CCNDBP1

gene
On this page

Also known as DIP1GCIPHHM

Summary

CCNDBP1 (cyclin D1 binding protein 1, HGNC:1587) is a protein-coding gene on chromosome 15q15.2, encoding Cyclin-D1-binding protein 1 (O95273). May negatively regulate cell cycle progression.

This gene was identified by the interaction of its gene product with Grap2, a leukocyte-specific adaptor protein important for immune cell signaling. The protein encoded by this gene was shown to interact with cyclin D. Transfection of this gene in cells was reported to reduce the phosphorylation of Rb gene product by cyclin D-dependent protein kinase, and inhibit E2F1-mediated transcription activity. This protein was also found to interact with helix-loop-helix protein E12 and is thought to be a negative regulator of liver-specific gene expression. Several alternatively spliced variants have been found for this gene.

Source: NCBI Gene 23582 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 71 total — 1 pathogenic, 1 likely-pathogenic
  • Druggable target: yes
  • MANE Select transcript: NM_012142

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1587
Approved symbolCCNDBP1
Namecyclin D1 binding protein 1
Location15q15.2
Locus typegene with protein product
StatusApproved
AliasesDIP1, GCIP, HHM
Ensembl geneENSG00000166946
Ensembl biotypeprotein_coding
OMIM607089
Entrez23582

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 7 retained_intron, 7 nonsense_mediated_decay, 6 protein_coding

ENST00000300213, ENST00000444658, ENST00000562553, ENST00000563065, ENST00000564630, ENST00000565296, ENST00000565958, ENST00000566515, ENST00000566833, ENST00000566882, ENST00000567434, ENST00000567690, ENST00000568507, ENST00000568936, ENST00000569745, ENST00000864042, ENST00000864043, ENST00000915942, ENST00000915943, ENST00000958193

RefSeq mRNA: 1 — MANE Select: NM_012142 NM_012142

CCDS: CCDS10092

Canonical transcript exons

ENST00000300213 — 11 exons

ExonStartEnd
ENSE000019302844318540343185607
ENSE000034932594319472743197177
ENSE000034969584319032543190398
ENSE000035002074319139543191675
ENSE000035236794319441543194461
ENSE000035335854319005543190151
ENSE000036077554319274343192803
ENSE000036335774318582043185879
ENSE000036606454319096643191042
ENSE000036770314318615443186233
ENSE000036933734318919943189280

Expression profiles

Bgee: expression breadth ubiquitous, 262 present calls, max score 98.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 42.1320 / max 868.3864, expressed in 1826 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
14629236.50841823
1462962.7584715
1462931.5885875
1462950.6589328
1462910.5311281
1462940.086626

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
trabecular bone tissueUBERON:000248398.44gold quality
ileal mucosaUBERON:000033198.06gold quality
cardiac muscle of right atriumUBERON:000337998.04gold quality
calcaneal tendonUBERON:000370198.02gold quality
bone marrowUBERON:000237197.88gold quality
right uterine tubeUBERON:000130297.73gold quality
bloodUBERON:000017897.68gold quality
left ventricle myocardiumUBERON:000656697.44gold quality
placentaUBERON:000198797.38gold quality
upper arm skinUBERON:000426397.29gold quality
leukocyteCL:000073897.24gold quality
monocyteCL:000057697.21gold quality
bone elementUBERON:000147497.21gold quality
granulocyteCL:000009497.01gold quality
tibialis anteriorUBERON:000138596.61gold quality
bone marrow cellCL:000209296.60gold quality
myocardiumUBERON:000234996.34gold quality
ponsUBERON:000098896.16gold quality
thoracic aortaUBERON:000151596.11gold quality
descending thoracic aortaUBERON:000234596.11gold quality
right coronary arteryUBERON:000162596.10gold quality
ascending aortaUBERON:000149696.09gold quality
spleenUBERON:000210696.06gold quality
lower esophagus mucosaUBERON:003583495.97gold quality
right lungUBERON:000216795.95gold quality
aortaUBERON:000094795.93gold quality
right adrenal gland cortexUBERON:003582795.90gold quality
right adrenal glandUBERON:000123395.87gold quality
bronchial epithelial cellCL:000232895.82gold quality
left coronary arteryUBERON:000162695.82gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-CURD-112yes42.63
E-MTAB-6701yes39.34
E-MTAB-10042yes34.39
E-MTAB-9221yes11.19
E-HCAD-9yes6.96
E-HCAD-10yes4.09
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

109 targeting CCNDBP1, 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-9-5P100.0072.282361
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-3163100.0077.238605
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-548AW99.9972.573559
HSA-MIR-428299.9975.366408
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-548N99.9871.944170
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-570-3P99.9672.414910
HSA-MIR-391099.9571.132227
HSA-MIR-651-3P99.9473.485177
HSA-MIR-335-3P99.9373.364958
HSA-MIR-539-5P99.9370.302855
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-10523-5P99.9169.222038
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-427199.8868.322244
HSA-MIR-394199.8670.542735

Literature-anchored findings (GeneRIF, showing 14)

  • In transgenic mice, GCIP functions as a transcriptional suppressor, regulates cyclin D1 expression, inhibits cell growth and colony formation in human HepG2 cells, suggesting GCIP plays a significant role in tumor initiation and development. (PMID:16501603)
  • CT847 interacts with mammalian Grap2 cyclin D-interacting protein (PMID:17532760)
  • P0 overexpression may cause tumorigenesis in breast and liver tissues at least in part by inhibiting GCIP-mediated tumor suppression. (PMID:17621266)
  • Data suggest that HHM/Maid regulates a subset of TGF-beta target genes including the Olig1-Smad synexpression group. (PMID:18923419)
  • decreased expression of GCIP in vivo is present in human breast carcinoma. (PMID:18983464)
  • Crystallization and preliminary X-ray diffraction analysis of GCIP/HHM transcriptional regulator (PMID:19153449)
  • It is proposed for the first time that Rad may promote carcinogenesis at least in part by inhibiting GCIP-mediated tumor suppression. (PMID:20460530)
  • The first structure of a free-standing human dominant-negative helix-loop-helix protein (DIP1) was reported. DIP1 adopts a V-shaped conformation, with N-terminal and C-terminal five-helix bundles connected by the HLH region. (PMID:22453338)
  • Data indicate that grap2 and cyclin D1 interacting protein (GCIP) and inhibitor of of DNA binding/differentiation 1 (Id1) are inversely expressed in non-small cell lung cancer (NSCLC) cell lines and specimens. (PMID:24970809)
  • Data suggest MAID/CCNDBP1 inhibits cell migration induced by TGFB1 (transforming growth factor-beta1) but not by BMP4 (bone morphogenetic protein-4); MAID does not alter cell proliferation, epithelial-mesenchymal transition, or TGFB3-induced apoptosis. (PMID:26002959)
  • GCIP underexpression is associated with Osteosarcoma. (PMID:26107195)
  • MEK2 is a critical modulating mechanism to down-regulate GCIP stability and function in cancer cells. (PMID:31907980)
  • Grap2 cyclin D interacting protein negatively regulates CREBbinding protein, inhibiting fibroblastlike synoviocyte growth. (PMID:33576455)
  • rs66651343 and rs12909095 confer lung cancer risk by regulating CCNDBP1 expression. (PMID:37058478)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioccndbp1ENSDARG00000039328
mus_musculusCcndbp1ENSMUSG00000023572
rattus_norvegicusCcndbp1ENSRNOG00000011379

Protein

Protein identifiers

Cyclin-D1-binding protein 1O95273 (reviewed: O95273)

Alternative names: Grap2 and cyclin-D-interacting protein, Human homolog of Maid

All UniProt accessions (4): O95273, H3BQA6, H3BR23, H3BUF4

UniProt curated annotations — full annotation on UniProt →

Function. May negatively regulate cell cycle progression. May act at least in part via inhibition of the cyclin-D1/CDK4 complex, thereby preventing phosphorylation of RB1 and blocking E2F-dependent transcription.

Subunit / interactions. Interacts with CCND1 and GRAP2. May also interact with COPS5, RPLP0, SIRT6, SYF2 and TCF3.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Ubiquitously expressed. Expression is down-regulated in a variety of tumor types including breast, colon, prostate and rectal tumors, and is up-regulated in certain hepatic carcinomas.

Post-translational modifications. Phosphorylated.

Induction. Expression is induced by sodium butyrate, an inhibitor of colon cancer cell proliferation.

Similarity. Belongs to the CCNDBP1 family.

Isoforms (4)

UniProt IDNamesCanonical?
O95273-11yes
O95273-22
O95273-33
O95273-44

RefSeq proteins (1): NP_036274* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR026907GCIP-likeFamily
IPR049317GCIP-like_NDomain
IPR049318GCIP_CDomain

Pfam: PF13324, PF20936

UniProt features (38 total): helix 13, sequence conflict 9, splice variant 5, region of interest 5, strand 2, initiator methionine 1, chain 1, turn 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3AY5X-RAY DIFFRACTION2.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95273-F187.380.71

Functional residue map

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

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 114 (showing top): MODULE_151, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, ONKEN_UVEAL_MELANOMA_UP, APPIERTO_RESPONSE_TO_FENRETINIDE_DN, DOUGLAS_BMI1_TARGETS_DN, MODULE_114, GOCC_NUCLEAR_BODY, DOANE_BREAST_CANCER_CLASSES_UP, WGTTNNNNNAAA_UNKNOWN, SCGGAAGY_ELK1_02, WAMUNYOKOLI_OVARIAN_CANCER_LMP_UP, DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN, BRUINS_UVC_RESPONSE_LATE, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), nuclear body (GO:0016604)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1
nucleoplasm1
intracellular membraneless organelle1

Protein interactions and networks

STRING

1287 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CCNDBP1SYF2O95926955
CCNDBP1GRAP2O75791914
CCNDBP1CCND1P24385549
CCNDBP1CDK4P11802543
CCNDBP1OLIG1Q8TAK6535
CCNDBP1TFPTP0C1Z6532
CCNDBP1E2F1Q01094500
CCNDBP1MRPL55Q7Z7F7455
CCNDBP1BEAN1Q3B7T3415
CCNDBP1GUCA1CO95843406
CCNDBP1RPLP0P05388399
CCNDBP1DDX43Q9NXZ2397
CCNDBP1SLCO6A1Q86UG4390
CCNDBP1GUCA1AP43080374
CCNDBP1LRRC57Q8N9N7363

IntAct

477 interactions, top by confidence:

ABTypeScore
CCNDBP1RPLP0psi-mi:“MI:0915”(physical association)0.800
RPLP0CCNDBP1psi-mi:“MI:0915”(physical association)0.800
RPL28CCNDBP1psi-mi:“MI:0915”(physical association)0.780
CCNDBP1TRAPPC5psi-mi:“MI:0915”(physical association)0.780
ZNF707CCNDBP1psi-mi:“MI:0915”(physical association)0.780
MRPL15CCNDBP1psi-mi:“MI:0915”(physical association)0.780
CCNDBP1RPL28psi-mi:“MI:0915”(physical association)0.780
CCNDBP1ZNF707psi-mi:“MI:0915”(physical association)0.780
TRAPPC5CCNDBP1psi-mi:“MI:0915”(physical association)0.780
CCNDBP1MRPL15psi-mi:“MI:0915”(physical association)0.780
IMP3CCNDBP1psi-mi:“MI:0915”(physical association)0.760
CCNDBP1IMP3psi-mi:“MI:0915”(physical association)0.760
PSMB10CCNDBP1psi-mi:“MI:0915”(physical association)0.740
ZNF136CCNDBP1psi-mi:“MI:0915”(physical association)0.740
CCNDBP1ZNF627psi-mi:“MI:0915”(physical association)0.740
THAP10CCNDBP1psi-mi:“MI:0915”(physical association)0.740
CCNDBP1PSMB10psi-mi:“MI:0915”(physical association)0.740
CCNDBP1ZNF136psi-mi:“MI:0915”(physical association)0.740

BioGRID (217): CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid), CCNDBP1 (Two-hybrid)

ESM2 similar proteins: A2CEI4, A3KNI7, B7ZC77, E7FBU4, G8JYB2, O35095, O43156, O46037, O75800, O88327, O95273, P0DX19, P26231, P35220, P35221, Q08CY4, Q0V9L1, Q14746, Q2KIZ9, Q2KJ97, Q3MHM6, Q3TVC7, Q4R809, Q59I72, Q5BK06, Q5RC06, Q5RFN4, Q5U4I3, Q65CL1, Q69ZR2, Q6GPP1, Q6NVK9, Q6NY52, Q7T006, Q803M5, Q8BTG3, Q8C3S2, Q8JGR7, Q8K2Z4, Q91V83

Diamond homologs: A3KNI7, O95273, Q2KIZ9, Q3TVC7, Q4R809, Q5BK06, Q5RFN4, Q5U4I3, Q2HJB9, Q6INX1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 64 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
Major pathway of rRNA processing in the nucleolus and cytosol58.6×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic1
Uncertain significance51
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
154069GRCh38/hg38 15q15.2-15.3(chr15:42785627-43342260)x1Pathogenic
980033GRCh37/hg19 15q15.2-15.3(chr15:43135272-43744542)x1Likely pathogenic

SpliceAI

1126 predictions. Top by Δscore:

VariantEffectΔscore
15:43185605:GGG:Gdonor_gain1.0000
15:43185606:GG:Gdonor_gain1.0000
15:43185606:GGG:Gdonor_gain1.0000
15:43185607:GG:Gdonor_gain1.0000
15:43185608:G:Cdonor_loss1.0000
15:43185608:G:GGdonor_gain1.0000
15:43185609:T:Adonor_loss1.0000
15:43185790:C:Aacceptor_gain1.0000
15:43189279:GG:Gdonor_gain1.0000
15:43189280:GG:Gdonor_gain1.0000
15:43189280:GGTA:Gdonor_loss1.0000
15:43189281:G:GGdonor_gain1.0000
15:43189281:GTA:Gdonor_loss1.0000
15:43189282:T:TCdonor_loss1.0000
15:43189290:A:Gdonor_gain1.0000
15:43190123:G:GTdonor_gain1.0000
15:43190123:G:Tdonor_gain1.0000
15:43190323:A:AGacceptor_gain1.0000
15:43190324:G:GCacceptor_gain1.0000
15:43190324:GCCCT:Gacceptor_gain1.0000
15:43190395:AGAGG:Adonor_loss1.0000
15:43190396:GAG:Gdonor_gain1.0000
15:43190397:AGGT:Adonor_loss1.0000
15:43190400:TGAG:Tdonor_loss1.0000
15:43190958:A:AGacceptor_gain1.0000
15:43190959:C:Gacceptor_gain1.0000
15:43190963:T:Gacceptor_gain1.0000
15:43190963:TA:Tacceptor_loss1.0000
15:43190964:A:ACacceptor_loss1.0000
15:43190964:A:AGacceptor_gain1.0000

AlphaMissense

2378 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:43191668:A:CS285R0.989
15:43191670:C:AS285R0.989
15:43191670:C:GS285R0.989
15:43191022:G:CA187P0.982
15:43191638:G:CD275H0.980
15:43194425:T:CL311P0.979
15:43191545:T:CC244R0.978
15:43191555:T:CL247P0.978
15:43192762:A:CS294R0.978
15:43192764:C:AS294R0.978
15:43192764:C:GS294R0.978
15:43191534:T:CL240P0.974
15:43191512:T:AW233R0.973
15:43191512:T:CW233R0.973
15:43189280:G:AG111R0.971
15:43189280:G:CG111R0.971
15:43191395:G:CA194P0.970
15:43189280:G:TG111W0.969
15:43191636:T:CL274P0.969
15:43194731:A:CS325R0.969
15:43194733:T:AS325R0.969
15:43194733:T:GS325R0.969
15:43191023:C:AA187E0.968
15:43191639:A:TD275V0.967
15:43192793:T:AV304E0.967
15:43192796:G:CR305P0.964
15:43190977:G:CA172P0.963
15:43190079:G:CR119P0.962
15:43191014:T:AV184E0.962
15:43191547:C:GC244W0.962

dbSNP variants (sampled 300 via entrez): RS1000290912 (15:43195853 T>G), RS1000395794 (15:43185269 A>C), RS1000851707 (15:43192189 A>G), RS1000882624 (15:43192577 A>G), RS1001087700 (15:43188005 G>T), RS1001120282 (15:43188366 G>A), RS1001457705 (15:43188326 T>C), RS1001604468 (15:43184675 A>G), RS1002090215 (15:43189572 C>G), RS1002122822 (15:43189976 T>C), RS1002163447 (15:43196480 GT>G), RS1002470725 (15:43197575 C>T), RS1002702186 (15:43193158 C>A,T), RS1002794074 (15:43195124 T>C), RS1002880184 (15:43183973 A>G)

Disease associations

OMIM: gene MIM:607089 | 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: yes

ChEMBL targets (1): CHEMBL4742266 (PROTEIN-PROTEIN INTERACTION)

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases abundance, increases expression2
Estradioldecreases expression2
Tretinoinincreases expression2
Valproic Acidaffects expression, decreases expression2
aristolochic acid Iincreases expression1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
beta-lapachoneincreases expression1
arseniteaffects binding, increases reaction1
butyraldehydedecreases expression1
pentanaldecreases expression1
perfluorooctane sulfonic acidincreases expression1
(+)-JQ1 compoundincreases expression1
Temozolomideincreases expression1
Decitabineaffects expression1
Air Pollutantsdecreases expression, increases abundance1
Air Pollutants, Occupationalaffects expression1
Aldehydesdecreases expression1
Arsenicincreases abundance, decreases expression1
Cannabidioldecreases expression1
Carbon Tetrachloridedecreases response to substance1
Cisplatinaffects expression1
Copperaffects binding, increases expression1
Diethylnitrosaminedecreases response to substance1
Dimethyl Sulfoxidedecreases expression1
Methyl Methanesulfonateincreases expression1
Smokedecreases expression1
Testosteroneincreases expression1
Thiosemicarbazonesaffects binding, increases expression1
Urethaneincreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4713784BindingProtac activity at CRBN/CCNDBP1 in human BxPC-3 cells assessed as CCNDBP1 degradation incubated for 16 hrs by proteomic analysisDiscovery of a Napabucasin PROTAC as an Effective Degrader of the E3 Ligase ZFP91. — J Med Chem

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.