050412Ig-like_Receptors_ImmuneRegFamily

Pfam: PF00047, PF13895

UniProt features (61 total): sequence conflict 17, sequence variant 13, compositionally biased region 5, glycosylation site 4, disulfide bond 4, domain 4, short sequence motif 3, region of interest 2, modified residue 2, topological domain 2, splice variant 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
8YOTELECTRON MICROSCOPY2.48

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O75022-F174.310.52

Antibody-complex structures (SAbDab): 18YOT

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 595, 625

Disulfide bonds (4): 49–98, 144–196, 245–296, 345–396

Glycosylation sites (4): 139, 280, 301, 340

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-198933Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-HSA-6798695Neutrophil degranulation
R-HSA-1280218Adaptive Immune System
R-HSA-168249Innate Immune System
R-HSA-168256Immune System

MSigDB gene sets: 176 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GOBP_MYELOID_CELL_DIFFERENTIATION, GOBP_NEGATIVE_REGULATION_OF_CELL_DEVELOPMENT, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_REGULATION_OF_OSTEOCLAST_DIFFERENTIATION, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOBP_RESPONSE_TO_PEPTIDE, GOCC_SECRETORY_GRANULE, MODULE_45, MODULE_64, GOZGIT_ESR1_TARGETS_DN, MODULE_478, GOBP_MYELOID_LEUKOCYTE_DIFFERENTIATION, GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION, GOBP_REGULATION_OF_IMMUNE_RESPONSE

GO Biological Process (7): adaptive immune response (GO:0002250), immune response-regulating signaling pathway (GO:0002764), defense response (GO:0006952), cell surface receptor signaling pathway (GO:0007166), cytokine-mediated signaling pathway (GO:0019221), negative regulation of osteoclast differentiation (GO:0045671), immune system process (GO:0002376)

GO Molecular Function (4): transmembrane signaling receptor activity (GO:0004888), inhibitory MHC class I receptor activity (GO:0032396), signaling receptor activity (GO:0038023), protein binding (GO:0005515)

GO Cellular Component (3): plasma membrane (GO:0005886), secretory granule membrane (GO:0030667), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Immune System2
Adaptive Immune System1
Innate Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
signal transduction2
immune response1
regulation of immune response1
response to stress1
cell surface receptor signaling pathway1
cellular response to cytokine stimulus1
negative regulation of myeloid leukocyte differentiation1
osteoclast differentiation1
regulation of osteoclast differentiation1
biological_process1
signaling receptor activity1
MHC class I receptor activity1
molecular transducer activity1
binding1
membrane1
cell periphery1
secretory granule1
cytoplasmic vesicle membrane1
bounding membrane of organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

1296 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LILRB3CD300CQ08708790
LILRB3CD22P20273659
LILRB3RNASE2P10153622
LILRB3HLA-FP30511532
LILRB3CD79AP11912527
LILRB3BLNKQ8WV28510
LILRB3TYROBPO43914507
LILRB3HLA-EP13747470
LILRB3CFLARO15519433
LILRB3FCARP24071430
LILRB3DNTTP04053427
LILRB3THBDP07204424
LILRB3EBF1Q9UH73423
LILRB3XBP1P17861421
LILRB3RPS9P46781410

IntAct

15 interactions, top by confidence:

ABTypeScore
LILRB3KRT18psi-mi:“MI:0914”(association)0.430
LILRB3KRT8psi-mi:“MI:0914”(association)0.430
LILRB3PTPN6psi-mi:“MI:0915”(physical association)0.400
PTPN6LILRB3psi-mi:“MI:0915”(physical association)0.400
BTNL8LILRB3psi-mi:“MI:0915”(physical association)0.400
LILRB3psi-mi:“MI:0915”(physical association)0.400
MOGLILRB3psi-mi:“MI:0915”(physical association)0.400
LILRB3MPZpsi-mi:“MI:0915”(physical association)0.400
LILRB3TNFRSF12Apsi-mi:“MI:0915”(physical association)0.400
LILRB3psi-mi:“MI:0915”(physical association)0.000

ESM2 similar proteins: A0A0K2S4Q6, A2A7V7, A6NI73, A8K4G0, O43699, O75019, O75022, O75023, O75871, O76036, P0C191, P20138, P24071, P40198, P59901, P80943, Q08708, Q13410, Q28110, Q3U497, Q496F6, Q64JA4, Q6GTX8, Q6ISS4, Q6PI73, Q6UXZ3, Q7TSN2, Q863H2, Q8C567, Q8K249, Q8MJZ2, Q8MJZ7, Q8N149, Q8N423, Q8N6C8, Q8NHJ6, Q8NHL6, Q8VBT3, Q8VCH2, Q95JB9

Diamond homologs: A0A0G2KBC9, A6NI73, C0HJX2, C0HJX3, D3ZQX2, O75019, O75022, O75023, O76036, P0C191, P24071, P43626, P43629, P43630, P59901, P83556, P97484, Q14943, Q14954, Q61450, Q64281, Q6GTX8, Q6ISS4, Q6PI73, Q7TQA1, Q863H2, Q8C567, Q8IYS5, Q8MJZ2, Q8MJZ7, Q8N109, Q8N149, Q8N423, Q8N6C8, Q8N743, Q8NHJ6, Q8NHK3, Q8NHL6, Q95JB9, Q9HCN6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

127 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance96
Likely benign15
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2187 predictions. Top by Δscore:

VariantEffectΔscore
19:54217236:CAGC:Cacceptor_gain1.0000
19:54217237:AGCCT:Aacceptor_loss1.0000
19:54217238:GC:Gacceptor_gain1.0000
19:54217238:GCCTG:Gacceptor_loss1.0000
19:54217239:CC:Cacceptor_gain1.0000
19:54217239:CCTG:Cacceptor_loss1.0000
19:54217240:C:CCacceptor_gain1.0000
19:54217240:CTGCA:Cacceptor_loss1.0000
19:54217314:CTCA:Cdonor_loss1.0000
19:54217315:TCAC:Tdonor_loss1.0000
19:54217316:CACCT:Cdonor_loss1.0000
19:54217317:A:ACdonor_gain1.0000
19:54217317:A:ATdonor_loss1.0000
19:54217318:C:CCdonor_gain1.0000
19:54217318:CCT:Cdonor_gain1.0000
19:54217318:CCTCA:Cdonor_gain1.0000
19:54217344:TCC:Tdonor_gain1.0000
19:54217473:CTCTG:Cacceptor_gain1.0000
19:54217474:TCTG:Tacceptor_loss1.0000
19:54217475:CTG:Cacceptor_gain1.0000
19:54217476:TG:Tacceptor_gain1.0000
19:54217477:GCTG:Gacceptor_loss1.0000
19:54217478:C:CCacceptor_gain1.0000
19:54217479:T:Aacceptor_loss1.0000
19:54218636:T:TAdonor_gain1.0000
19:54218643:A:ACdonor_gain1.0000
19:54218644:C:CCdonor_gain1.0000
19:54218764:T:TAdonor_gain1.0000
19:54219125:TCAC:Tdonor_loss1.0000
19:54219126:CACC:Cdonor_loss1.0000

AlphaMissense

1012 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000122357 (19:54217595 C>A,T), RS1000270962 (19:54219632 C>T), RS1000860231 (19:54215812 C>G), RS1001012017 (19:54218618 C>G), RS1002063044 (19:54218938 A>G), RS1002066934 (19:54217723 C>T), RS1002264870 (19:54216894 T>A,C,G), RS1002658153 (19:54218881 A>C), RS1002722103 (19:54216755 C>T), RS1003015521 (19:54216958 C>G,T), RS1004965931 (19:54215907 C>T), RS1005191721 (19:54217862 C>T), RS1005710436 (19:54217651 C>T), RS1006044366 (19:54216498 G>T), RS1006104722 (19:54216315 T>C)

Disease associations

OMIM: gene MIM:604820 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

StudyTraitp-value
GCST006575_26Takayasu arteritis2.000000e-08
GCST006575_50Takayasu arteritis4.000000e-08
GCST008362_34Birth weight1.000000e-11
GCST90002393_673Monocyte count3.000000e-10

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004344birth weight
EFO:0005091monocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
Methotrexatedecreases expression2
GSK-J4increases expression1
triphenyl phosphateaffects expression1
di-n-butylphosphoric acidaffects expression1
azoxystrobindecreases expression1
chloropicrinincreases expression1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamidedecreases expression1
pyrimidifendecreases expression1
ICG 001increases expression1
picoxystrobindecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Benzo(a)pyrenedecreases expression1
Nickelincreases expression1
Rotenonedecreases expression1
Tretinoinincreases expression1
Valproic Aciddecreases expression, increases methylation1
Zidovudineaffects cotreatment, increases expression1
Aflatoxin B1increases methylation1
Antirheumatic Agentsdecreases expression1
Cadmium Chlorideincreases expression1

Cellosaurus cell lines

2 cell lines: 1 spontaneously immortalized cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E6R1Genomeditech CHO-K1 H_LILRB3(ILT5)Spontaneously immortalized cell lineFemale
CVCL_E6UFGenomeditech HEK-293 H_LILRB3(ILT5)Transformed cell lineFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.