CLEC4D

gene
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Also known as MpclCD368MCLDectin-3

Summary

CLEC4D (C-type lectin domain family 4 member D, HGNC:14554) is a protein-coding gene on chromosome 12p13.31, encoding C-type lectin domain family 4 member D (Q8WXI8). Calcium-dependent lectin that acts as a pattern recognition receptor (PRR) of the innate immune system: recognizes damage-associated molecular patterns (DAMPs) of pathogen-associated molecular patterns (PAMPs) of bacteria and fungi.

This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signalling, glycoprotein turnover, and roles in inflammation and immune response. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region.

Source: NCBI Gene 338339 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 44 total
  • MANE Select transcript: NM_080387

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14554
Approved symbolCLEC4D
NameC-type lectin domain family 4 member D
Location12p13.31
Locus typegene with protein product
StatusApproved
AliasesMpcl, CD368, MCL, Dectin-3
Ensembl geneENSG00000166527
Ensembl biotypeprotein_coding
OMIM609964
Entrez338339

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000299665, ENST00000382064, ENST00000959647

RefSeq mRNA: 1 — MANE Select: NM_080387 NM_080387

CCDS: CCDS8593

Canonical transcript exons

ENST00000299665 — 6 exons

ExonStartEnd
ENSE0000110386085181648518274
ENSE0000110386785152368515328
ENSE0000110387085190098519160
ENSE0000110387485202268520341
ENSE0000123402585211248522366
ENSE0000123403585135038513760

Expression profiles

Bgee: expression breadth ubiquitous, 130 present calls, max score 91.56.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 2.0182 / max 598.0148, expressed in 170 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
1239711.7460147
1239700.191884
1239720.03419
1239660.01904
1239680.01274
1239690.00844
1239650.00341
1239670.00271

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
bone marrowUBERON:000237191.56gold quality
monocyteCL:000057691.35gold quality
leukocyteCL:000073890.78gold quality
bone marrow cellCL:000209289.00gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.76gold quality
bloodUBERON:000017883.23gold quality
granulocyteCL:000009482.36gold quality
trabecular bone tissueUBERON:000248380.93gold quality
right lungUBERON:000216775.00gold quality
vermiform appendixUBERON:000115474.32gold quality
spleenUBERON:000210671.65gold quality
caecumUBERON:000115366.99gold quality
upper lobe of left lungUBERON:000895265.51gold quality
upper lobe of lungUBERON:000894863.61gold quality
buccal mucosa cellCL:000233659.56gold quality
tendon of biceps brachiiUBERON:000818857.71silver quality
lungUBERON:000204856.99gold quality
myocardiumUBERON:000234956.26gold quality
left uterine tubeUBERON:000130355.58gold quality
descending thoracic aortaUBERON:000234554.92gold quality
smooth muscle tissueUBERON:000113554.84gold quality
gall bladderUBERON:000211054.74gold quality
oviduct epitheliumUBERON:000480454.50gold quality
lymph nodeUBERON:000002954.07gold quality
omental fat padUBERON:001041453.84gold quality
peritoneumUBERON:000235853.80gold quality
hindlimb stylopod muscleUBERON:000425253.62gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450253.61gold quality
adipose tissue of abdominal regionUBERON:000780853.24gold quality
fallopian tubeUBERON:000388950.95gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting CLEC4D, 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-8485100.0077.574731
HSA-MIR-548AW99.9972.573559
HSA-MIR-366299.9973.825684
HSA-MIR-56899.9869.862084
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-60799.9773.625593
HSA-MIR-548AN99.9770.912817
HSA-MIR-314899.9775.066478
HSA-MIR-365899.9673.874379
HSA-MIR-767-5P99.9570.85993
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-627-3P99.9071.423316
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-17-5P99.8973.832665
HSA-MIR-95-5P99.8972.173973
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-526B-3P99.8874.062587
HSA-MIR-93-5P99.8873.982606
HSA-MIR-394199.8670.542735
HSA-MIR-6875-3P99.8270.262983
HSA-MIR-129999.7771.242389
HSA-MIR-1213099.7565.47452
HSA-MIR-674599.7465.331321
HSA-MIR-494-3P99.7071.452795
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-1251-3P99.6467.211408

Literature-anchored findings (GeneRIF, showing 6)

  • Cross-linking of the receptor leads to a rapid internalization suggesting that CLECSF8 constitutes and endocytic receptor. (PMID:14971047)
  • CLECSF8 functions as an activation receptor on myeloid cells and associates with a novel adaptor molecule (PMID:22689578)
  • Results show the molecular mechanism of glycolipid recognition through C-type lectin receptors, which may provide clues to rational design for effective adjuvants. (PMID:24101491)
  • The Syk-Coupled C-Type Lectin Receptors Dectin-2 and Dectin-3 Are Involved in Paracoccidioides brasiliensis Recognition by Human Plasmacytoid Dendritic Cells. (PMID:29616019)
  • The Mincle/Syk/NF-kappaB Signaling Circuit Is Essential for Maintaining the Protumoral Activities of Tumor-Associated Macrophages. (PMID:32532809)
  • C-type lectin receptor Dectin3 deficiency balances the accumulation and function of FoxO1-mediated LOX-1(+) M-MDSCs in relieving lupus-like symptoms. (PMID:34480018)

Cross-species orthologs

21 orthologs

OrganismSymbolGene ID
danio_rerioasgr1c.2ENSDARG00000046092
danio_reriosi:dkey-61f9.1ENSDARG00000070414
danio_rerioasgr1aENSDARG00000095963
danio_reriosi:cabz01007816.2ENSDARG00000102537
danio_rerioasgr1bENSDARG00000103480
danio_reriosi:ch211-283g2.5ENSDARG00000108953
danio_rerioENSDARG00000111755
danio_rerioENSDARG00000112842
mus_musculusClec4dENSMUSG00000030144
rattus_norvegicusClec4dENSRNOG00000067848
drosophila_melanogastertfcFBGN0035199
drosophila_melanogasterCG14866FBGN0038315
drosophila_melanogasterlectin-46CbFBGN0040092
drosophila_melanogasterlectin-46CaFBGN0040093
drosophila_melanogasterlectin-33AFBGN0040096
drosophila_melanogasterCG34033FBGN0054033
caenorhabditis_elegansclec-87WBGENE00007709
caenorhabditis_elegansclec-91WBGENE00014117
caenorhabditis_elegansWBGENE00016088
caenorhabditis_elegansWBGENE00018692
caenorhabditis_elegansWBGENE00019606

Paralogs (14): CD209 (ENSG00000090659), FCER2 (ENSG00000104921), CLEC4M (ENSG00000104938), CLEC4A (ENSG00000111729), CD207 (ENSG00000116031), CLEC10A (ENSG00000132514), ASGR1 (ENSG00000141505), CLEC4F (ENSG00000152672), ASGR2 (ENSG00000161944), CLEC4E (ENSG00000166523), CLEC4G (ENSG00000182566), CLEC17A (ENSG00000187912), CLEC4C (ENSG00000198178), CLEC6A (ENSG00000205846)

Protein

Protein identifiers

C-type lectin domain family 4 member DQ8WXI8 (reviewed: Q8WXI8)

Alternative names: C-type lectin superfamily member 8, C-type lectin-like receptor 6, Dendritic cell-associated C-type lectin 3

All UniProt accessions (2): A6NHA5, Q8WXI8

UniProt curated annotations — full annotation on UniProt →

Function. Calcium-dependent lectin that acts as a pattern recognition receptor (PRR) of the innate immune system: recognizes damage-associated molecular patterns (DAMPs) of pathogen-associated molecular patterns (PAMPs) of bacteria and fungi. The PAMPs include alpha-mannans on C.albicans hypheas and mycobacterial trehalose 6,6’-dimycolate (TDM). Interacts with signaling adapter Fc receptor gamma chain/FCER1G, likely via CLEC4E, to form a functional complex in myeloid cells. Binding of mycobacterial TDM or C.albicans alpha-mannans to this receptor complex leads to phosphorylation of the immunoreceptor tyrosine-based activation motif (ITAM) of FCER1G, triggering activation of SYK, CARD9 and NF-kappa-B, consequently driving maturation of antigen-presenting cells and shaping antigen-specific priming of T-cells toward effector T-helper 1 and T-helper 17 cell subtypes. The heterodimer formed with CLEC6A is active against fungal infection. Functions as an endocytic receptor. May be involved in antigen uptake at the site of infection, either for clearance of the antigen, or for processing and further presentation to T-cells.

Subunit / interactions. Heterodimer with CLEC4E; disulfide-linked. CLEC4E acts as a bridge for interaction between CLEC4D and FCER1G to form a functional complex. Heterodimer with CLEC6A; this heterodimer forms a pattern recognition receptor (PRR) against fungal infection.

Subcellular location. Cell membrane.

Tissue specificity. Expressed weakly in peripheral blood leukocytes, bone marrow and spleen. Expression is confined mostly in monocytes and macrophage and seems to be up-regulated by IL-6, IL-10, TNF and IFN-gamma.

Induction. By autocrine inflammatory stimuli.

RefSeq proteins (1): NP_525126* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001304C-type_lectin-likeDomain
IPR016186C-type_lectin-like/link_sfHomologous_superfamily
IPR016187CTDL_foldHomologous_superfamily
IPR033989CD209-like_CTLDDomain
IPR050111C-type_lectin/snaclec_domainFamily

Pfam: PF00059

UniProt features (32 total): strand 11, binding site 4, glycosylation site 3, disulfide bond 3, topological domain 2, mutagenesis site 2, helix 2, chain 1, sequence variant 1, transmembrane region 1, turn 1, domain 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
3WHDX-RAY DIFFRACTION2.29
2LS8SOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8WXI8-F186.580.68

Functional residue map

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

Ligand- & substrate-binding residues (4): 173; 175; 195; 196

Disulfide bonds (3): 84–95, 112–207, 182–199

Glycosylation sites (3): 102, 111, 45

Mutagenesis-validated functional residues (2):

PositionPhenotype
173no effect on already low affinity binding to trehalose-6,6’-dimycolate.
175no effect on already low affinity binding to trehalose-6,6’-dimycolate.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-5621480Dectin-2 family
R-HSA-6798695Neutrophil degranulation

MSigDB gene sets: 185 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_DN, GOBP_REGULATION_OF_CELL_ACTIVATION, REACTOME_INNATE_IMMUNE_SYSTEM, GOCC_SECRETORY_GRANULE, GOBP_T_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION, GOCC_CELL_SURFACE, AP4_Q6, CAGCTG_AP4_Q5, GOBP_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, TCF4_Q5, GOBP_REGULATION_OF_IMMUNE_RESPONSE, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_T_CELL_DIFFERENTIATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_MYELOID_LEUKOCYTE_ACTIVATION

GO Biological Process (9): adaptive immune response (GO:0002250), T cell differentiation involved in immune response (GO:0002292), positive regulation of myeloid dendritic cell activation (GO:0030887), Fc-gamma receptor signaling pathway (GO:0038094), defense response to bacterium (GO:0042742), positive regulation of canonical NF-kappaB signal transduction (GO:0043123), antifungal innate immune response (GO:0061760), immune system process (GO:0002376), innate immune response (GO:0045087)

GO Molecular Function (6): D-mannose binding (GO:0005537), carbohydrate binding (GO:0030246), immunoglobulin receptor binding (GO:0034987), pattern recognition receptor activity (GO:0038187), metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (6): plasma membrane (GO:0005886), external side of plasma membrane (GO:0009897), specific granule membrane (GO:0035579), tertiary granule membrane (GO:0070821), ficolin-1-rich granule membrane (GO:0101003), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
C-type lectin receptors (CLRs)1
Innate Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
immune response3
secretory granule membrane3
binding2
tertiary granule2
T cell activation involved in immune response1
T cell differentiation1
myeloid dendritic cell activation1
positive regulation of leukocyte activation1
regulation of myeloid dendritic cell activation1
Fc receptor signaling pathway1
defense response1
response to bacterium1
canonical NF-kappaB signal transduction1
regulation of canonical NF-kappaB signal transduction1
positive regulation of intracellular signal transduction1
innate immune response1
defense response to fungus1
biological_process1
defense response to symbiont1
monosaccharide binding1
signaling receptor binding1
signaling receptor activity1
cation binding1
membrane1
cell periphery1
plasma membrane1
cell surface1
side of membrane1
specific granule1
ficolin-1-rich granule1
cellular anatomical structure1

Protein interactions and networks

STRING

936 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CLEC4DCLEC6AQ6EIG7950
CLEC4DFCER1GP30273851
CLEC4DSYKP43405798
CLEC4DCLEC7AQ9BXN2798
CLEC4DCLEC4EQ9ULY5739
CLEC4DCARD9Q9H257706
CLEC4DCLEC9AQ6UXN8698
CLEC4DCLEC1AQ8NC01578
CLEC4DPRRG4Q9BZD6572
CLEC4DMALT1Q9UDY8521
CLEC4DBCL10O95999517
CLEC4DIL6P05231517
CLEC4DCLEC12AQ5QGZ9493
CLEC4DCLEC12BQ2HXU8458
CLEC4DVNN1O95497438

IntAct

13 interactions, top by confidence:

ABTypeScore
ACTN2CLEC4Dpsi-mi:“MI:0915”(physical association)0.560
JAGN1CLEC4Dpsi-mi:“MI:0915”(physical association)0.560
ZDHHC22CLEC4Dpsi-mi:“MI:0915”(physical association)0.560
ANKRD46CLEC4Dpsi-mi:“MI:0915”(physical association)0.560
ZDHHC22CLEC4Dpsi-mi:“MI:0915”(physical association)0.000
ANKRD46CLEC4Dpsi-mi:“MI:0915”(physical association)0.000

BioGRID (313): CLEC4D (Two-hybrid), JAGN1 (Two-hybrid), ZDHHC22 (Two-hybrid), ANKRD46 (Two-hybrid), MYO1C (Affinity Capture-MS), PGRMC1 (Affinity Capture-MS), CLIC1 (Affinity Capture-MS), IPO5 (Affinity Capture-MS), CLGN (Affinity Capture-MS), SPTBN2 (Affinity Capture-MS), SEC16A (Affinity Capture-MS), ARPC3 (Affinity Capture-MS), SPINT2 (Affinity Capture-MS), MYO1B (Affinity Capture-MS), LANCL1 (Affinity Capture-MS)

ESM2 similar proteins: A4KWA5, A4KWA6, A4KWA8, B2KG20, D4AD02, O54709, O70215, P26717, P26718, P27471, P27811, P27814, P37217, P61252, Q07108, Q07444, Q0H8B9, Q149M0, Q504P2, Q5DT36, Q5DT37, Q5DT39, Q5M9I1, Q5RFR2, Q60652, Q60654, Q68D85, Q6QLQ4, Q6UXN8, Q80XD9, Q80ZC8, Q8C1T8, Q8MI05, Q8MJH1, Q8VBX4, Q8VI21, Q8WXI8, Q91V08, Q925N7, Q95MI4

Diamond homologs: A5PMY6, A6QP79, D3ZWT9, O14594, P02706, P02707, P05451, P06734, P07306, P07307, P07897, P07898, P08290, P08661, P10716, P10758, P11226, P13608, P13611, P16112, P19999, P20693, P22897, P24721, P34927, P41317, P43137, P48304, P49300, P49301, P55066, P55067, P60883, P70194, P81282, P82596, P86854, Q28343, Q28670, Q29011

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance35
Likely benign4
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

775 predictions. Top by Δscore:

VariantEffectΔscore
12:8513761:G:GGdonor_gain1.0000
12:8515234:A:AGacceptor_gain1.0000
12:8515235:G:GGacceptor_gain1.0000
12:8518282:GT:Gdonor_gain1.0000
12:8518280:GAGT:Gdonor_gain0.9900
12:8519002:A:AGacceptor_gain0.9900
12:8519002:ACTT:Aacceptor_gain0.9900
12:8520338:GAGT:Gdonor_gain0.9900
12:8520340:GT:Gdonor_gain0.9900
12:8521122:A:AGacceptor_gain0.9900
12:8521123:G:GGacceptor_gain0.9900
12:8513757:AAACG:Adonor_loss0.9800
12:8513759:ACG:Adonor_loss0.9800
12:8513760:CG:Cdonor_loss0.9800
12:8513761:G:Cdonor_loss0.9800
12:8513762:T:Gdonor_loss0.9800
12:8513763:GAGTA:Gdonor_loss0.9800
12:8513764:AGTAC:Adonor_loss0.9800
12:8515227:T:TAacceptor_gain0.9800
12:8519005:T:TAacceptor_gain0.9800
12:8519008:G:Aacceptor_gain0.9800
12:8520342:G:GGdonor_gain0.9800
12:8521118:TTTCA:Tacceptor_loss0.9800
12:8521119:TTCA:Tacceptor_loss0.9800
12:8521120:TCA:Tacceptor_loss0.9800
12:8521121:CAGA:Cacceptor_loss0.9800
12:8521122:AGAT:Aacceptor_loss0.9800
12:8513759:AC:Adonor_gain0.9700
12:8515234:AGT:Aacceptor_gain0.9700
12:8515235:GTG:Gacceptor_gain0.9700

AlphaMissense

1441 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:8519098:A:CS108R0.937
12:8519100:T:AS108R0.937
12:8519100:T:GS108R0.937
12:8519091:G:CW105C0.924
12:8519091:G:TW105C0.924
12:8520265:T:CF142L0.917
12:8520267:C:AF142L0.917
12:8520267:C:GF142L0.917
12:8520309:G:CW156C0.908
12:8520309:G:TW156C0.908
12:8521199:G:CW192C0.904
12:8521199:G:TW192C0.904
12:8519040:G:CW88C0.901
12:8519040:G:TW88C0.901
12:8521205:G:CW194C0.895
12:8521205:G:TW194C0.895
12:8521130:G:CW169C0.888
12:8521130:G:TW169C0.888
12:8519047:T:CF91L0.885
12:8519049:C:AF91L0.885
12:8519049:C:GF91L0.885
12:8520303:G:CW154C0.882
12:8520303:G:TW154C0.882
12:8520229:T:CF130L0.869
12:8520231:T:AF130L0.869
12:8520231:T:GF130L0.869
12:8521242:T:AC207S0.869
12:8521243:G:CC207S0.869
12:8521203:T:AW194R0.863
12:8521203:T:CW194R0.863

dbSNP variants (sampled 300 via entrez): RS1000013317 (12:8530297 G>C), RS1000033961 (12:8514735 C>T), RS1000218007 (12:8512616 C>T), RS1000246294 (12:8517468 G>A,T), RS1000460248 (12:8511620 G>C), RS1000923363 (12:8522711 A>T), RS1000954094 (12:8523090 G>A), RS1001157723 (12:8528559 A>C), RS1001195402 (12:8524331 C>G), RS1001231782 (12:8512708 A>T), RS1001266200 (12:8528818 G>A), RS1001300101 (12:8518788 G>A), RS1001422210 (12:8528882 T>C), RS1001605625 (12:8519132 T>C), RS1001806911 (12:8512900 G>A,T)

Disease associations

OMIM: gene MIM:609964 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression3
alpha phellandrenedecreases expression1
triphenyl phosphateaffects expression1
bisphenol Adecreases methylation1
sulforaphaneincreases expression1
cobaltous chlorideincreases expression1
butyraldehydeincreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneincreases methylation1
Lipopolysaccharidesincreases expression1
Nickelincreases expression1
Paraquatdecreases expression1
Tretinoinincreases expression1
Antirheumatic Agentsdecreases expression1
Nanotubes, Carbonincreases 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.