CILP

gene
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Also known as HsT18872CILP1

Summary

CILP (cartilage intermediate layer protein, HGNC:1980) is a protein-coding gene on chromosome 15q22.31, encoding Cartilage intermediate layer protein 1 (O75339). Probably plays a role in cartilage scaffolding.

Major alterations in the composition of the cartilage extracellular matrix occur in joint disease, such as osteoarthrosis. This gene encodes the cartilage intermediate layer protein (CILP), which increases in early osteoarthrosis cartilage. The encoded protein was thought to encode a protein precursor for two different proteins; an N-terminal CILP and a C-terminal homolog of NTPPHase, however, later studies identified no nucleotide pyrophosphatase phosphodiesterase (NPP) activity. The full-length and the N-terminal domain of this protein was shown to function as an IGF-1 antagonist. An allelic variant of this gene has been associated with lumbar disc disease.

Source: NCBI Gene 8483 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 241 total
  • MANE Select transcript: NM_003613

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1980
Approved symbolCILP
Namecartilage intermediate layer protein
Location15q22.31
Locus typegene with protein product
StatusApproved
AliasesHsT18872, CILP1
Ensembl geneENSG00000138615
Ensembl biotypeprotein_coding
OMIM603489
Entrez8483

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000261883, ENST00000888802, ENST00000888803, ENST00000941156, ENST00000941157

RefSeq mRNA: 1 — MANE Select: NM_003613 NM_003613

CCDS: CCDS10203

Canonical transcript exons

ENST00000261883 — 9 exons

ExonStartEnd
ENSE000006936736520187265202029
ENSE000006936766520336265203470
ENSE000006936796520426865204582
ENSE000006936836520528765205466
ENSE000006936886520678265207051
ENSE000006936936520767265207764
ENSE000012008646521142865211473
ENSE000012008716520969565209861
ENSE000012878436519476065199099

Expression profiles

Bgee: expression breadth ubiquitous, 218 present calls, max score 99.27.

FANTOM5 (CAGE): breadth broad, TPM avg 2.5243 / max 214.0913, expressed in 194 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1505352.5243194

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370199.27gold quality
tendon of biceps brachiiUBERON:000818897.96gold quality
tendonUBERON:000004397.64gold quality
synovial jointUBERON:000221797.04gold quality
pericardiumUBERON:000240794.37gold quality
subcutaneous adipose tissueUBERON:000219090.12gold quality
skin of hipUBERON:000155489.81gold quality
diaphragmUBERON:000110389.72gold quality
gall bladderUBERON:000211089.24gold quality
deciduaUBERON:000245088.77gold quality
tibiaUBERON:000097988.67gold quality
layer of synovial tissueUBERON:000761688.60gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451188.53gold quality
trabecular bone tissueUBERON:000248388.44gold quality
connective tissueUBERON:000238488.13gold quality
adipose tissueUBERON:000101388.09gold quality
body of tongueUBERON:001187688.06gold quality
nippleUBERON:000203087.50gold quality
esophagogastric junction muscularis propriaUBERON:003584187.43gold quality
smooth muscle tissueUBERON:000113587.30gold quality
left uterine tubeUBERON:000130387.13gold quality
triceps brachiiUBERON:000150987.03gold quality
hindlimb stylopod muscleUBERON:000425287.00gold quality
olfactory bulbUBERON:000226486.69silver quality
endocervixUBERON:000045886.57gold quality
tibialis anteriorUBERON:000138586.54gold quality
deltoidUBERON:000147686.47gold quality
adipose tissue of abdominal regionUBERON:000780886.46gold quality
omental fat padUBERON:001041486.33gold quality
peritoneumUBERON:000235886.25gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

TargetRegulation
ACTA2Repression
CCN2Repression

Upstream regulators (CollecTRI, top): IGF1, SMAD3, TGFB1

miRNA regulators (miRDB)

53 targeting CILP, 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-548AW99.9972.573559
HSA-MIR-548N99.9871.944170
HSA-MIR-569699.9872.364487
HSA-MIR-548AN99.9770.912817
HSA-MIR-302E99.9670.742669
HSA-LET-7C-3P99.9573.422862
HSA-MIR-129799.9173.413162
HSA-MIR-3180-5P99.8269.122422
HSA-MIR-520F-3P99.8271.321216
HSA-MIR-313399.8170.923506
HSA-MIR-26A-5P99.7873.522303
HSA-MIR-26B-5P99.7873.512305
HSA-MIR-498-5P99.7669.641807
HSA-MIR-446599.7172.562096
HSA-MIR-472999.6972.184233
HSA-MIR-58699.6570.402051
HSA-MIR-4804-3P99.6567.78866
HSA-MIR-5197-5P99.6469.081494
HSA-MIR-451B99.5568.281380
HSA-MIR-4687-3P99.4866.41968
HSA-MIR-608399.4768.732393
HSA-MIR-582-5P99.4770.792635
HSA-MIR-4797-5P99.3968.011354
HSA-MIR-569799.3967.741249
HSA-MIR-542-3P99.3467.581270
HSA-MIR-3678-3P99.3167.101432
HSA-MIR-797499.2465.481137
HSA-MIR-312599.1468.492269
HSA-MIR-391698.9968.042155
HSA-MIR-6859-5P98.9968.072049

Literature-anchored findings (GeneRIF, showing 11)

  • CILP regulates TGF-beta signaling and that this regulation has a crucial role in the etiology and pathogenesis of LDD. (PMID:15864306)
  • These observations, together with the finding that CILP protein binds and inhibits TGF-beta1, suggest that CILP and TGF-beta1 may form a functional feedback loop that controls chondrocyte metabolism. (PMID:16413503)
  • SNP analysis suggested that the CILP gene is not a major risk factor for symptoms of lumbar disc disease in Finnish or Chinese populations. (PMID:17220213)
  • the CILP gene 1184T/C polymorphism is a significant risk factor for lumbar disc degeneration occurrence in Japanese collegiate judo athletes (PMID:19569011)
  • The researchers found that the single nucleotide polymorphism (1184T/C) of the CILP gene is associated an increased risk of lumbar disc degeneration in male athletes. (PMID:20724643)
  • CILP is involved in the etiology of intervertebral disc degeneration among young adults. (PMID:22107760)
  • Meta-analysis. Our results confirm the positive association between CILP and intervertebral disc degeneration, providing novel clues for clarifying the role of CILP in the development of IVD. (PMID:27359356)
  • CILP rs2073711 TT is associated with increased risk of symmetrical hand osteoarthritis particularly in individuals with low variation in work tasks. (PMID:29233086)
  • CILP gene polymorphism (rs2073711) is associated with a lower risk of lumbar disc degeneration. (PMID:30288688)
  • CILP is a potential pan-cancer marker: combined silico study and in vitro analyses. (PMID:37968343)
  • CILP-1 Is a Biomarker for Backward Failure and Right Ventricular Dysfunction in HFrEF. (PMID:38132152)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriocilpENSDARG00000053362
mus_musculusCilpENSMUSG00000042254
rattus_norvegicusCilpENSRNOG00000029911

Paralogs (1): CILP2 (ENSG00000160161)

Protein

Protein identifiers

Cartilage intermediate layer protein 1O75339 (reviewed: O75339)

Alternative names: Cartilage intermediate-layer protein

All UniProt accessions (1): O75339

UniProt curated annotations — full annotation on UniProt →

Function. Probably plays a role in cartilage scaffolding. May act by antagonizing TGF-beta1 (TGFB1) and IGF1 functions. Has the ability to suppress IGF1-induced proliferation and sulfated proteoglycan synthesis, and inhibits ligand-induced IGF1R autophosphorylation. May inhibit TGFB1-mediated induction of cartilage matrix genes via its interaction with TGFB1. Overexpression may lead to impair chondrocyte growth and matrix repair and indirectly promote inorganic pyrophosphate (PPi) supersaturation in aging and osteoarthritis cartilage.

Subunit / interactions. Monomer. Interacts with TGFB1.

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Tissue specificity. Specifically expressed in cartilage. Localizes in the intermediates layer of articular cartilage but neither in the superficial nor in the deepest regions. Specifically and highly expressed in intervertebral disk tissue. Expression increases with aging in hip articular cartilage. Overexpressed in articular hyaline cartilage from patients with calcium pyrophosphate dihydrate crystal deposition disease (CPPD). Expression in intervertebral disk tissue from individuals with lumbar disk disease increases as disk degeneration progresses.

Post-translational modifications. Cleaved into 2 chains possibly by a furin-like protease upon or preceding secretion.

Disease relevance. Intervertebral disc disease (IDD) [MIM:603932] A common musculo-skeletal disorder caused by degeneration of intervertebral disks of the lumbar spine. It results in low-back pain and unilateral leg pain. Disease susceptibility is associated with variants affecting the gene represented in this entry.

Miscellaneous. Antibodies against CILP are detected in patients with early-stage knee osteoarthritis and rheumatoid arthritis.

RefSeq proteins (1): NP_003604* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000884TSP1_rptRepeat
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR007110Ig-like_domDomain
IPR008969CarboxyPept-like_regulatoryHomologous_superfamily
IPR013783Ig-like_foldHomologous_superfamily
IPR025155WxxW_domainDomain
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR036383TSP1_rpt_sfHomologous_superfamily
IPR039675CILP1/CILP2Family
IPR056255CILP-1/2_domDomain
IPR056256CILP-1/2_b-sand_dom2Domain
IPR056257CILP-1/2_8thDomain
IPR056258CILP-1/2_CDomain

Pfam: PF00090, PF13330, PF13927, PF23591, PF23599, PF23708, PF23730

UniProt features (35 total): sequence variant 11, glycosylation site 8, disulfide bond 4, sequence conflict 4, chain 3, domain 2, signal peptide 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O75339-F180.300.35

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 (4): 161–195, 165–200, 177–185, 330–376

Glycosylation sites (8): 346, 420, 550, 631, 1000, 1056, 129, 132

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-2404192Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R)

MSigDB gene sets: 118 (showing top): GOBP_SMAD_PROTEIN_SIGNAL_TRANSDUCTION, TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, MODULE_64, SMID_BREAST_CANCER_RELAPSE_IN_LUNG_DN, CAGCTG_AP4_Q5, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_INSULIN_LIKE_GROWTH_FACTOR_RECEPTOR_SIGNALING_PATHWAY, GOBP_REGULATION_OF_TRANSMEMBRANE_RECEPTOR_PROTEIN_SERINE_THREONINE_KINASE_SIGNALING_PATHWAY, GOBP_RESPONSE_TO_TRANSFORMING_GROWTH_FACTOR_BETA, GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_TRANSFORMING_GROWTH_FACTOR_BETA_STIMULUS, GOBP_RESPONSE_TO_GROWTH_FACTOR, GOBP_REGULATION_OF_INSULIN_LIKE_GROWTH_FACTOR_RECEPTOR_SIGNALING_PATHWAY, GOBP_TRANSFORMING_GROWTH_FACTOR_BETA_RECEPTOR_SIGNALING_PATHWAY

GO Biological Process (4): negative regulation of gene expression (GO:0010629), negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512), negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569), negative regulation of SMAD protein signal transduction (GO:0060392)

GO Molecular Function (1): extracellular matrix structural constituent (GO:0005201)

GO Cellular Component (4): obsolete extracellular space (GO:0005615), extracellular matrix (GO:0031012), extracellular exosome (GO:0070062), extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Signaling by Receptor Tyrosine Kinases1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway2
gene expression1
regulation of gene expression1
negative regulation of macromolecule biosynthetic process1
transforming growth factor beta receptor signaling pathway1
regulation of transforming growth factor beta receptor signaling pathway1
negative regulation of signal transduction1
regulation of insulin-like growth factor receptor signaling pathway1
insulin-like growth factor receptor signaling pathway1
regulation of SMAD protein signal transduction1
SMAD protein signal transduction1
negative regulation of intracellular signal transduction1
structural molecule activity1
extracellular matrix1
external encapsulating structure1
extracellular vesicle1
cellular anatomical structure1

Protein interactions and networks

STRING

956 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CILPASPNQ9BXN1843
CILPCOL9A3Q14050819
CILPCOL9A2Q14055803
CILPCOL11A1P12107755
CILPTHBS2P35442646
CILPFURINP09958611
CILPLUMP51884566
CILPPRELPP51888559
CILPACANP16112548
CILPCOMPP49747524
CILPCHADO15335517
CILPPRG4Q92954502
CILPFMODQ06828493
CILPFN1P02751487
CILPHAPLN1P10915469

IntAct

5 interactions, top by confidence:

ABTypeScore
TGFB1CILPpsi-mi:“MI:0914”(association)0.430
CILPTGFB1psi-mi:“MI:0403”(colocalization)0.430
ATG16L1ESYT2psi-mi:“MI:0914”(association)0.350
ATG16L1psi-mi:“MI:0914”(association)0.350

BioGRID (4): ERH (Cross-Linking-MS (XL-MS)), CILP (Affinity Capture-MS), CILP (Affinity Capture-MS), CILP (Affinity Capture-MS)

ESM2 similar proteins: A0A8M9PFP2, A1L2K1, A4IGL3, A4IH88, A8WFR0, B0S5G3, F1LW30, L7VG99, O42146, O73746, O75339, O93449, O97591, P12032, P15203, P16035, P16176, P16368, P20614, P23667, P25785, P26652, P30120, P30121, P30970, P35625, P39876, P48032, P61269, P79121, Q01H84, Q09199, Q28GB8, Q3KTM2, Q5PXZ9, Q60453, Q66K08, Q6DDG2, Q6UXZ4, Q7ZV46

Diamond homologs: D3Z7H8, O15394, O19112, O35136, O75339, P20241, P70193, P98167, Q66K08, Q6PDN3, Q8IUL8, Q8WZ42, A4IGL7, G5ECS8, P35440, Q2TBA3, Q7TQM3, Q91V87, Q92626, Q96JA1, Q9UDY8, A2ASS6, D3YXG0, P17948, Q15746, Q2EY14, Q2EY15, Q2VWP7, Q2VWP9, Q3UH53, Q589G5, Q58EX2, Q6UWL6, Q6V4S5, Q7Z5N4, Q8AV57, Q8BQC3, Q8IVU1, Q96RW7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance216
Likely benign14
Benign6

Top pathogenic / likely-pathogenic (0)

SpliceAI

1393 predictions. Top by Δscore:

VariantEffectΔscore
15:65201866:GCTTA:Gdonor_loss1.0000
15:65201867:CTTAC:Cdonor_loss1.0000
15:65201869:TAC:Tdonor_loss1.0000
15:65201870:A:ACdonor_gain1.0000
15:65201870:A:Cdonor_loss1.0000
15:65201871:C:CCdonor_gain1.0000
15:65201871:C:Tdonor_loss1.0000
15:65202027:TAC:Tacceptor_gain1.0000
15:65202030:C:CCacceptor_gain1.0000
15:65202030:CTGC:Cacceptor_loss1.0000
15:65202031:T:Aacceptor_loss1.0000
15:65207670:A:ACdonor_gain1.0000
15:65207670:ACTCT:Adonor_gain1.0000
15:65207671:C:CCdonor_gain1.0000
15:65207671:CT:Cdonor_gain1.0000
15:65207671:CTCT:Cdonor_gain1.0000
15:65207671:CTCTC:Cdonor_gain1.0000
15:65207674:T:Adonor_gain1.0000
15:65207761:CTCC:Cacceptor_gain1.0000
15:65207763:CC:Cacceptor_gain1.0000
15:65207763:CCCT:Cacceptor_loss1.0000
15:65207764:CC:Cacceptor_gain1.0000
15:65207764:CCTG:Cacceptor_loss1.0000
15:65207765:C:CCacceptor_gain1.0000
15:65207766:T:Aacceptor_loss1.0000
15:65209712:T:TAdonor_gain1.0000
15:65199100:C:CCacceptor_gain0.9900
15:65201870:AC:Adonor_gain0.9900
15:65201871:CC:Cdonor_gain0.9900
15:65201871:CCT:Cdonor_gain0.9900

AlphaMissense

7814 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:65197001:G:CC1095W0.999
15:65197003:A:GC1095R0.999
15:65197002:C:GC1095S0.998
15:65197003:A:TC1095S0.998
15:65197257:C:GC1010S0.998
15:65197258:A:GC1010R0.998
15:65197258:A:TC1010S0.998
15:65197424:G:CC954W0.998
15:65197425:C:TC954Y0.998
15:65197426:A:GC954R0.998
15:65197454:C:AW944C0.998
15:65197454:C:GW944C0.998
15:65197002:C:TC1095Y0.997
15:65197256:G:CC1010W0.997
15:65197271:A:CC1005W0.997
15:65197273:A:GC1005R0.997
15:65197451:C:AW945C0.997
15:65197451:C:GW945C0.997
15:65197456:A:GW944R0.997
15:65197456:A:TW944R0.997
15:65197002:C:AC1095F0.996
15:65197057:A:CY1077D0.996
15:65197189:A:GC1033R0.996
15:65197257:C:TC1010Y0.996
15:65197310:G:CS992R0.996
15:65197310:G:TS992R0.996
15:65197312:T:GS992R0.996
15:65197425:C:AC954F0.996
15:65198164:A:GW708R0.996
15:65198164:A:TW708R0.996

dbSNP variants (sampled 300 via entrez): RS1000004789 (15:65206722 C>G,T), RS1000037823 (15:65196134 G>C), RS1000104363 (15:65194792 A>G), RS1000214808 (15:65212014 C>T), RS1000410232 (15:65196537 G>A), RS1000656709 (15:65201400 G>A), RS1000880630 (15:65201651 C>T), RS1000890024 (15:65195686 C>G), RS1000975125 (15:65202091 G>A), RS1001127455 (15:65207611 C>A,T), RS1001490829 (15:65207371 A>C,G,T), RS1001520853 (15:65212688 C>T), RS1001541937 (15:65203132 C>A,G,T), RS1001656579 (15:65202831 C>A,G,T), RS1001727479 (15:65208973 A>G)

Disease associations

OMIM: gene MIM:603489 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST010796_4774Electrocardiogram morphology (amplitude at temporal datapoints)5.000000e-11
GCST010796_4775Electrocardiogram morphology (amplitude at temporal datapoints)2.000000e-09
GCST010796_4776Electrocardiogram morphology (amplitude at temporal datapoints)4.000000e-09
GCST010796_4777Electrocardiogram morphology (amplitude at temporal datapoints)5.000000e-09
GCST010796_4778Electrocardiogram morphology (amplitude at temporal datapoints)2.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004327electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aincreases expression, affects cotreatment2
Dexamethasoneincreases expression, affects cotreatment2
Estradiolaffects cotreatment, increases expression2
Nickeldecreases expression2
Genisteinincreases expression2
methylmercuric chlorideincreases expression1
pirinixic acidaffects binding, increases activity, increases expression1
sodium arseniteincreases expression1
perfluorooctanoic acidincreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
perfluorooctane sulfonic acidincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Acetaminophenincreases expression1
Calcitriolincreases expression1
Cisplatinaffects response to substance1
Copperaffects binding, decreases expression1
Diethylstilbestrolincreases expression1
Disulfiramaffects binding, decreases expression1
Doxorubicindecreases expression1
Indomethacinaffects cotreatment, increases expression1
Lipopolysaccharidesaffects response to substance, increases expression1
Plant Extractsdecreases expression, affects cotreatment1
Progesteroneincreases expression, affects cotreatment1
Tobacco Smoke Pollutiondecreases expression1
Valproic Acidincreases methylation1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Aflatoxin B1increases methylation1
Medroxyprogesterone Acetatedecreases 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.