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CDKN1B (cyclin-dependent kinase inhibitor 1 B)

Written1998-05Chrystele Bilhou-Nabera
Cytogénétique,Laboratoire d'Hématologie-Pr RAPHAEL, Pav BROCA - 4eme étage, 78 rue du Général Leclerc, 94275 LE KREMLIN-BICETRE, France

(Note : for Links provided by Atlas : click)

Identity

Alias (NCBI)KIP1
P27KIP1
HGNC (Hugo) CDKN1B
HGNC Alias symbKIP1
P27KIP1
HGNC Previous namecyclin-dependent kinase inhibitor 1B (p27, Kip1)
LocusID (NCBI) 1027
Atlas_Id 116
Location 12p13.1  [Link to chromosome band 12p13]
Location_base_pair Starts at 12717270 and ends at 12722382 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping CDKN1B.png]
Local_order centromere - CDNK1B - ETV6 - PRB - KCNA5 - CACNL1A1 - telomere
 
  CDK1B (12p3) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
APOLD1 (12p13.1)::CDKN1B (12p13.1)CDKN1B (12p13.1)::ADGRG1 (16q21)CDKN1B (12p13.1)::CDKN1B (12p13.1)
ETV6 (12p13.2)::CDKN1B (12p13.1)FN1 (2q35)::CDKN1B (12p13.1)VDAC3 (8p11.21)::CDKN1B (12p13.1)

DNA/RNA

Description coding region from two exons
Transcription 2.5 Kb mRNA; CDKN1B gene regulation by extracellular antiproliferative signals occurs at a post-transcriptional level

Protein

Description 198 amino-acids; 22 kDa; homology to WAF1, limited to a 60 amino acid segment in the N-term half of the protein (residues 28-88); putative bipartite nuclear localization signal near the C-term (153-169); C-term extension of 23 amino acids that contains a consensus Cdc2 phosphorylation site.
Expression expressed in all tissues tested; high levels in skeletal muscle, low levels in liver and kidney.
Localisation nuclear.
Function - CDKN1B is a negative regulator implicated in G1 arrest mediated by TGFb, cell-cell contact, agents that elevate cyclic AMP and rapamycin; CDKN1B binds to and acts as a stoichiometric inhibitor of G1-cyclin-cyclin dependent kinase complexes (cyclin E-Cdk2, cyclin A-Cdk2, cyclin D-Cdk4 (restriction point), controlling G1 to S phase transition or exit from the cell cycle; CDKN1B coordinates the varied inputs from the extracellular environment; post-translational ubiquitin-mediated proteasomal proteolysis represents the major regulatory influence of CDKN1B protein level. - in CDKN1B knockout mouse, CDKN1B defect causes multi-organ hyperplasia with features of gigantism, abnormalities of thymus, retina, pituitary, adrenal glands and gonadal organs (ovulatory defect and female sterility).
Homology Cip1/WAF1

Implicated in

Note
  
Entity haematological malignancies.
Note hemizygous interstitial deletion is found in 10% of cytogenetically normal AML; monoallelic deletion found in 5% AML cases, but not described in ALL; no case so far of CDKN1B mutations in leukemia samples.
  
  
Entity primary breast cancers
Prognosis a low nuclear expression of CDKN1B protein is a significant predictor of poor disease-free survival; in contrary, high level of CDKN1B protein expression combined with low level expression of its target (cyclin E-Cdk2) correlates with about 90% 10-yr overall survival in the lymph node-negative subgroup.
  
  
Entity primary colorectal carcinomas
Prognosis CDKN1B is an independent prognostic marker: low levels are significantly correlated with a poor prognosis.
  

Bibliography

Deletions of CDKN1B and ETV6 in acute myeloid leukemia and myelodysplastic syndromes without cytogenetic evidence of 12p abnormalities.
Andreasson P, Johansson B, Arheden K, Billström R, Mitelman F, Höglund M
Genes, chromosomes & cancer. 1997 ; 19 (2) : 77-83.
PMID 9171997
 
Decreased levels of the cell-cycle inhibitor p27Kip1 protein: prognostic implications in primary breast cancer.
Catzavelos C, Bhattacharya N, Ung YC, Wilson JA, Roncari L, Sandhu C, Shaw P, Yeger H, Morava-Protzner I, Kapusta L, Franssen E, Pritchard KI, Slingerland JM
Nature medicine. 1997 ; 3 (2) : 227-230.
PMID 9018244
 
Molecular analysis of cyclin-dependent kinase inhibitors in human leukemias.
Hayette S, Thomas X, Bertrand Y, Tigaud I, Callanan M, Thiebaut A, Charrin C, Archimbaud E, Magaud JP, Rimokh R
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 1997 ; 11 (10) : 1696-1699.
PMID 9324291
 
Translational control of p27Kip1 accumulation during the cell cycle.
Hengst L, Reed SI
Science (New York, N.Y.). 1996 ; 271 (5257) : 1861-1864.
PMID 8596954
 
Increased proteasome-dependent degradation of the cyclin-dependent kinase inhibitor p27 in aggressive colorectal carcinomas.
Loda M, Cukor B, Tam SW, Lavin P, Fiorentino M, Draetta GF, Jessup JM, Pagano M
Nature medicine. 1997 ; 3 (2) : 231-234.
PMID 9018245
 
Assignment of the human p27Kip1 gene to 12p13 and its analysis in leukemias.
Pietenpol JA, Bohlander SK, Sato Y, Papadopoulos N, Liu B, Friedman C, Trask BJ, Roberts JM, Kinzler KW, Rowley JD
Cancer research. 1995 ; 55 (6) : 1206-1210.
PMID 7882309
 
Cloning of p27Kip1, a cyclin-dependent kinase inhibitor and a potential mediator of extracellular antimitogenic signals.
Polyak K, Lee MH, Erdjument-Bromage H, Koff A, Roberts JM, Tempst P, Massagué J
Cell. 1994 ; 78 (1) : 59-66.
PMID 8033212
 
Expression of cell-cycle regulators p27Kip1 and cyclin E, alone and in combination, correlate with survival in young breast cancer patients.
Porter PL, Malone KE, Heagerty PJ, Alexander GM, Gatti LA, Firpo EJ, Daling JR, Roberts JM
Nature medicine. 1997 ; 3 (2) : 222-225.
PMID 9018243
 
Germline configuration of the p27(Kip1) gene in childhood acute lymphoblastic leukemia (ALL).
Seriu T, Erz D, Bartram CR
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 1996 ; 10 (2) : page 345.
PMID 8637245
 
Cancer prognostics: past, present and p27.
Steeg PS, Abrams JS
Nature medicine. 1997 ; 3 (2) : 152-154.
PMID 9018230
 
p27, a novel inhibitor of G1 cyclin-Cdk protein kinase activity, is related to p21.
Toyoshima H, Hunter T
Cell. 1994 ; 78 (1) : 67-74.
PMID 8033213
 

Citation

This paper should be referenced as such :
Bilhou-Nabera, C
CDKN1B (cyclin-dependent kinase inhibitor 1 B )
Atlas Genet Cytogenet Oncol Haematol. 1998;2(4):115-116.
Free journal version : [ pdf ]   [ DOI ]


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 8 ]
  12p abnormalities in myeloid malignancies
Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)
Classification of myelodysplastic syndromes 2015
Classification of myelodysplasic syndromes 1999
der(12)t(1;12)(q11-21;p11-13)
t(8;12)(q12;p13)
t(10;12)(q24;p13) ETV6::GOT1
t(12;12)(p13;p13) ETV6::CDKN1B


External links

 

Nomenclature
HGNC (Hugo)CDKN1B   1785
Cards
AtlasCDKN1BID116
Entrez_Gene (NCBI)CDKN1B    cyclin dependent kinase inhibitor 1B
AliasesCDKN4; KIP1; MEN1B; MEN4; 
P27KIP1
GeneCards (Weizmann)CDKN1B
Ensembl hg19 (Hinxton)ENSG00000111276 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000111276 [Gene_View]  ENSG00000111276 [Sequence]  chr12:12717270-12722382 [Contig_View]  CDKN1B [Vega]
ICGC DataPortalENSG00000111276
TCGA cBioPortalCDKN1B
AceView (NCBI)CDKN1B
Genatlas (Paris)CDKN1B
SOURCE (Princeton)CDKN1B
Genetics Home Reference (NIH)CDKN1B
Genomic and cartography
GoldenPath hg38 (UCSC)CDKN1B  -     chr12:12717270-12722382 +  12p13.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CDKN1B  -     12p13.1   [Description]    (hg19-Feb_2009)
GoldenPathCDKN1B - 12p13.1 [CytoView hg19]  CDKN1B - 12p13.1 [CytoView hg38]
ImmunoBaseENSG00000111276
Genome Data Viewer NCBICDKN1B [Mapview hg19]  
OMIM600778   610755   
Gene and transcription
Genbank (Entrez)AA833962 AB451291 AB451423 AF247551 AJ616234
RefSeq transcript (Entrez)NM_004064
Consensus coding sequences : CCDS (NCBI)CDKN1B
Gene ExpressionCDKN1B [ NCBI-GEO ]   CDKN1B [ EBI - ARRAY_EXPRESS ]   CDKN1B [ SEEK ]   CDKN1B [ MEM ]
Gene Expression Viewer (FireBrowse)CDKN1B [ Firebrowse - Broad ]
GenevisibleExpression of CDKN1B in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1027
GTEX Portal (Tissue expression)CDKN1B
Human Protein AtlasENSG00000111276-CDKN1B [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP46527   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP46527  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP46527
PhosPhoSitePlusP46527
Domains : Interpro (EBI)CDI    CDKN1B   
Domain families : Pfam (Sanger)CDI (PF02234)   
Domain families : Pfam (NCBI)pfam02234   
Conserved Domain (NCBI)CDKN1B
PDB (RSDB)1H27    1JSU    2AST    5UQ3    6ATH    6P8E    6P8F    6P8G   
PDB Europe1H27    1JSU    2AST    5UQ3    6ATH    6P8E    6P8F    6P8G   
PDB (PDBSum)1H27    1JSU    2AST    5UQ3    6ATH    6P8E    6P8F    6P8G   
PDB (IMB)1H27    1JSU    2AST    5UQ3    6ATH    6P8E    6P8F    6P8G   
Structural Biology KnowledgeBase1H27    1JSU    2AST    5UQ3    6ATH    6P8E    6P8F    6P8G   
SCOP (Structural Classification of Proteins)1H27    1JSU    2AST    5UQ3    6ATH    6P8E    6P8F    6P8G   
CATH (Classification of proteins structures)1H27    1JSU    2AST    5UQ3    6ATH    6P8E    6P8F    6P8G   
SuperfamilyP46527
AlphaFold pdb e-kbP46527   
Human Protein Atlas [tissue]ENSG00000111276-CDKN1B [tissue]
HPRD02867
Protein Interaction databases
DIP (DOE-UCLA)P46527
IntAct (EBI)P46527
BioGRIDCDKN1B
STRING (EMBL)CDKN1B
ZODIACCDKN1B
Ontologies - Pathways
QuickGOP46527
Ontology : AmiGOregulation of cyclin-dependent protein serine/threonine kinase activity  G1/S transition of mitotic cell cycle  G1/S transition of mitotic cell cycle  G1/S transition of mitotic cell cycle  response to hypoxia  placenta development  protein kinase inhibitor activity  cyclin-dependent protein serine/threonine kinase inhibitor activity  cyclin-dependent protein serine/threonine kinase inhibitor activity  protein binding  nucleus  nucleus  nucleoplasm  nucleoplasm  cytoplasm  cytoplasm  endosome  cytosol  potassium ion transport  DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest  regulation of exit from mitosis  Notch signaling pathway  heart development  sensory perception of sound  positive regulation of cell population proliferation  negative regulation of cell population proliferation  negative regulation of cell population proliferation  negative regulation of cell population proliferation  response to glucose  positive regulation of cell death  cytokine-mediated signaling pathway  protein kinase binding  protein phosphatase binding  negative regulation of cell growth  cyclin binding  cyclin binding  Hsp70 protein binding  positive regulation of microtubule polymerization  Cul4A-RING E3 ubiquitin ligase complex  response to estradiol  negative regulation of kinase activity  negative regulation of phosphorylation  response to drug  negative regulation of apoptotic process  response to amino acid  intracellular membrane-bounded organelle  response to peptide hormone  protein-containing complex binding  positive regulation of protein catabolic process  negative regulation of cyclin-dependent protein serine/threonine kinase activity  negative regulation of cyclin-dependent protein serine/threonine kinase activity  positive regulation of cyclin-dependent protein serine/threonine kinase activity  negative regulation of cell cycle  positive regulation of cell cycle  negative regulation of transcription, DNA-templated  negative regulation of mitotic cell cycle  negative regulation of mitotic cell cycle  response to cadmium ion  autophagic cell death  inner ear development  chaperone binding  negative regulation of cellular component movement  regulation of cell cycle  regulation of cell cycle  regulation of cell cycle  regulation of cell cycle  negative regulation of epithelial cell proliferation involved in prostate gland development  cellular response to antibiotic  cellular response to lithium ion  cellular response to organic cyclic compound  regulation of lens fiber cell differentiation  regulation of cell cycle G1/S phase transition  negative regulation of cyclin-dependent protein kinase activity  negative regulation of vascular associated smooth muscle cell proliferation  negative regulation of cardiac muscle tissue regeneration  
Ontology : EGO-EBIregulation of cyclin-dependent protein serine/threonine kinase activity  G1/S transition of mitotic cell cycle  G1/S transition of mitotic cell cycle  G1/S transition of mitotic cell cycle  response to hypoxia  placenta development  protein kinase inhibitor activity  cyclin-dependent protein serine/threonine kinase inhibitor activity  cyclin-dependent protein serine/threonine kinase inhibitor activity  protein binding  nucleus  nucleus  nucleoplasm  nucleoplasm  cytoplasm  cytoplasm  endosome  cytosol  potassium ion transport  DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest  regulation of exit from mitosis  Notch signaling pathway  heart development  sensory perception of sound  positive regulation of cell population proliferation  negative regulation of cell population proliferation  negative regulation of cell population proliferation  negative regulation of cell population proliferation  response to glucose  positive regulation of cell death  cytokine-mediated signaling pathway  protein kinase binding  protein phosphatase binding  negative regulation of cell growth  cyclin binding  cyclin binding  Hsp70 protein binding  positive regulation of microtubule polymerization  Cul4A-RING E3 ubiquitin ligase complex  response to estradiol  negative regulation of kinase activity  negative regulation of phosphorylation  response to drug  negative regulation of apoptotic process  response to amino acid  intracellular membrane-bounded organelle  response to peptide hormone  protein-containing complex binding  positive regulation of protein catabolic process  negative regulation of cyclin-dependent protein serine/threonine kinase activity  negative regulation of cyclin-dependent protein serine/threonine kinase activity  positive regulation of cyclin-dependent protein serine/threonine kinase activity  negative regulation of cell cycle  positive regulation of cell cycle  negative regulation of transcription, DNA-templated  negative regulation of mitotic cell cycle  negative regulation of mitotic cell cycle  response to cadmium ion  autophagic cell death  inner ear development  chaperone binding  negative regulation of cellular component movement  regulation of cell cycle  regulation of cell cycle  regulation of cell cycle  regulation of cell cycle  negative regulation of epithelial cell proliferation involved in prostate gland development  cellular response to antibiotic  cellular response to lithium ion  cellular response to organic cyclic compound  regulation of lens fiber cell differentiation  regulation of cell cycle G1/S phase transition  negative regulation of cyclin-dependent protein kinase activity  negative regulation of vascular associated smooth muscle cell proliferation  negative regulation of cardiac muscle tissue regeneration  
Pathways : BIOCARTARegulation of p27 Phosphorylation during Cell Cycle Progression [Genes]    Cyclins and Cell Cycle Regulation [Genes]    CTCF: First Multivalent Nuclear Factor [Genes]    Cell Cycle: G1/S Check Point [Genes]    CDK Regulation of DNA Replication [Genes]    PTEN dependent cell cycle arrest and apoptosis [Genes]    Influence of Ras and Rho proteins on G1 to S Transition [Genes]   
Pathways : KEGGErbB signaling pathway    HIF-1 signaling pathway    FoxO signaling pathway    Cell cycle    PI3K-Akt signaling pathway    Hepatitis B    Measles    Epstein-Barr virus infection    Pathways in cancer    Transcriptional misregulation in cancer    Viral carcinogenesis    MicroRNAs in cancer    Prostate cancer    Chronic myeloid leukemia    Small cell lung cancer   
REACTOMEP46527 [protein]
REACTOME PathwaysR-HSA-9634638 [pathway]   
NDEx NetworkCDKN1B
Atlas of Cancer Signalling NetworkCDKN1B
Wikipedia pathwaysCDKN1B
Orthology - Evolution
OrthoDB1027
GeneTree (enSembl)ENSG00000111276
Phylogenetic Trees/Animal Genes : TreeFamCDKN1B
Homologs : HomoloGeneCDKN1B
Homology/Alignments : Family Browser (UCSC)CDKN1B
Gene fusions - Rearrangements
Fusion : MitelmanAPOLD1::CDKN1B [12p13.1/12p13.1]  
Fusion : QuiverCDKN1B
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCDKN1B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CDKN1B
dbVarCDKN1B
ClinVarCDKN1B
MonarchCDKN1B
1000_GenomesCDKN1B 
Exome Variant ServerCDKN1B
GNOMAD BrowserENSG00000111276
Varsome BrowserCDKN1B
ACMGCDKN1B variants
VarityP46527
Genomic Variants (DGV)CDKN1B [DGVbeta]
DECIPHERCDKN1B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCDKN1B 
Mutations
ICGC Data PortalCDKN1B 
TCGA Data PortalCDKN1B 
Broad Tumor PortalCDKN1B
OASIS PortalCDKN1B [ Somatic mutations - Copy number]
Cancer Gene: CensusCDKN1B 
Somatic Mutations in Cancer : COSMICCDKN1B  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DCDKN1B
Mutations and Diseases : HGMDCDKN1B
intOGen PortalCDKN1B
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaCDKN1B
DgiDB (Drug Gene Interaction Database)CDKN1B
DoCM (Curated mutations)CDKN1B
CIViC (Clinical Interpretations of Variants in Cancer)CDKN1B
OncoKBCDKN1B
NCG (London)CDKN1B
Cancer3DCDKN1B
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600778    610755   
Orphanet121    20350   
DisGeNETCDKN1B
MedgenCDKN1B
Genetic Testing Registry CDKN1B
NextProtP46527 [Medical]
GENETestsCDKN1B
Target ValidationCDKN1B
Huge Navigator CDKN1B [HugePedia]
ClinGenCDKN1B
Clinical trials, drugs, therapy
MyCancerGenomeCDKN1B
Protein Interactions : CTDCDKN1B
Pharm GKB GenePA105
Pharm GKB PathwaysPA152241951   
PharosP46527
Clinical trialCDKN1B
Miscellaneous
canSAR (ICR)CDKN1B
HarmonizomeCDKN1B
DataMed IndexCDKN1B
Other databasehttp://cancergenome.broadinstitute.org/index.php?tgene=CDKN1B
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXCDKN1B
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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