CLEC2B

gene
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Also known as AICLHP10085

Summary

CLEC2B (C-type lectin domain family 2 member B, HGNC:2053) is a protein-coding gene on chromosome 12p13.31, encoding C-type lectin domain family 2 member B (Q92478). Membrane-bound protein expressed on myeloid cells which acts as a ligand to stimulate the activating receptor NKp80/KLRF1, expressed on the surface of natural killer (NK) cells.

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. The encoded type 2 transmembrane protein may function as a cell activation antigen. An alternative splice variant has been described but its full-length sequence has not been determined. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region.

Source: NCBI Gene 9976 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 28 total
  • MANE Select transcript: NM_005127

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2053
Approved symbolCLEC2B
NameC-type lectin domain family 2 member B
Location12p13.31
Locus typegene with protein product
StatusApproved
AliasesAICL, HP10085
Ensembl geneENSG00000110852
Ensembl biotypeprotein_coding
OMIM603242
Entrez9976

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 2 retained_intron

ENST00000228438, ENST00000538152, ENST00000539028, ENST00000540743, ENST00000893503, ENST00000893504, ENST00000893505, ENST00000893506, ENST00000893507, ENST00000893508, ENST00000964946

RefSeq mRNA: 1 — MANE Select: NM_005127 NM_005127

CCDS: CCDS8605

Canonical transcript exons

ENST00000228438 — 5 exons

ExonStartEnd
ENSE0000071871798543819854484
ENSE0000071872398574749857637
ENSE0000082183198523699853408
ENSE0000221288998692059869354
ENSE0000367357198624999862573

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 98.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.7580 / max 2037.3463, expressed in 1095 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
12943931.22361062
1294402.2128722
1294430.6224180
1294380.3785191
1294420.175177
1294410.145774

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
upper leg skinUBERON:000426298.85gold quality
skin of hipUBERON:000155498.60gold quality
periodontal ligamentUBERON:000826697.80gold quality
gluteal muscleUBERON:000200097.62gold quality
vena cavaUBERON:000408796.95gold quality
pericardiumUBERON:000240796.69gold quality
mononuclear cellCL:000084296.63gold quality
penisUBERON:000098996.61gold quality
monocyteCL:000057696.58gold quality
mammalian vulvaUBERON:000099796.55gold quality
leukocyteCL:000073896.53gold quality
granulocyteCL:000009496.19gold quality
deciduaUBERON:000245096.13gold quality
gingivaUBERON:000182896.12gold quality
upper arm skinUBERON:000426395.90gold quality
gingival epitheliumUBERON:000194995.80gold quality
mucosa of urinary bladderUBERON:000125995.44gold quality
skin of legUBERON:000151195.43gold quality
zone of skinUBERON:000001495.30gold quality
visceral pleuraUBERON:000240195.17gold quality
skin of abdomenUBERON:000141695.09gold quality
left ovaryUBERON:000211995.08gold quality
palpebral conjunctivaUBERON:000181294.53gold quality
pleuraUBERON:000097794.50gold quality
spleenUBERON:000210694.40gold quality
esophagus squamous epitheliumUBERON:000692094.31gold quality
calcaneal tendonUBERON:000370194.10gold quality
bone marrowUBERON:000237194.07gold quality
right ovaryUBERON:000211894.03gold quality
subcutaneous adipose tissueUBERON:000219093.93gold quality

Single-cell (SCXA)

Detected in 18 experiment(s), a significant marker in 14.

ExperimentMarker?Max mean expression
E-MTAB-8884yes1182.12
E-GEOD-110499yes282.56
E-CURD-122yes44.93
E-HCAD-1yes43.44
E-HCAD-8yes33.87
E-HCAD-4yes29.06
E-MTAB-10287yes28.23
E-HCAD-10yes28.00
E-CURD-46yes19.65
E-CURD-88yes16.05
E-MTAB-8410yes12.83
E-GEOD-135922yes11.10
E-MTAB-5061yes5.93
E-CURD-95no783.72
E-MTAB-10290no584.46

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): GLI2

miRNA regulators (miRDB)

60 targeting CLEC2B, 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-477599.9875.006394
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-302E99.9670.742669
HSA-MIR-3912-5P99.9566.11925
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-311999.9271.342390
HSA-LET-7A-2-3P99.8770.531921
HSA-LET-7G-3P99.8570.431929
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-205299.7969.372031
HSA-MIR-57799.7869.132479
HSA-MIR-548A-3P99.7670.583524
HSA-MIR-4446-5P99.7269.192544
HSA-MIR-561-3P99.6470.903647
HSA-MIR-488-3P99.6168.791731
HSA-MIR-6832-5P99.5864.821132
HSA-MIR-1212299.5669.331672
HSA-MIR-582-5P99.4770.792635
HSA-MIR-312399.4767.152693
HSA-MIR-568399.3668.592083
HSA-MIR-19A-5P99.3666.931675
HSA-MIR-19B-1-5P99.3667.071669

Literature-anchored findings (GeneRIF, showing 9)

  • NKp80 is expressed on a highly responsive subset of effector memory CD8 T cells with an inflammatory NK-like phenotype and promotes T-cell responses toward AICL-expressing cells. (PMID:18922855)
  • expressed in primary liver cancers (PMID:20663776)
  • our data report a previously unrecognized regulatory circuit enabling autonomous control of human NK cell responses via the NKp80-AICL axis. (PMID:23929856)
  • Lipid rafts do not directly contribute to CLEC-2 receptor activation in platelets. (PMID:25462818)
  • Data suggest that vascular smooth muscle cells (VSMCs) stimulate platelets through platelet receptor CLEC-2, possibly leading to thrombus formation after plaque erosion. (PMID:26418160)
  • Review of C-type lectin-like receptor 2 and podoplanin interactions [review] (PMID:27960039)
  • our data demonstrate that AICL expression and surfacing are tightly controlled by several independent cellular posttranslational mechanisms. (PMID:29980609)
  • Plasma soluble C-type lectin-like receptor-2 is associated with the risk of coronary artery disease. (PMID:31280468)
  • Association between c-type lectin-like receptor 2 and microsatellite instability in colorectal cancer: a cross-sectional study. (PMID:35902826)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriosi:ch211-193e13.5ENSDARG00000052656
danio_rerioENSDARG00000074732
danio_reriosi:dkey-26c10.5ENSDARG00000088023
danio_reriosi:ch211-170d8.8ENSDARG00000090945
drosophila_melanogasterrgnFBGN0261258
caenorhabditis_elegansWBGENE00009156
caenorhabditis_elegansWBGENE00013008

Paralogs (23): CLEC2D (ENSG00000069493), CD69 (ENSG00000110848), KLRB1 (ENSG00000111796), KLRD1 (ENSG00000134539), KLRC1 (ENSG00000134545), KLRG1 (ENSG00000139187), KLRF1 (ENSG00000150045), CLEC1A (ENSG00000150048), CLEC1B (ENSG00000165682), CLEC7A (ENSG00000172243), CLEC12A (ENSG00000172322), OLR1 (ENSG00000173391), KLRC4 (ENSG00000183542), CLEC2A (ENSG00000188393), KLRG2 (ENSG00000188883), CLEC9A (ENSG00000197992), KLRC2 (ENSG00000205809), KLRC3 (ENSG00000205810), KLRK1 (ENSG00000213809), CLEC2L (ENSG00000236279), CLEC12B (ENSG00000256660), KLRF2 (ENSG00000256797), CLEC5A (ENSG00000258227)

Protein

Protein identifiers

C-type lectin domain family 2 member BQ92478 (reviewed: Q92478)

Alternative names: Activation-induced C-type lectin, C-type lectin superfamily member 2, IFN-alpha-2b-inducing-related protein 1

All UniProt accessions (2): Q92478, F5H631

UniProt curated annotations — full annotation on UniProt →

Function. Membrane-bound protein expressed on myeloid cells which acts as a ligand to stimulate the activating receptor NKp80/KLRF1, expressed on the surface of natural killer (NK) cells. In turn, stimulates NK-cell cytotoxicity and cytokine production leading to the cytolysis of malignant CLEC2B-expressing myeloid cells.

Subunit / interactions. Homodimer. Interacts with NKp80/KLRF1.

Subcellular location. Cell membrane. Golgi apparatus membrane.

Tissue specificity. Expressed preferentially in lymphoid tissues, and in most hematopoietic cell types.

Post-translational modifications. (Microbial infection) Ubiquitinated by human herpesvirus 8 protein K5, leading to endolysosomal degradation. N-linked glycosylated; required to enable surface expression and the extent of surface expression correlates with the number of functional conventional N-glycosylation sites.

Induction. By TLR activation. By IL12 and IL18.

RefSeq proteins (1): NP_005118* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001304C-type_lectin-likeDomain
IPR016186C-type_lectin-like/link_sfHomologous_superfamily
IPR016187CTDL_foldHomologous_superfamily
IPR033992NKR-like_CTLDDomain
IPR050828C-type_lectin/matrix_domainFamily

Pfam: PF00059

UniProt features (15 total): disulfide bond 3, sequence conflict 3, glycosylation site 3, topological domain 2, chain 1, mutagenesis site 1, transmembrane region 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q92478-F192.250.79

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): 123–136, 35–46, 63–144

Glycosylation sites (3): 57, 62, 100

Mutagenesis-validated functional residues (1):

PositionPhenotype
87complete loss of dimerization.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-198933Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell

MSigDB gene sets: 235 (showing top): MCLACHLAN_DENTAL_CARIES_UP, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, MODULE_151, MODULE_45, MODULE_64, GOBP_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY, HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_DN, MODULE_118, GOBP_REGULATION_OF_IMMUNE_RESPONSE, MODULE_75, ONKEN_UVEAL_MELANOMA_UP, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, BLALOCK_ALZHEIMERS_DISEASE_UP, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, MODULE_410

GO Biological Process (2): NK T cell activation (GO:0051132), signal transduction (GO:0007165)

GO Molecular Function (4): carbohydrate binding (GO:0030246), identical protein binding (GO:0042802), receptor ligand activity (GO:0048018), protein binding (GO:0005515)

GO Cellular Component (4): Golgi membrane (GO:0000139), plasma membrane (GO:0005886), Golgi apparatus (GO:0005794), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Adaptive Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
alpha-beta T cell activation1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
protein binding1
signaling receptor binding1
signal transduction1
signaling receptor activator activity1
Golgi apparatus1
bounding membrane of organelle1
membrane1
cell periphery1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

718 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CLEC2BKLRF1Q9NZS2987
CLEC2BSLAMF6Q96DU3783
CLEC2BKLRC4O43908780
CLEC2BKLRF2D3W0D1726
CLEC2BNCR1O76036693
CLEC2BHLA-EP13747669
CLEC2BNCR2O95944641
CLEC2BNCR3O14931625
CLEC2BMICBP79525611
CLEC2BKLRK1P26718516
CLEC2BCLEC3AO75596513
CLEC2BICAM1P05362499
CLEC2BOLR1P78380488
CLEC2BCD27P26842482
CLEC2BTLR9Q9NR96474

IntAct

27 interactions, top by confidence:

ABTypeScore
CLEC2BCLEC2Bpsi-mi:“MI:0407”(direct interaction)0.560
CLEC2BCLEC2Bpsi-mi:“MI:0195”(covalent binding)0.560
CLEC2BA2Mpsi-mi:“MI:0915”(physical association)0.560
CLEC2BDNM2psi-mi:“MI:0915”(physical association)0.560
CLEC2BTOR1Apsi-mi:“MI:0915”(physical association)0.560
HTTCLEC2Bpsi-mi:“MI:0915”(physical association)0.560
CLEC2BASPHD2psi-mi:“MI:0914”(association)0.530
CLEC2BKLRF1psi-mi:“MI:0407”(direct interaction)0.440
ENO1psi-mi:“MI:0914”(association)0.350
CLEC2BDEGS1psi-mi:“MI:0914”(association)0.350
CLEC2BADAM10psi-mi:“MI:0914”(association)0.350
AFG2AESYT2psi-mi:“MI:0914”(association)0.350

BioGRID (147): CLEC2B (Affinity Capture-MS), TGFBR3 (Affinity Capture-MS), DGAT1 (Affinity Capture-MS), ADAMTS2 (Affinity Capture-MS), FAR2 (Affinity Capture-MS), EIF2B1 (Affinity Capture-MS), FAM69A (Affinity Capture-MS), FAM114A2 (Affinity Capture-MS), SUN1 (Affinity Capture-MS), EXTL2 (Affinity Capture-MS), TMEM199 (Affinity Capture-MS), PON2 (Affinity Capture-MS), USP22 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), SLC4A7 (Affinity Capture-MS)

ESM2 similar proteins: A0A0E4BZH1, A4KWA1, D3W0D1, O35778, O54707, P27471, P27812, P27814, P78380, P79391, Q0VCS6, Q0ZUP0, Q0ZUP1, Q12918, Q13241, Q2HXU8, Q38HS3, Q49BZ4, Q58DF9, Q5NKN2, Q5NKN4, Q5QGZ9, Q60651, Q60652, Q60653, Q60660, Q60682, Q63378, Q64329, Q6QLQ4, Q6UVW9, Q80ZC8, Q863H3, Q8BWY2, Q8C567, Q8CJC7, Q8HZR8, Q8MHY9, Q8NC01, Q8VD98

Diamond homologs: A4D1S0, O88713, P0C7M8, P0C7M9, Q0ZCA7, Q3UM83, Q92478, Q96E93, A4KWA5, A4KWA6, A4KWA8, O70156, O89335, P06734, P08290, P14370, P37217, P49259, P79391, Q07108, Q0H8B9, Q5M9I1, Q5QGZ9, Q60660, Q6QLQ4, Q6UVW9, Q6UXN8, Q80XD9, Q8BWY2, Q8C1T8, Q8N1N0, Q8VI21, Q91V08, Q925N7, Q9D676, Q9UBG0, Q9UHP7, Q9WVF9, Q9XTA8, A4KWA1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance19
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

682 predictions. Top by Δscore:

VariantEffectΔscore
12:9857638:C:CCacceptor_gain1.0000
12:9857633:TTTAA:Tacceptor_gain0.9900
12:9857634:TTAA:Tacceptor_gain0.9900
12:9857635:TAA:Tacceptor_gain0.9900
12:9854379:A:ACdonor_gain0.9800
12:9854380:C:CCdonor_gain0.9800
12:9854482:ATT:Aacceptor_gain0.9800
12:9857468:ACTT:Adonor_loss0.9800
12:9857469:CTT:Cdonor_loss0.9800
12:9857470:TTA:Tdonor_loss0.9800
12:9857471:TAC:Tdonor_loss0.9800
12:9857472:ACCAT:Adonor_loss0.9800
12:9857473:C:Tdonor_loss0.9800
12:9854480:AAATT:Aacceptor_gain0.9700
12:9857472:A:ACdonor_gain0.9700
12:9857473:C:CCdonor_gain0.9700
12:9857634:TTAAC:Tacceptor_loss0.9700
12:9857636:AA:Aacceptor_gain0.9700
12:9857637:AC:Aacceptor_loss0.9700
12:9857638:CTGGA:Cacceptor_loss0.9700
12:9857639:T:Aacceptor_loss0.9700
12:9857650:C:CTacceptor_loss0.9700
12:9857651:A:Tacceptor_loss0.9700
12:9869538:A:ACdonor_gain0.9700
12:9869539:C:CCdonor_gain0.9700
12:9854481:AATT:Aacceptor_gain0.9600
12:9869539:CTTT:Cdonor_gain0.9600
12:9853408:CCTGC:Cacceptor_loss0.9500
12:9853409:C:CGacceptor_loss0.9500
12:9853410:T:Gacceptor_loss0.9500

AlphaMissense

994 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:9854446:C:AW92C0.995
12:9854446:C:GW92C0.995
12:9857543:C:AW56C0.995
12:9857543:C:GW56C0.995
12:9854407:C:AW105C0.991
12:9854407:C:GW105C0.991
12:9854479:A:CF81L0.989
12:9854479:A:TF81L0.989
12:9854481:A:GF81L0.989
12:9853319:C:GC144S0.985
12:9853320:A:TC144S0.985
12:9853330:T:AR140S0.985
12:9853330:T:GR140S0.985
12:9854448:A:GW92R0.985
12:9854448:A:TW92R0.985
12:9857534:A:CS59R0.984
12:9857534:A:TS59R0.984
12:9857536:T:GS59R0.984
12:9857523:C:GC63S0.983
12:9857524:A:TC63S0.983
12:9853373:A:GL126P0.982
12:9857594:C:AW39C0.981
12:9857594:C:GW39C0.981
12:9857545:A:GW56R0.980
12:9857545:A:TW56R0.980
12:9857585:G:CF42L0.980
12:9857585:G:TF42L0.980
12:9857587:A:GF42L0.980
12:9857522:A:CC63W0.979
12:9853326:A:GW142R0.978

dbSNP variants (sampled 300 via entrez): RS1000135230 (12:9868848 C>A), RS1000265699 (12:9862790 A>C,G), RS1000271193 (12:9869920 G>A), RS1000299787 (12:9863078 T>C), RS1000525124 (12:9856392 C>T), RS1000569259 (12:9869145 C>G), RS1000734502 (12:9864717 CTAAT>C), RS1000744545 (12:9865146 C>G,T), RS1000799929 (12:9857969 A>G), RS1000895109 (12:9856031 C>T), RS1000962746 (12:9858324 C>T), RS1001450876 (12:9861935 T>A,C), RS1001450984 (12:9869955 T>G), RS1001485350 (12:9863164 A>G), RS1001545748 (12:9868317 T>C)

Disease associations

OMIM: gene MIM:603242 | 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
GCST010725_46Malaria1.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

54 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression2
Air Pollutantsincreases abundance, decreases expression, affects expression2
Diuronincreases expression, decreases expression2
Tobacco Smoke Pollutiondecreases expression, increases expression2
Particulate Matterdecreases expression, increases abundance2
GSK-J4increases expression1
sotorasibdecreases expression, affects cotreatment1
urushioldecreases expression1
testosterone enanthateaffects expression1
triphenyl phosphateaffects expression1
2-methyl-4-isothiazolin-3-oneincreases expression1
3,4-dichloroanilineincreases expression1
arseniteincreases reaction, affects binding1
sulforaphaneincreases expression1
cobaltous chlorideincreases expression1
zinc chromateincreases abundance, increases expression1
cupric chlorideincreases expression1
hydroquinonedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent ionincreases abundance, increases expression1
perfluorooctane sulfonic aciddecreases expression1
perfluoro-n-nonanoic aciddecreases expression1
corosolic aciddecreases expression1
2-palmitoylglycerolincreases expression1
entinostatincreases expression1
2,2’,4,4’,5-brominated diphenyl etherincreases expression1
abrineincreases expression1
jinfukangincreases expression1
incobotulinumtoxinAincreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_E1TUHAP1 CLEC2B (-)Cancer cell lineMale

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.