KIR3DL3

gene
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Also known as KIRC1KIR3DL7KIR44CD158Z

Summary

KIR3DL3 (killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3, HGNC:16312) is a protein-coding gene on chromosome 19q13.42, encoding Killer cell immunoglobulin-like receptor 3DL3 (Q8N743). Receptor on natural killer cells.

Killer cell immunoglobulin-like receptors (KIRs) are transmembrane glycoproteins expressed by natural killer cells and subsets of T cells. The KIR genes are polymorphic and highly homologous and they are found in a cluster on chromosome 19q13.4 within the 1 Mb leukocyte receptor complex (LRC). The gene content of the KIR gene cluster varies among haplotypes, although several “framework” genes are found in all haplotypes (KIR3DL3, KIR3DP1, KIR3DL4, KIR3DL2). The KIR proteins are classified by the number of extracellular immunoglobulin domains (2D or 3D) and by whether they have a long (L) or short (S) cytoplasmic domain. KIR proteins with the long cytoplasmic domain transduce inhibitory signals upon ligand binding via an immune tyrosine-based inhibitory motif (ITIM), while KIR proteins with the short cytoplasmic domain lack the ITIM motif and instead associate with the TYRO protein tyrosine kinase binding protein to transduce activating signals. The ligands for several KIR proteins are subsets of HLA class I molecules; thus, KIR proteins are thought to play an important role in regulation of the immune response. This gene is one of the “framework” loci that is present on all haplotypes.

Source: NCBI Gene 115653 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 63 total
  • MANE Select transcript: NM_153443

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16312
Approved symbolKIR3DL3
Namekiller cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
Location19q13.42
Locus typegene with protein product
StatusApproved
AliasesKIRC1, KIR3DL7, KIR44, CD158Z
Ensembl geneENSG00000242019
Ensembl biotypeprotein_coding
OMIM610095
Entrez115653

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000291860

RefSeq mRNA: 1 — MANE Select: NM_153443 NM_153443

CCDS: CCDS12903

Canonical transcript exons

ENST00000291860 — 8 exons

ExonStartEnd
ENSE000011775635472444254724530
ENSE000011805955473597154736632
ENSE000024336675473582054735872
ENSE000024481645473525354735357
ENSE000024593035472761154727910
ENSE000024651835472949354729786
ENSE000025152095472524754725282
ENSE000025343625472605354726337

Expression profiles

Bgee: expression breadth tissue_specific, 3 present calls, max score 78.91.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047378.91silver quality
bone marrow cellCL:000209240.04gold quality
sural nerveUBERON:001548838.11gold quality
granulocyteCL:000009437.64gold quality
colonic epitheliumUBERON:000039737.20gold quality
ventricular zoneUBERON:000305336.48gold quality
cortical plateUBERON:000534336.47gold quality
hindlimb stylopod muscleUBERON:000425236.36silver quality
ganglionic eminenceUBERON:000402335.49gold quality
bloodUBERON:000017833.82silver quality
bone marrowUBERON:000237133.73gold quality
skeletal muscle tissueUBERON:000113433.38gold quality
duodenumUBERON:000211432.66gold quality
muscle tissueUBERON:000238531.06gold quality
tonsilUBERON:000237230.42gold quality
stromal cell of endometriumCL:000225529.87gold quality
leukocyteCL:000073829.25gold quality
liverUBERON:000210729.17gold quality
prefrontal cortexUBERON:000045129.04gold quality
monocyteCL:000057627.62gold quality
lymph nodeUBERON:000002927.57gold quality
uterine cervixUBERON:000000227.36gold quality
spleenUBERON:000210627.36gold quality
urinary bladderUBERON:000125526.82gold quality
rectumUBERON:000105226.66gold quality
islet of LangerhansUBERON:000000626.55gold quality
vermiform appendixUBERON:000115426.42gold quality
gall bladderUBERON:000211025.98gold quality
olfactory segment of nasal mucosaUBERON:000538625.89gold quality
placentaUBERON:000198725.81gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-CURD-84yes34.11
E-ANND-3no0.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting KIR3DL3, 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-453199.9969.703181
HSA-MIR-430299.8967.941187
HSA-MIR-6505-5P99.7369.251595
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-7157-5P99.6669.331829
HSA-MIR-6513-3P99.5969.771102
HSA-MIR-431099.5968.842527
HSA-MIR-549A-3P99.5468.17825
HSA-MIR-766-3P99.4765.241811
HSA-MIR-569799.3967.741249
HSA-MIR-133A-5P99.2869.13941
HSA-MIR-10B-3P99.0466.98988
HSA-MIR-432698.9767.63962
HSA-MIR-3922-5P98.7766.531059
HSA-MIR-1211498.7063.45730
HSA-MIR-3144-5P97.6465.45646
HSA-MIR-4676-5P97.5465.29715
HSA-MIR-57597.5465.18718
HSA-MIR-6781-3P97.4466.85970
HSA-MIR-2682-3P97.1066.16840
HSA-MIR-429696.3563.551233
HSA-MIR-426596.1864.68557
HSA-MIR-432296.1864.85539
HSA-MIR-191-3P83.9061.2544

Literature-anchored findings (GeneRIF, showing 11)

  • an inhibitory element was identified in the KIR2DL4 promoter and an activating element was found in the KIR3DL3 promoter; AML-2 acts as a repressor of expression of both KIR2DL4 and KIR3DL3 in mature NK cells (PMID:15778373)
  • KIR3DL3 gene is not a pseudogene but encodes a protein that is not expressed in healthy individuals. (PMID:16391939)
  • Allelic sequence polymorphism at the KIR3DL3 is associated with pre-Eclampsia (PMID:16823588)
  • Seventeen novel alleles have been added to the already extensive KIR3DL3 diversity. (PMID:17900289)
  • The frequencies of alleles of killer cell immunoglobulin-like receptor genes, KIR3DL3 and KIR3DL2, and the carrier frequency of KIR2DL4 alleles have been determined from a population of African Americans by DNA sequencing of the coding regions. (PMID:21607693)
  • Array CGH showed a 95 Kb de novo duplication on chromosome 19q13.4 encompassing four killer cell immunoglobulin-like receptor (KIR) genes. (PMID:23952617)
  • Higher proportion of NK cells expressing inhibitory CD158b and CD158e receptors is associated with significant liver injury in children with chronic hepatitis C. (PMID:28611271)
  • KIR3DL3 Is an Inhibitory Receptor for HHLA2 that Mediates an Alternative Immunoinhibitory Pathway to PD1. (PMID:33229411)
  • KIR3DL3-HHLA2 is a human immunosuppressive pathway and a therapeutic target. (PMID:34244312)
  • KIR3DL3-HHLA2 and TMIGD2-HHLA2 pathways: The dual role of HHLA2 in immune responses and its potential therapeutic approach for cancer immunotherapy. (PMID:35933091)
  • Polymorphic KIR3DL3 expression modulates tissue-resident and innate-like T cells. (PMID:37390222)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
mus_musculusKir3dl1ENSMUSG00000031424
mus_musculusKir3dl2ENSMUSG00000057439
rattus_norvegicusKir3dl1ENSRNOG00000027843

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), LILRB3 (ENSG00000204577), KIR2DS4 (ENSG00000221957), LILRA4 (ENSG00000239961), LILRA2 (ENSG00000239998), KIR3DL2 (ENSG00000240403), KIR2DL3 (ENSG00000243772), LILRA6 (ENSG00000244482), TARM1 (ENSG00000248385)

Protein

Protein identifiers

Killer cell immunoglobulin-like receptor 3DL3Q8N743 (reviewed: Q8N743)

Alternative names: CD158 antigen-like family member Z, Killer cell inhibitory receptor 1

All UniProt accessions (1): A0A8I5QEB2

UniProt curated annotations — full annotation on UniProt →

Function. Receptor on natural killer cells. May inhibit the activity of NK cells thus preventing cell lysis.

Subcellular location. Cell membrane.

Polymorphism. Various different KIR3DL3 alleles are known: KIR3DL300101, KIR3DL300102, KIR3DL300103, KIR3DL300201, KIR3DL300202, KIR3DL300203, KIR3DL300204, KIR3DL300205, KIR3DL300206, KIR3DL300207, KIR3DL30030101 KIR3DL30030102, KIR3DL300401, KIR3DL300402, KIR3DL3005, KIR3DL300601, KIR3DL300602, KIR3DL3007, KIR3DL300801, KIR3DL300802, KIR3DL300901, KIR3DL300902, KIR3DL3010, KIR3DL301101, KIR3DL301102, KIR3DL3012, KIR3DL301301, KIR3DL301302, KIR3DL301303, KIR3DL301304, KIR3DL301305, KIR3DL301306, KIR3DL301307, KIR3DL301401, KIR3DL301402, KIR3DL301403, KIR3DL301404, KIR3DL301405, KIR3DL3015 KIR3DL3016, KIR3DL3017, KIR3DL3018, KIR3DL3019, KIR3DL3020, KIR3DL3021, KIR3DL3022, KIR3DL3023, KIR3DL3024, KIR3DL3025, KIR3DL3026, KIR3DL3027, KIR3DL3028, KIR3DL3029, KIR3DL3030 and KIR3DL3031. The sequence shown corresponds to the alleles KIR3DL3002.

Similarity. Belongs to the immunoglobulin superfamily.

RefSeq proteins (1): NP_703144* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF00047

UniProt features (28 total): sequence variant 14, glycosylation site 3, disulfide bond 3, domain 3, topological domain 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N743-F180.200.55

Functional residue map

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

Disulfide bonds (3): 49–95, 144–195, 244–293

Glycosylation sites (3): 273, 179, 239

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 30 (showing top): GOBP_REGULATION_OF_IMMUNE_RESPONSE, GNF2_IL2RB, KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION, SHEN_SMARCA2_TARGETS_DN, GOMF_TRANSMEMBRANE_SIGNALING_RECEPTOR_ACTIVITY, HAHTOLA_SEZARY_SYNDROM_DN, LI_INDUCED_T_TO_NATURAL_KILLER_UP, GOBP_IMMUNE_RESPONSE_REGULATING_SIGNALING_PATHWAY, GOBP_IMMUNE_RESPONSE_INHIBITING_SIGNAL_TRANSDUCTION, JNK_DN.V1_DN, GOMF_IMMUNE_RECEPTOR_ACTIVITY, NFKBIA_TARGET_GENES, MIR5697, MIR6781_3P, MIR2682_3P

GO Biological Process (2): immune response-regulating signaling pathway (GO:0002764), cell communication (GO:0007154)

GO Molecular Function (0):

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
signal transduction1
regulation of immune response1
cellular process1
membrane1
cell periphery1
cellular anatomical structure1

Protein interactions and networks

STRING

320 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KIR3DL3STACQ99469859
KIR3DL3HHLA2Q9UM44837
KIR3DL3SORBS1Q9BX66822
KIR3DL3SPARTQ8N0X7806
KIR3DL3HLA-BP01889801
KIR3DL3TRIM45Q9H8W5767
KIR3DL3HLA-AP01891739
KIR3DL3HLA-CP04222733
KIR3DL3RUNX3Q13761715
KIR3DL3FCHSD2O94868713
KIR3DL3NCAM1P13591684
KIR3DL3KLRD1Q13241625
KIR3DL3KIR2DL1P43626583
KIR3DL3KIR2DL4P78400581
KIR3DL3ETV7Q9Y603518

IntAct

310 interactions, top by confidence:

ABTypeScore
EDDM3BKIR3DL3psi-mi:“MI:0915”(physical association)0.560
GIMAP5KIR3DL3psi-mi:“MI:0915”(physical association)0.560
SLC35A1KIR3DL3psi-mi:“MI:0915”(physical association)0.560
EMP3KIR3DL3psi-mi:“MI:0915”(physical association)0.560
LAPTM5KIR3DL3psi-mi:“MI:0915”(physical association)0.560
ASIC1KIR3DL3psi-mi:“MI:0915”(physical association)0.560
TNMDKIR3DL3psi-mi:“MI:0915”(physical association)0.560
C5KIR3DL3psi-mi:“MI:0915”(physical association)0.560
UPK2KIR3DL3psi-mi:“MI:0915”(physical association)0.560
ADAM33KIR3DL3psi-mi:“MI:0915”(physical association)0.560
CMTM5KIR3DL3psi-mi:“MI:0915”(physical association)0.560
AGTRAPKIR3DL3psi-mi:“MI:0915”(physical association)0.560
OLFM4KIR3DL3psi-mi:“MI:0915”(physical association)0.560
JAGN1KIR3DL3psi-mi:“MI:0915”(physical association)0.560
CTXN3KIR3DL3psi-mi:“MI:0915”(physical association)0.560
KIR3DL3CMTM5psi-mi:“MI:0915”(physical association)0.560
CD53KIR3DL3psi-mi:“MI:0915”(physical association)0.560
KIR3DL3GIMAP5psi-mi:“MI:0915”(physical association)0.560

BioGRID (29): KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid), KIR3DL3 (Two-hybrid)

ESM2 similar proteins: A0A0G2KBC9, A1YIY0, B6A8R8, C0HJX2, C0HJX3, D3ZQX2, P08101, P0C1X9, P0DTI4, P12314, P12318, P26151, P43626, P43627, P43628, P43629, P43630, P43631, P43632, P83555, P83556, P97484, Q01965, Q13291, Q14943, Q14952, Q14953, Q14954, Q28942, Q3B8P2, Q60513, Q61450, Q63203, Q64281, Q68SN8, Q6UX27, Q7TQA1, Q7Z6M3, Q8BG84, Q8BHK6

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.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 105 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Ras activation upon Ca2+ influx through NMDA receptor546.8×3e-06
Unblocking of NMDA receptors, glutamate binding and activation544.6×3e-06
Negative regulation of NMDA receptor-mediated neuronal transmission544.6×3e-06
Long-term potentiation539.0×6e-06
Assembly and cell surface presentation of NMDA receptors833.3×9e-09
Neurexins and neuroligins929.1×4e-09
Protein-protein interactions at synapses521.8×1e-04

GO biological processes:

GO termPartnersFoldFDR
establishment or maintenance of epithelial cell apical/basal polarity1059.9×3e-13
receptor clustering851.5×5e-10
protein localization to synapse647.4×4e-07
regulation of postsynaptic membrane neurotransmitter receptor levels630.7×4e-06
cell-cell adhesion1010.5×4e-06
protein-containing complex assembly89.4×1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance55
Likely benign6
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

910 predictions. Top by Δscore:

VariantEffectΔscore
19:54724529:TGG:Tdonor_loss1.0000
19:54724531:G:Tdonor_loss1.0000
19:54726254:GGACC:Gdonor_gain1.0000
19:54726255:G:Tdonor_gain1.0000
19:54735248:TCCA:Tacceptor_loss1.0000
19:54735249:CCA:Cacceptor_loss1.0000
19:54735250:CA:Cacceptor_loss1.0000
19:54735251:A:AGacceptor_gain1.0000
19:54735251:AG:Aacceptor_gain1.0000
19:54735252:G:GGacceptor_gain1.0000
19:54735252:GG:Gacceptor_gain1.0000
19:54735252:GGT:Gacceptor_gain1.0000
19:54735252:GGTA:Gacceptor_gain1.0000
19:54735252:GGTAA:Gacceptor_gain1.0000
19:54735353:AAAGA:Adonor_gain1.0000
19:54735354:AAGA:Adonor_gain1.0000
19:54735355:AGA:Adonor_gain1.0000
19:54735356:GA:Gdonor_gain1.0000
19:54735356:GAG:Gdonor_gain1.0000
19:54735358:G:GGdonor_gain1.0000
19:54724527:GTTG:Gdonor_gain0.9900
19:54724531:G:GGdonor_gain0.9900
19:54726213:G:GTdonor_gain0.9900
19:54735355:AGAG:Adonor_loss0.9900
19:54735357:AGTAA:Adonor_loss0.9900
19:54735358:G:Adonor_loss0.9900
19:54735359:TAAGT:Tdonor_loss0.9900
19:54735360:AA:Adonor_loss0.9900
19:54735361:AGTCT:Adonor_loss0.9900
19:54735745:ATGTT:Aacceptor_gain0.9900

AlphaMissense

2665 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:54727883:A:CS210R0.956
19:54727885:T:AS210R0.956
19:54727885:T:GS210R0.956
19:54727712:T:CF153L0.954
19:54727714:C:AF153L0.954
19:54727714:C:GF153L0.954
19:54729759:A:CS308R0.946
19:54729761:T:AS308R0.946
19:54729761:T:GS308R0.946
19:54726154:T:CF58L0.943
19:54726156:C:AF58L0.943
19:54726156:C:GF58L0.943
19:54729567:T:AC244S0.929
19:54729568:G:CC244S0.929
19:54729717:T:CF294L0.928
19:54729719:C:AF294L0.928
19:54729719:C:GF294L0.928
19:54726259:T:GY93D0.927
19:54726168:A:CK62N0.925
19:54726168:A:TK62N0.925
19:54729675:T:CF280L0.923
19:54729677:C:AF280L0.923
19:54729677:C:GF280L0.923
19:54726310:A:CS110R0.921
19:54726312:C:AS110R0.921
19:54726312:C:GS110R0.921
19:54729562:T:CL242S0.921
19:54729714:T:AC293S0.917
19:54729715:G:CC293S0.917
19:54727685:T:AC144S0.914

dbSNP variants (sampled 300 via entrez): RS1000235612 (19:54725272 G>A,T), RS1000499370 (19:54724291 G>A,T), RS1000571618 (19:54723973 C>G,T), RS1001119231 (19:54731005 T>G), RS1002892303 (19:54726885 A>G), RS1003367262 (19:54725555 C>T), RS1004598589 (19:54728800 G>A), RS1006240523 (19:54734443 A>G), RS1006826642 (19:54723955 G>A,C), RS1006929219 (19:54723863 A>G), RS1007367212 (19:54726087 C>A,G,T), RS1008032877 (19:54733838 G>C), RS1008063788 (19:54733522 C>CA), RS1008609098 (19:54732126 G>A), RS1008860136 (19:54724777 G>A)

Disease associations

OMIM: gene MIM:610095 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST90002394_566Monocyte percentage of white cells4.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007989monocyte percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

ChemicalActions (top 5)PubMed papers
quercitrinaffects expression1
CGP 52608affects binding, increases reaction1
Arsenicaffects expression1
Benzo(a)pyreneincreases expression1
Cadmiumdecreases expression1
Valproic Acidincreases methylation1
Copper Sulfateincreases expression1

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.