CLEC3A

gene
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Summary

CLEC3A (C-type lectin domain family 3 member A, HGNC:2052) is a protein-coding gene on chromosome 16q23.1, encoding C-type lectin domain family 3 member A (O75596). Promotes cell adhesion to laminin-332 and fibronectin.

Predicted to enable carbohydrate binding activity. Predicted to be involved in ossification. Predicted to be located in extracellular region. Predicted to be active in extracellular space.

Source: NCBI Gene 10143 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 36 total — 1 pathogenic, 1 likely-pathogenic
  • MANE Select transcript: NM_005752

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2052
Approved symbolCLEC3A
NameC-type lectin domain family 3 member A
Location16q23.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000166509
Ensembl biotypeprotein_coding
OMIM613588
Entrez10143

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000299642, ENST00000565808, ENST00000567430, ENST00000651443

RefSeq mRNA: 1 — MANE Select: NM_005752 NM_005752

CCDS: CCDS10927

Canonical transcript exons

ENST00000299642 — 3 exons

ExonStartEnd
ENSE000011037087802810778028190
ENSE000011037127803044778032101
ENSE000038958287802254878022741

Expression profiles

Bgee: expression breadth broad, 79 present calls, max score 91.96.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0963 / max 34.7786, expressed in 22 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1550780.096322

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tibiaUBERON:000097991.96gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047378.02gold quality
pancreatic ductal cellCL:000207973.19silver quality
tibialis anteriorUBERON:000138567.73silver quality
ileal mucosaUBERON:000033166.65silver quality
gall bladderUBERON:000211065.34gold quality
cardiac muscle of right atriumUBERON:000337965.02gold quality
left ventricle myocardiumUBERON:000656664.63gold quality
deltoidUBERON:000147660.17gold quality
urinary bladderUBERON:000125558.03gold quality
right coronary arteryUBERON:000162557.57gold quality
epithelial cell of pancreasCL:000008356.25gold quality
myocardiumUBERON:000234955.91gold quality
quadriceps femorisUBERON:000137754.87gold quality
kidney epitheliumUBERON:000481953.93gold quality
upper arm skinUBERON:000426353.52gold quality
vastus lateralisUBERON:000137953.22gold quality
cartilage tissueUBERON:000241851.69gold quality
calcaneal tendonUBERON:000370151.59gold quality
left coronary arteryUBERON:000162651.57gold quality
coronary arteryUBERON:000162151.41gold quality
ascending aortaUBERON:000149650.90gold quality
thoracic aortaUBERON:000151549.87gold quality
mucosa of stomachUBERON:000119949.21gold quality
descending thoracic aortaUBERON:000234549.19gold quality
tracheaUBERON:000312649.03gold quality
nasal cavity epitheliumUBERON:000538448.29gold quality
aortaUBERON:000094748.27gold quality
tendonUBERON:000004348.06gold quality
fundus of stomachUBERON:000116047.50gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.93
E-CURD-7no73.02

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

73 targeting CLEC3A, 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-4262100.0073.263931
HSA-MIR-318599.9968.121959
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-548P99.9872.253784
HSA-MIR-25-3P99.9874.601817
HSA-MIR-32-5P99.9875.211964
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-570-3P99.9672.414910
HSA-LET-7C-3P99.9573.422862
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-137-3P99.8774.742401
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-449599.8272.083080
HSA-MIR-117999.7168.701040
HSA-MIR-119799.7067.751027
HSA-MIR-518A-5P99.7069.012209
HSA-MIR-52799.7069.012209
HSA-MIR-561-3P99.6470.903647
HSA-MIR-6716-5P99.5668.621244
HSA-MIR-5004-3P99.5468.271371
HSA-MIR-186-3P99.5166.241685
HSA-MIR-5584-5P99.4968.222814
HSA-MIR-4762-3P99.4369.722363
HSA-MIR-302A-5P99.3968.211913
HSA-MIR-103A-1-5P99.3967.781545

Literature-anchored findings (GeneRIF, showing 4)

  • CLEC3A binds to heparan sulfate proteoglycans on cell surface, leading to the enhancement of cell adhesion to integrin ligands on ECM; cleavage of CLEC3A by MMP-7 weakens the stable adhesion of tumor cells to the matrix (PMID:19173304)
  • we demonstrated that the recurrence potential in PNETs is characterized by the upregulation of genes related to ECM organization and cell adhesion. This study identified three genes-CLEC3, MMP7, and LCN2-that contribute to the prediction of postoperative recurrence of PNETs in clinical practice. (PMID:31129920)
  • Suppression of CLEC3A inhibits osteosarcoma cell proliferation and promotes their chemosensitivity through the AKT1/mTOR/HIF1alpha signaling pathway. (PMID:32319617)
  • C-type lectin domain-containing protein CLEC3A regulates proliferation, regeneration and maintenance of nucleus pulposus cells. (PMID:35864364)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioCLEC3AENSDARG00000110756
mus_musculusClec3aENSMUSG00000008874
rattus_norvegicusClec3aENSRNOG00000070954

Paralogs (2): CLEC11A (ENSG00000105472), CLEC3B (ENSG00000163815)

Protein

Protein identifiers

C-type lectin domain family 3 member AO75596 (reviewed: O75596)

Alternative names: C-type lectin superfamily member 1, Cartilage-derived C-type lectin

All UniProt accessions (3): O75596, H3BTK1, J3KNC9

UniProt curated annotations — full annotation on UniProt →

Function. Promotes cell adhesion to laminin-332 and fibronectin.

Subcellular location. Secreted.

Tissue specificity. Restricted to cartilage and breast. Also expressed in breast cancers.

RefSeq proteins (1): NP_005743* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001304C-type_lectin-likeDomain
IPR016186C-type_lectin-like/link_sfHomologous_superfamily
IPR016187CTDL_foldHomologous_superfamily
IPR018378C-type_lectin_CSConserved_site
IPR051663CLec_Tetranectin-domainFamily

Pfam: PF00059

UniProt features (7 total): disulfide bond 3, signal peptide 1, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O75596-F192.500.77

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): 68–78, 95–191, 167–183

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 49 (showing top): GOBP_SKELETAL_SYSTEM_DEVELOPMENT, MODULE_205, NF1_Q6_01, TGCTGAY_UNKNOWN, MODULE_410, GOBP_OSSIFICATION, MODULE_207, MODULE_95, TCTGATC_MIR383, AR_Q6, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, MODULE_163, chr16q23, MIR1468_3P, MIR548P

GO Biological Process (2): skeletal system development (GO:0001501), ossification (GO:0001503)

GO Molecular Function (1): carbohydrate binding (GO:0030246)

GO Cellular Component (2): obsolete extracellular space (GO:0005615), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
system development1
multicellular organismal process1
binding1
cellular anatomical structure1

Protein interactions and networks

STRING

626 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CLEC3AMMP7P09237673
CLEC3ALAMA1P25391669
CLEC3AVAT1LQ9HCJ6536
CLEC3ACLEC1BQ9P126531
CLEC3ACLEC2BQ92478513
CLEC3ACHRDL2Q6WN34485
CLEC3ACYTL1Q9NRR1481
CLEC3AWWOXQ9NZC7450
CLEC3ACDYL2Q8N8U2443
CLEC3ASYF2O95926441
CLEC3AFN1P02751437
CLEC3ACNMDO75829429
CLEC3ATAF1DQ9H5J8398
CLEC3ACILPO75339385
CLEC3APRELPP51888380

IntAct

11 interactions, top by confidence:

ABTypeScore
HIKESHICLEC3Apsi-mi:“MI:0914”(association)0.530
CLEC3AZZEF1psi-mi:“MI:0914”(association)0.530
CLEC3AZNF593psi-mi:“MI:0914”(association)0.350
TOR1ACLEC3Apsi-mi:“MI:0914”(association)0.350
RCAN1CLEC3Apsi-mi:“MI:0914”(association)0.350
FAAP20FANCGpsi-mi:“MI:0914”(association)0.350
CLEC3AMACROH2A1psi-mi:“MI:0914”(association)0.350
CLEC3ATRIP4psi-mi:“MI:0914”(association)0.350

BioGRID (79): RNASEH1 (Affinity Capture-MS), PHF10 (Affinity Capture-MS), YY1AP1 (Affinity Capture-MS), ZNF430 (Affinity Capture-MS), CACTIN (Affinity Capture-MS), RBM23 (Affinity Capture-MS), KBTBD7 (Affinity Capture-MS), CTNNBL1 (Affinity Capture-MS), LSM14B (Affinity Capture-MS), C1QBP (Affinity Capture-MS), CLEC3A (Affinity Capture-MS), RBM27 (Affinity Capture-MS), KBTBD6 (Affinity Capture-MS), ZNF638 (Affinity Capture-MS), CLEC3A (Affinity Capture-MS)

ESM2 similar proteins: A3FM55, B4XSY7, B4XSY8, B4XSZ1, C0HKZ6, D1MGU0, F1QVU0, O09037, O60449, O75596, O89103, O93426, P06681, P14371, P18292, P19221, P21180, P23132, P25031, P28824, P30836, P35230, P35231, P49259, P49260, P81017, P81112, P98131, Q08731, Q09GJ8, Q09GK0, Q13018, Q28008, Q3SYW2, Q4PRD2, Q568T5, Q5R880, Q60767, Q62028, Q6T7B5

Diamond homologs: O02659, O75596, P06734, P06908, P07307, P08290, P08427, P08661, P11226, P12842, P19999, P20693, P23805, P24721, P34927, P35242, P35247, P35248, P39039, P41317, P49300, P49301, P49874, P50403, P50404, P82596, Q17QH6, Q1PBC5, Q28008, Q2KIS7, Q2LK54, Q2LK94, Q2LK95, Q5M8X6, Q5MIZ0, Q5U3G1, Q5U9S1, Q66KU1, Q66S37, Q66S41

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic1
Uncertain significance26
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
4279196GRCh37/hg19 16q23.1(chr16:77960665-78530885)x1Pathogenic
624464GRCh37/hg19 16q23.1(chr16:77981957-79037091)x1Likely pathogenic

SpliceAI

401 predictions. Top by Δscore:

VariantEffectΔscore
16:78022716:G:GTdonor_gain1.0000
16:78030445:A:AGacceptor_gain1.0000
16:78030446:G:GGacceptor_gain1.0000
16:78030446:GTCT:Gacceptor_gain1.0000
16:78022738:AGAG:Adonor_gain0.9900
16:78022739:GAG:Gdonor_gain0.9900
16:78022739:GAGG:Gdonor_gain0.9900
16:78022740:AG:Adonor_loss0.9900
16:78022741:GGTAA:Gdonor_loss0.9900
16:78022742:G:GAdonor_loss0.9900
16:78022743:T:Adonor_loss0.9900
16:78030446:GT:Gacceptor_gain0.9900
16:78030446:GTC:Gacceptor_gain0.9900
16:78028186:GACAG:Gdonor_gain0.9800
16:78028190:GGTA:Gdonor_loss0.9800
16:78028191:GTAAG:Gdonor_loss0.9800
16:78028192:T:Adonor_loss0.9800
16:78030430:A:AGacceptor_gain0.9800
16:78028094:A:Gacceptor_gain0.9700
16:78030431:C:Gacceptor_gain0.9700
16:78030442:CACA:Cacceptor_loss0.9700
16:78030444:CA:Cacceptor_loss0.9700
16:78030445:A:ATacceptor_loss0.9700
16:78022734:A:AGdonor_gain0.9600
16:78022735:G:GGdonor_gain0.9600
16:78022880:GGGAT:Gdonor_gain0.9600
16:78028105:A:AGacceptor_gain0.9600
16:78028106:G:GGacceptor_gain0.9600
16:78022736:TGAG:Tdonor_gain0.9500
16:78028104:CAGAC:Cacceptor_loss0.9500

AlphaMissense

1300 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:78030531:G:AC95Y0.998
16:78030532:C:GC95W0.998
16:78030709:G:CW154C0.998
16:78030709:G:TW154C0.998
16:78030479:T:AC78S0.997
16:78030480:G:CC78S0.997
16:78030518:G:CA91P0.997
16:78030530:T:AC95S0.997
16:78030531:G:CC95S0.997
16:78030634:G:CW129C0.996
16:78030634:G:TW129C0.996
16:78030779:T:AW178R0.996
16:78030779:T:CW178R0.996
16:78030818:T:AC191S0.996
16:78030819:G:AC191Y0.996
16:78030819:G:CC191S0.996
16:78030449:T:AC68S0.995
16:78030450:G:CC68S0.995
16:78030479:T:CC78R0.995
16:78030530:T:CC95R0.995
16:78030746:T:AC167S0.995
16:78030747:G:CC167S0.995
16:78030748:T:GC167W0.995
16:78030481:C:GC78W0.994
16:78030531:G:TC95F0.994
16:78030632:T:AW129R0.994
16:78030632:T:CW129R0.994
16:78030747:G:AC167Y0.994
16:78030449:T:CC68R0.993
16:78030451:T:GC68W0.993

dbSNP variants (sampled 300 via entrez): RS1000055292 (16:78025309 C>G), RS1000415948 (16:78022176 A>G), RS1000488111 (16:78022317 A>G,T), RS1000716427 (16:78027396 G>A), RS1000751192 (16:78023065 G>C), RS1000784392 (16:78026519 A>C,G), RS1000807323 (16:78023128 G>C), RS1000826529 (16:78023201 G>A,C,T), RS1000879497 (16:78023012 G>A,C), RS1001142481 (16:78022295 C>T), RS1001370340 (16:78025853 C>A), RS1001490737 (16:78031133 T>A), RS1001827637 (16:78032034 A>G), RS1001867649 (16:78028654 T>G), RS1002339908 (16:78032200 TG>T)

Disease associations

OMIM: gene MIM:613588 | disease phenotypes: MIM:616211

GenCC curated gene-disease

Mondo (2): developmental and epileptic encephalopathy, 28 (MONDO:0014533), autism spectrum disorder (MONDO:0005258)

Orphanet (2): Non-specific early-onset epileptic encephalopathy (Orphanet:442835), NON RARE IN EUROPE: Autism (Orphanet:106)

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST002307_5Systolic blood pressure (alcohol consumption interaction)9.000000e-07
GCST003209_15Colorectal or endometrial cancer1.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004329alcohol drinking
EFO:0006335systolic blood pressure
EFO:0004230endometrial neoplasm

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
Benzo(a)pyreneaffects methylation, increases expression, increases methylation2
tungsten carbideaffects binding, decreases expression1
(+)-JQ1 compounddecreases expression1
Cadmiumdecreases expression1
Carbamazepineaffects expression1
Cobaltaffects binding, decreases expression1
Aflatoxin B1increases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00391261PHASE4COMPLETEDAn Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT01028820PHASE4COMPLETEDFMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01333865PHASE4COMPLETEDA Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700PHASE4COMPLETEDMilnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200PHASE4COMPLETEDOmega-3 Fatty Acids in Autism Spectrum Disorders
NCT02096952PHASE4COMPLETEDMethylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02235467PHASE4COMPLETEDMultisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02940574PHASE4COMPLETEDNeural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629PHASE4COMPLETEDPromoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646PHASE4COMPLETEDEvaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431PHASE4COMPLETEDImproving Driving in Young People With Autism Spectrum Disorders
NCT03757585PHASE4COMPLETEDNatural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353PHASE4COMPLETEDPragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656PHASE4COMPLETEDBiomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245PHASE4UNKNOWNSafety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339PHASE4RECRUITINGAWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052PHASE4TERMINATEDA Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665PHASE4RECRUITINGThe TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697PHASE4COMPLETEDPilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804PHASE4COMPLETEDPilot RCT Using Homeopathic Medicines in ASD
NCT07439042PHASE4NOT_YET_RECRUITINGBuspirone for Anxiety in Autistic Youth
NCT01302964PHASE3COMPLETEDMirtazapine Treatment of Anxiety in Children and Adolescents With Pervasive Developmental Disorders
NCT01706523PHASE3TERMINATEDOpen Label Extension Study of STX209 (Arbaclofen) in Autism Spectrum Disorders
NCT01825798PHASE3COMPLETEDTreatment of Overweight Induced by Antipsychotic Medication in Young People With Autism Spectrum Disorders (ASD)
NCT01972074PHASE3COMPLETEDBehavioral and Neural Response to Memantine in Adolescents With Autism Spectrum Disorder
NCT02985749PHASE3COMPLETEDA Study of Oxytocin for the Treatment of Social Impairment in Individuals With High Functioning Autism Spectrum Disorder
NCT03197922PHASE3COMPLETEDTreatment of Encopresis in Children With Autism Spectrum Disorders
NCT03504917PHASE3TERMINATEDA Study of Balovaptan in Adults With Autism Spectrum Disorder With a 2-Year Open-Label Extension
NCT03553875PHASE3TERMINATEDMemantine for the Treatment of Social Deficits in Youth With Disorders of Impaired Social Interactions
NCT03640156PHASE3COMPLETEDModulating Socially Adaptive Mirror System Functioning in Autism by Oxytocin
NCT03715153PHASE3TERMINATEDEfficacy and Safety of Bumetanide Oral Liquid Formulation in Children Aged From 2 to Less Than 7 Years Old With Autism Spectrum Disorder.
NCT03715166PHASE3TERMINATEDEfficacy and Safety of Bumetanide Oral Liquid Formulation in Children and Adolescents Aged From 7 to Less Than 18 Years Old With Autism Spectrum Disorder
NCT04233502PHASE3WITHDRAWNEfficacy and Safety of Slenyto for Insomnia in Children With ASD
NCT04578756PHASE3COMPLETEDOpen-Label, Flexible-dose Study to Evaluate the Long-Term Safety and Tolerability of Cariprazine in the Treatment of Pediatric Participants With Schizophrenia, Bipolar I Disorder, or Autism Spectrum Disorder
NCT04623398PHASE3COMPLETEDEffect of Lithium in Patients With Autism Spectrum Disorder and Phelan-McDermid Syndrome (SHANK3 Haploinsufficiency)
NCT04725383PHASE3TERMINATEDAmitriptyline for Repetitive Behaviors in Autism Spectrum Disorders
NCT05212493PHASE3COMPLETEDThe Effects of Medical Cannabis in Children With Autistic Spectrum Disorder
NCT05361707PHASE3UNKNOWNEvaluating the Effects of Tasimelteon in Individuals With Autism Spectrum Disorder (ASD) and Sleep Disturbances
NCT05439616PHASE3COMPLETEDStudy of Cariprazine Oral Capsules or Solution to Assess Adverse Events and Change in Irritability Due to Autism Spectrum Disorder (ASD) in Participants Aged 5-17 Years With ASD
NCT06229210PHASE3RECRUITINGSafety and Tolerability Trial of Lumateperone in Pediatric Patients With Schizophrenia, Bipolar Disorder or Autism Spectrum Disorder