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CDKN3 cyclin dependent kinase inhibitor 3 [ Homo sapiens (human) ]

Gene ID: 1033, updated on 5-Mar-2024

Summary

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Official Symbol
CDKN3provided by HGNC
Official Full Name
cyclin dependent kinase inhibitor 3provided by HGNC
Primary source
HGNC:HGNC:1791
See related
Ensembl:ENSG00000100526 MIM:123832; AllianceGenome:HGNC:1791
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KAP; CDI1; CIP2; KAP1
Summary
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]
Expression
Biased expression in testis (RPKM 79.3), bone marrow (RPKM 10.8) and 5 other tissues See more
Orthologs
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Genomic context

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See CDKN3 in Genome Data Viewer
Location:
14q22.2
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (54397007..54420218)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (48602154..48625376)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (54863725..54886936)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATP synthase F1 subunit gamma pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8409 Neighboring gene uncharacterized LOC105370507 Neighboring gene NANOG hESC enhancer GRCh37_chr14:54551221-54551722 Neighboring gene uncharacterized LOC105370505 Neighboring gene Sharpr-MPRA regulatory region 2316 Neighboring gene HNF4 motif-containing MPRA enhancer 145 Neighboring gene Sharpr-MPRA regulatory region 14732 Neighboring gene VISTA enhancer hs1414 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:54718298-54719497 Neighboring gene NANOG hESC enhancer GRCh37_chr14:54806435-54806956 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:54828631-54829198 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:54829199-54829766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:54836737-54837238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:54860347-54860846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5761 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:54907701-54908499 Neighboring gene cornichon family member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8411 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5764 Neighboring gene glia maturation factor beta

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Identification of cell cycle-associated and -unassociated regulators for expression of a hepatocellular carcinoma oncogene cyclin-dependent kinase inhibitor 3. Mori J, et al. Biochem Biophys Res Commun, 2022 Oct 15. PMID 35944363
  2. Integrated transcriptomics explored the cancer-promoting genes CDKN3 in esophageal squamous cell cancer. Wang W, et al. J Cardiothorac Surg, 2021 May 27. PMID 34044866, Free PMC Article
  3. CDKN3 expression predicates poor prognosis and regulates adriamycin sensitivity in hepatocellular carcinoma in vitro. Dai W, et al. J Int Med Res, 2020 Jul. PMID 32721244, Free PMC Article
  4. Expression and alternative splicing of the cyclin-dependent kinase inhibitor-3 gene in human cancer. Cress WD, et al. Int J Biochem Cell Biol, 2017 Oct. PMID 28504190, Free PMC Article
  5. Cyclin-Dependent Kinase Inhibitor 3 Promotes Cancer Cell Proliferation and Tumorigenesis in Nasopharyngeal Carcinoma by Targeting p27. Wang H, et al. Oncol Res, 2017 Nov 2. PMID 28109073, Free PMC Article

See all (65) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. MicroRNA-127-3p Inhibits Cardiomyocyte Inflammation and Apoptosis after Acute Myocardial Infarction via Targeting CDKN3.
    Title: MicroRNA-127-3p Inhibits Cardiomyocyte Inflammation and Apoptosis after Acute Myocardial Infarction via Targeting CDKN3.
  2. PSMD12 interacts with CDKN3 and facilitates pancreatic cancer progression.
    Title: PSMD12 interacts with CDKN3 and facilitates pancreatic cancer progression.
  3. Cyclin dependent kinase inhibitor 3 (CDKN3) upregulation is associated with unfavorable prognosis in clear cell renal cell carcinoma and shapes tumor immune microenvironment: A bioinformatics analysis.
    Title: Cyclin dependent kinase inhibitor 3 (CDKN3) upregulation is associated with unfavorable prognosis in clear cell renal cell carcinoma and shapes tumor immune microenvironment: A bioinformatics analysis.
  4. GID2 Interacts With CDKN3 and Regulates Pancreatic Cancer Growth and Apoptosis.
    Title: GID2 Interacts With CDKN3 and Regulates Pancreatic Cancer Growth and Apoptosis.
  5. Identifying key genes related to inflammasome in severe COVID-19 patients based on a joint model with random forest and artificial neural network.
    Title: Identifying key genes related to inflammasome in severe COVID-19 patients based on a joint model with random forest and artificial neural network.
  6. Identification of cell cycle-associated and -unassociated regulators for expression of a hepatocellular carcinoma oncogene cyclin-dependent kinase inhibitor 3.
    Title: Identification of cell cycle-associated and -unassociated regulators for expression of a hepatocellular carcinoma oncogene cyclin-dependent kinase inhibitor 3.
  7. CDKN3 expression predicates poor prognosis and regulates adriamycin sensitivity in hepatocellular carcinoma in vitro.
    Title: CDKN3 expression predicates poor prognosis and regulates adriamycin sensitivity in hepatocellular carcinoma in vitro.
  8. Integrated transcriptomics explored the cancer-promoting genes CDKN3 in esophageal squamous cell cancer.
    Title: Integrated transcriptomics explored the cancer-promoting genes CDKN3 in esophageal squamous cell cancer.
  9. CDKN3 regulates cisplatin resistance to colorectal cancer through TIPE1.
    Title: CDKN3 regulates cisplatin resistance to colorectal cancer through TIPE1.
  10. The aberrant expression of miR-181d-5p and cyclin-dependent kinase inhibitor 3 (CDKN3) in non-small-cell lung cancer (NSCLC) was screened by microarray analysis. There was a high expression of CDKN3, whereas miR-181d-5p was downregulated in NSCLC.
    Title: Tumor-suppressive effects of microRNA-181d-5p on non-small-cell lung cancer through the CDKN3-mediated Akt signaling pathway in vivo and in vitro.
Submit: New GeneRIF Correction See all GeneRIFs (37)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association scan of dental caries in the permanent dentition.
EBI GWAS Catalog
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
EBI GWAS Catalog
Genome-wide pharmacogenomic study of neurocognition as an indicator of antipsychotic treatment response in schizophrenia.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ25787, MGC70625

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables myosin phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein serine/threonine phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein tyrosine phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein tyrosine phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein tyrosine/serine/threonine phosphatase activity TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in G1/S transition of mitotic cell cycle TAS
Traceable Author Statement
more info
 PubMed 
involved_in dephosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of cell population proliferation TAS
Traceable Author Statement
more info
 PubMed 
acts_upstream_of_or_within regulation of cell cycle IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of cyclin-dependent protein serine/threonine kinase activity TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
cyclin-dependent kinase inhibitor 3
Names
CDK2-associated dual specificity phosphatase
Cdk-associated protein phosphatase
cyclin-dependent kinase inhibitor
cyclin-dependent kinase interacting protein 2
cyclin-dependent kinase interactor 1
kinase-associated phosphatase
NP_001124323.1
NP_001317102.1
NP_005183.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_023235.1 RefSeqGene

    Range
    5053..28264
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001130851.2 → NP_001124323.1  cyclin-dependent kinase inhibitor 3 isoform 2

    See identical proteins and their annotated locations for NP_001124323.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame segment in the CDS, as compared to variant 1. The resulting isoform (2) lacks an internal segment, as compared to isoform 1.
    Source sequence(s)
    BC064965
    Consensus CDS
    CCDS45109.1
    UniProtKB/TrEMBL
    Q9BPV5
    Related
    ENSP00000415333.2, ENST00000442975.6
    Conserved Domains (1) summary
    cl21483
    Location:11 → 128
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

  2. NM_001330173.2 → NP_001317102.1  cyclin-dependent kinase inhibitor 3 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate exon in the 3' coding region, resulting in a frameshift compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL049778, AL359792
    Consensus CDS
    CCDS81804.1
    UniProtKB/TrEMBL
    G3V2J7, Q9C043
    Related
    ENSP00000450711.1, ENST00000556102.6
    Conserved Domains (1) summary
    pfam05706
    Location:1 → 168
    CDKN3; Cyclin-dependent kinase inhibitor 3 (CDKN3)

  3. NM_005192.4 → NP_005183.2  cyclin-dependent kinase inhibitor 3 isoform 1

    See identical proteins and their annotated locations for NP_005183.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK098653, BC064965
    Consensus CDS
    CCDS9716.1
    UniProtKB/Swiss-Prot
    Q16667, Q53ZU6, Q5U0M4, Q6P1N8, Q99585, Q9BPW7, Q9BY36, Q9C042, Q9C046, Q9C047, Q9C049, Q9C051, Q9C053
    UniProtKB/TrEMBL
    H7C0S3
    Related
    ENSP00000335357.6, ENST00000335183.11
    Conserved Domains (1) summary
    pfam05706
    Location:1 → 168
    CDKN3; Cyclin-dependent kinase inhibitor 3 (CDKN3)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    54397007..54420218
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    48602154..48625376
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q16667.1 GenPept UniProtKB/Swiss-Prot:Q16667

Gene LinkOut

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