Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CDKN3 Gene

Aliases for CDKN3 Gene

  • Cyclin Dependent Kinase Inhibitor 3 2 3 5
  • CDK2-Associated Dual Specificity Phosphatase 2 3
  • Cyclin-Dependent Kinase Interactor 1 3 4
  • Cyclin-Dependent Kinase Inhibitor 2 3
  • Kinase-Associated Phosphatase 3 4
  • CDI1 3 4
  • CIP2 3 4
  • KAP 3 4
  • Cyclin-Dependent Kinase Interacting Protein 2 3
  • Cyclin-Dependent Kinase-Interacting Protein 2 4
  • CDK2-Associated Dual-Specificity Phosphatase 4
  • Cyclin-Dependent Kinase Inhibitor 3 3
  • Cdk-Associated Protein Phosphatase 3
  • Kinase Associated Phosphatase 2
  • EC 4
  • EC 4
  • KAP1 3

External Ids for CDKN3 Gene

Previous GeneCards Identifiers for CDKN3 Gene

  • GC14P052187
  • GC14P048659
  • GC14P052853
  • GC14P053933
  • GC14P054863
  • GC14P035026

Summaries for CDKN3 Gene

Entrez Gene Summary for CDKN3 Gene

  • The protein encoded by this gene belongs to the dual specificity protein phosphatase family. It was identified as a cyclin-dependent kinase inhibitor, and has been shown to interact with, and dephosphorylate CDK2 kinase, thus prevent the activation of CDK2 kinase. This gene was reported to be deleted, mutated, or overexpressed in several kinds of cancers. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

GeneCards Summary for CDKN3 Gene

CDKN3 (Cyclin Dependent Kinase Inhibitor 3) is a Protein Coding gene. Diseases associated with CDKN3 include Hepatocellular Carcinoma and Bannayan-Riley-Ruvalcaba Syndrome. GO annotations related to this gene include phosphatase activity and phosphoprotein phosphatase activity.

UniProtKB/Swiss-Prot for CDKN3 Gene

  • May play a role in cell cycle regulation. Dual specificity phosphatase active toward substrates containing either phosphotyrosine or phosphoserine residues. Dephosphorylates CDK2 at Thr-160 in a cyclin-dependent manner.

Gene Wiki entry for CDKN3 Gene

Additional gene information for CDKN3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDKN3 Gene

Genomics for CDKN3 Gene

Regulatory Elements for CDKN3 Gene

Enhancers for CDKN3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH14H054439 1.1 ENCODE 0.3 +44.2 44158 2.5 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 YY1 ZNF207 ZNF143 DEK ZNF592 ATG14 CNIH1 WDHD1 MAPK1IP1L CDKN3
GH14H054438 0.6 Ensembl 0.3 +42.1 42052 0.2 ZNF398 GATA3 ZNF766 PATZ1 GLIS1 ZNF341 IKZF1 PRDM1 SP7 CNIH1 CDKN3
GH14H054420 0.5 ENCODE 0.3 +23.8 23819 0.1 CTCF MAZ ZNF511 RAD21 CDKN3 CNIH1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CDKN3 on UCSC Golden Path with GeneCards custom track

Promoters for CDKN3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000068682 152 1600 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF416 ZNF143 ZNF548

Genomic Locations for CDKN3 Gene

Genomic Locations for CDKN3 Gene
23,370 bases
Plus strand

Genomic View for CDKN3 Gene

Genes around CDKN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDKN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDKN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDKN3 Gene

Proteins for CDKN3 Gene

  • Protein details for CDKN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Cyclin-dependent kinase inhibitor 3
    Protein Accession:
    Secondary Accessions:
    • Q53ZU6
    • Q5U0M4
    • Q6P1N8
    • Q99585
    • Q9BPW7
    • Q9BY36
    • Q9C042
    • Q9C046
    • Q9C047
    • Q9C049
    • Q9C051
    • Q9C053

    Protein attributes for CDKN3 Gene

    212 amino acids
    Molecular mass:
    23805 Da
    Quaternary structure:
    • Interacts with cyclin-dependent kinases such as CDK1, CDK2 and CDK3. Does not interact with CDK4. Interacts (via C-terminus) with phosphorylated CDK2 (via C-terminal helix). Interacts with MS4A3 (via C-terminus); the interaction enhances CDKN3 enzymatic activity.

    Three dimensional structures from OCA and Proteopedia for CDKN3 Gene

    Alternative splice isoforms for CDKN3 Gene


neXtProt entry for CDKN3 Gene

Post-translational modifications for CDKN3 Gene

  • Ubiquitination at posLast=184184
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CDKN3 Gene

Domains & Families for CDKN3 Gene

Gene Families for CDKN3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for CDKN3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the protein-tyrosine phosphatase family.
  • Belongs to the protein-tyrosine phosphatase family.
genes like me logo Genes that share domains with CDKN3: view

Function for CDKN3 Gene

Molecular function for CDKN3 Gene

GENATLAS Biochemistry:
cyclin dependent kinases CDC2 (CDK1) and CDK2 (CDC2/CDK2) inhibitor,expressed at the G1 to S transition of the cell cycle
UniProtKB/Swiss-Prot CatalyticActivity:
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
UniProtKB/Swiss-Prot CatalyticActivity:
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate.
UniProtKB/Swiss-Prot Function:
May play a role in cell cycle regulation. Dual specificity phosphatase active toward substrates containing either phosphotyrosine or phosphoserine residues. Dephosphorylates CDK2 at Thr-160 in a cyclin-dependent manner.
UniProtKB/Swiss-Prot Induction:
Up-regulated in breast and prostate cancer cells.

Enzyme Numbers (IUBMB) for CDKN3 Gene

Phenotypes From GWAS Catalog for CDKN3 Gene

Gene Ontology (GO) - Molecular Function for CDKN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004721 phosphoprotein phosphatase activity IEA --
GO:0004722 protein serine/threonine phosphatase activity IDA 12745075
GO:0004725 protein tyrosine phosphatase activity IEA,IDA 8242750
GO:0005515 protein binding IPI 8242750
GO:0008138 protein tyrosine/serine/threonine phosphatase activity TAS 8242750
genes like me logo Genes that share ontologies with CDKN3: view
genes like me logo Genes that share phenotypes with CDKN3: view

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CDKN3 Gene

Localization for CDKN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDKN3 Gene

Cytoplasm, perinuclear region.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CDKN3 gene
Compartment Confidence
cytosol 5
nucleus 4

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CDKN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
GO:0048471 perinuclear region of cytoplasm IDA,IEA 10669749
genes like me logo Genes that share ontologies with CDKN3: view

Pathways & Interactions for CDKN3 Gene

SuperPathways for CDKN3 Gene

No Data Available

Pathways by source for CDKN3 Gene

1 GeneTex pathway for CDKN3 Gene

Gene Ontology (GO) - Biological Process for CDKN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity TAS 8242750
GO:0000082 G1/S transition of mitotic cell cycle TAS 8127873
GO:0006470 protein dephosphorylation IEA --
GO:0007049 cell cycle IEA --
GO:0007050 cell cycle arrest IDA 8242750
genes like me logo Genes that share ontologies with CDKN3: view

No data available for SIGNOR curated interactions for CDKN3 Gene

Drugs & Compounds for CDKN3 Gene

(78) Drugs for CDKN3 Gene - From: ApexBio, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
AT7519 Investigational Pharma Multi-CDK inhibitor 0
calcium Nutra 0
Kenpaullone Pharma 0

(56) Additional Compounds for CDKN3 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)

(8) ApexBio Compounds for CDKN3 Gene

Compound Action Cas Number
AT7519 Multi-CDK inhibitor 844442-38-2
Kenpaullone 142273-20-9
ML167 Clk4 inhibitor,highly selective 1285702-20-6
Nu 6027 ATR/CDK inhibitor, potent and selective 220036-08-8
PHA-848125 CDK inhibitor,potent and ATP-competitive 802539-81-7
Purvalanol B CDK1/CDK2/CDK4 inhibitor 212844-54-7
R547 CDK1/2/4 inhibitor,ATP-competitive 741713-40-6
Ro 3306 An ATP-competitive, potent CDK1 inhibitor 872573-93-8
genes like me logo Genes that share compounds with CDKN3: view

Drug Products

Transcripts for CDKN3 Gene

Unigene Clusters for CDKN3 Gene

Cyclin-dependent kinase inhibitor 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CDKN3 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c · 8d
SP3: -
SP4: -
SP6: -

Relevant External Links for CDKN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CDKN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDKN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CDKN3 Gene

This gene is overexpressed in Testis (x23.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CDKN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of CDKN3 Gene:


SOURCE GeneReport for Unigene cluster for CDKN3 Gene:

genes like me logo Genes that share expression patterns with CDKN3: view

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDKN3 Gene

Orthologs for CDKN3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CDKN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CDKN3 33 34
  • 99.53 (n)
(Bos Taurus)
Mammalia CDKN3 34
  • 92 (a)
(Canis familiaris)
Mammalia CDKN3 33 34
  • 91.67 (n)
(Mus musculus)
Mammalia Cdkn3 33 16 34
  • 88.47 (n)
(Monodelphis domestica)
Mammalia CDKN3 34
  • 83 (a)
(Ornithorhynchus anatinus)
Mammalia CDKN3 34
  • 64 (a)
(Gallus gallus)
Aves CDKN3 33 34
  • 69.42 (n)
(Anolis carolinensis)
Reptilia CDKN3 34
  • 66 (a)
(Danio rerio)
Actinopterygii cdkn3 33 34
  • 64.08 (n)
Dr.24317 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4052 33
Species where no ortholog for CDKN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CDKN3 Gene

Gene Tree for CDKN3 (if available)
Gene Tree for CDKN3 (if available)

Paralogs for CDKN3 Gene

No data available for Paralogs for CDKN3 Gene

Variants for CDKN3 Gene

Sequence variations from dbSNP and Humsavar for CDKN3 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs144479038 Hepatocellular carcinoma (HCC) [MIM:114550] 54,411,612(+) ATCCA(A/G)TCGCA reference, missense
rs760687800 Hepatocellular carcinoma (HCC) [MIM:114550] 54,411,563(+) CCAAA(C/G)CTTCT reference, missense
VAR_013842 Hepatocellular carcinoma (HCC) [MIM:114550]
VAR_013843 Hepatocellular carcinoma (HCC) [MIM:114550]
VAR_013844 Hepatocellular carcinoma (HCC) [MIM:114550]

Structural Variations from Database of Genomic Variants (DGV) for CDKN3 Gene

Variant ID Type Subtype PubMed ID
nsv952844 CNV deletion 24416366
nsv832801 CNV gain 17160897

Variation tolerance for CDKN3 Gene

Residual Variation Intolerance Score: 69.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.66; 14.00% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CDKN3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDKN3 Gene

Disorders for CDKN3 Gene

MalaCards: The human disease database

(14) MalaCards diseases for CDKN3 Gene - From: HGMD, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
hepatocellular carcinoma
  • hepatocellular carcinoma, somatic
bannayan-riley-ruvalcaba syndrome
  • bannayan-zonana syndrome
cataract 18, autosomal recessive
  • cataract 18
leopard syndrome
  • capute-rimoin-konigsmark-esterly-richardson syndrome
charcot-marie-tooth disease, type 4b1
  • charcot-marie-tooth disease type 4b1
- elite association - COSMIC cancer census association via MalaCards
Search CDKN3 in MalaCards View complete list of genes associated with diseases


  • Hepatocellular carcinoma (HCC) [MIM:114550]: A primary malignant neoplasm of epithelial liver cells. The major risk factors for HCC are chronic hepatitis B virus (HBV) infection, chronic hepatitis C virus (HCV) infection, prolonged dietary aflatoxin exposure, alcoholic cirrhosis, and cirrhosis due to other causes. {ECO:0000269 PubMed:10987270}. Note=The gene represented in this entry may be involved in disease pathogenesis.

Relevant External Links for CDKN3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CDKN3: view

No data available for Genatlas for CDKN3 Gene

Publications for CDKN3 Gene

  1. Cdi1, a human G1 and S phase protein phosphatase that associates with Cdk2. (PMID: 8242750) Gyuris J … Brent R (Cell 1993) 2 3 4 22 60
  2. Binding of HTm4 to cyclin-dependent kinase (Cdk)-associated phosphatase (KAP).Cdk2.cyclin A complex enhances the phosphatase activity of KAP, dissociates cyclin A, and facilitates KAP dephosphorylation of Cdk2. (PMID: 15671017) Chinami M … Adra CN (The Journal of biological chemistry 2005) 3 4 22 60
  3. Abolishment of the interaction between cyclin-dependent kinase 2 and Cdk-associated protein phosphatase by a truncated KAP mutant. (PMID: 12745075) Yeh CT … Chao ML (Biochemical and biophysical research communications 2003) 3 4 22 60
  4. Overexpression of kinase-associated phosphatase (KAP) in breast and prostate cancer and inhibition of the transformed phenotype by antisense KAP expression. (PMID: 10669749) Lee SW … Aaronson SA (Molecular and cellular biology 2000) 3 4 22 60
  5. Chromosomal mapping of the genes for the human cell cycle proteins cyclin C (CCNC), cyclin E (CCNE), p21 (CDKN1) and KAP (CDKN3). (PMID: 7698009) Demetrick DJ … Beach DH (Cytogenetics and cell genetics 1995) 2 3 22 60

Products for CDKN3 Gene

Sources for CDKN3 Gene

Loading form....