CDKN2D Gene (Protein Coding)

Cyclin Dependent Kinase Inhibitor 2D

GC19M010566
GIFtS:
40
The protein encoded by this gene is a member of the INK4 family of cyclin-dependent kinase inhibitors. This protein has been shown to form a stable complex with CDK4 or CDK6, and prevent the activation of the CDK kinases, thus function as a cell growth regulator that controls cell cycle G1 progression. The abundance of the transcript of this gene was found to oscillate in a cel... See more...

Aliases for CDKN2D Gene

Aliases for CDKN2D Gene

  • Cyclin Dependent Kinase Inhibitor 2D 2 3 5
  • Cyclin-Dependent Kinase Inhibitor 2D (P19, Inhibits CDK4) 2 3
  • Cyclin-Dependent Kinase 4 Inhibitor D 3 4
  • INK4D 2 3
  • P19 2 3
  • Cell Cycle Inhibitor, Nur77 Associating Protein 3
  • Cyclin-Dependent Kinase 4 Inhibitor D P19 3
  • Inhibitor Of Cyclin-Dependent Kinase 4d 3
  • CDK Inhibitor P19INK4d 3
  • P19-INK4D 3
  • P19-INK4d 4
  • CDKN2D 5

External Ids for CDKN2D Gene

Previous GeneCards Identifiers for CDKN2D Gene

  • GC19M010808
  • GC19M010899
  • GC19M010522
  • GC19M010538
  • GC19M010677
  • GC19M010255

Summaries for CDKN2D Gene

Entrez Gene Summary for CDKN2D Gene

  • The protein encoded by this gene is a member of the INK4 family of cyclin-dependent kinase inhibitors. This protein has been shown to form a stable complex with CDK4 or CDK6, and prevent the activation of the CDK kinases, thus function as a cell growth regulator that controls cell cycle G1 progression. The abundance of the transcript of this gene was found to oscillate in a cell-cycle dependent manner with the lowest expression at mid G1 and a maximal expression during S phase. The negative regulation of the cell cycle involved in this protein was shown to participate in repressing neuronal proliferation, as well as spermatogenesis. Two alternatively spliced variants of this gene, which encode an identical protein, have been reported. [provided by RefSeq, Jul 2008]

GeneCards Summary for CDKN2D Gene

CDKN2D (Cyclin Dependent Kinase Inhibitor 2D) is a Protein Coding gene. Diseases associated with CDKN2D include Adult Central Nervous System Primitive Neuroectodermal Neoplasm and Parathyroid Adenoma. Among its related pathways are Oncogene Induced Senescence and Cyclins and Cell Cycle Regulation. Gene Ontology (GO) annotations related to this gene include protein kinase binding and cyclin-dependent protein serine/threonine kinase inhibitor activity. An important paralog of this gene is CDKN2C.

UniProtKB/Swiss-Prot Summary for CDKN2D Gene

Gene Wiki entry for CDKN2D Gene

Additional gene information for CDKN2D Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CDKN2D Gene

Genomics for CDKN2D Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CDKN2D Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH19J010564 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 624.6 +1.7 1715 5.9 BRCA1 SP1 HNRNPL CREB1 GATAD2A PRDM10 ZNF629 TFE3 RFX1 LEF1 KRI1 CDKN2D ILF3 PPAN DNMT1 ZNF627 FBXL12 LOC100419831 TIMM29 ZNF561
GH19J010601 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 33.8 -35.0 -34998 4.5 ZNF629 IKZF1 KDM1A ZNF692 BACH1 LARP7 MTA2 ZNF143 ZIC2 POLR2A SLC44A2 CDKN2D KRI1 ICAM3 ILF3 ZNF627 PRKCSH TYK2 DNM2 S1PR5
GH19J010345 Promoter/Enhancer 1.4 FANTOM5 Ensembl ENCODE 32.8 +222.3 222326 0.3 GATAD2A REST RFX1 JUND PHF21A PKNOX1 SP1 DPF2 HDAC1 FOXJ2 piR-61101-324 CDKN2D ICAM3 SLC44A2 TYK2 RAVER1 DNM2 ICAM1 ATG4D
GH19J010595 Promoter/Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 28.1 -27.2 -27184 1.9 ZBTB33 ZSCAN4 IKZF2 TRIM22 KLF9 DPF2 RELB RUNX3 TCF12 ARNT KRI1 CDKN2D SLC44A2 ICAM3 ATG4D ILF3 TYK2 DNM2 C19orf38 S1PR5
GH19J010580 Promoter/Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas 23.6 -12.1 -12104 0.5 HNRNPL GATAD2A CTCF PRDM10 TFE3 NFKBIZ ZNF692 JUND LARP7 ZNF143 MF281430-039 CDKN2D AP1M2 lnc-TIMM29-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDKN2D on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CDKN2D

Top Transcription factor binding sites by QIAGEN in the CDKN2D gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • NF-Y
  • p53

Genomic Locations for CDKN2D Gene

Genomic Locations for CDKN2D Gene
chr19:10,566,460-10,569,059
(GRCh38/hg38)
Size:
2,600 bases
Orientation:
Minus strand
chr19:10,677,138-10,679,735
(GRCh37/hg19)
Size:
2,598 bases
Orientation:
Minus strand

Genomic View for CDKN2D Gene

Genes around CDKN2D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDKN2D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDKN2D Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CDKN2D Gene

Proteins for CDKN2D Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for CDKN2D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P55273-CDN2D_HUMAN
    Recommended name:
    Cyclin-dependent kinase 4 inhibitor D
    Protein Accession:
    P55273
    Secondary Accessions:
    • Q13102
    • Q6FGE9

    Protein attributes for CDKN2D Gene

    Size:
    166 amino acids
    Molecular mass:
    17700 Da
    Quaternary structure:
    • Interacts with CDK6.

    Three dimensional structures from OCA and Proteopedia for CDKN2D Gene

neXtProt entry for CDKN2D Gene

Protein Expression for CDKN2D Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CDKN2D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CDKN2D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CDKN2D Gene

Domains & Families for CDKN2D Gene

Gene Families for CDKN2D Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for CDKN2D Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CDKN2D Gene

GenScript: Design optimal peptide antigens:
  • p19-INK4d (CDN2D_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P55273

UniProtKB/Swiss-Prot:

CDN2D_HUMAN :
  • Belongs to the CDKN2 cyclin-dependent kinase inhibitor family.
Family:
  • Belongs to the CDKN2 cyclin-dependent kinase inhibitor family.
genes like me logo Genes that share domains with CDKN2D: view

Function for CDKN2D Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for CDKN2D Gene

UniProtKB/Swiss-Prot Function:
Interacts strongly with CDK4 and CDK6 and inhibits them.
GENATLAS Biochemistry:
cyclin dependent kinase 4 and 6 (CDK4/CDK6) inhibitor,p19,regulator of the cell cycle,passage through the G1 checkpoint,expressed primarily in hematopoietic tissues

Phenotypes From GWAS Catalog for CDKN2D Gene

Gene Ontology (GO) - Molecular Function for CDKN2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004861 cyclin-dependent protein serine/threonine kinase inhibitor activity IDA 8741839
GO:0005515 protein binding IPI 9751050
GO:0016301 kinase activity IEA --
GO:0019901 protein kinase binding IPI 8741839
genes like me logo Genes that share ontologies with CDKN2D: view
genes like me logo Genes that share phenotypes with CDKN2D: view

Animal Models for CDKN2D Gene

MGI Knock Outs for CDKN2D:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDKN2D

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CDKN2D Gene

Localization for CDKN2D Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDKN2D Gene

Nucleus. Cytoplasm.

Subcellular locations from

COMPARTMENTS
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 CDKN2D gene
Compartment Confidence
nucleus 5
cytosol 4
extracellular 3
cytoskeleton 2
plasma membrane 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CDKN2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 8741839
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA,IDA 15750620
GO:0005829 cytosol TAS --
GO:0097129 cyclin D2-CDK4 complex IEA --
genes like me logo Genes that share ontologies with CDKN2D: view

Pathways & Interactions for CDKN2D Gene

genes like me logo Genes that share pathways with CDKN2D: view

Pathways by source for CDKN2D Gene

1 BioSystems pathway for CDKN2D Gene
2 KEGG pathways for CDKN2D Gene
1 GeneGo (Thomson Reuters) pathway for CDKN2D Gene
  • Immune response IL-10 signaling pathway
5 Qiagen pathways for CDKN2D Gene
  • Cyclins and Cell Cycle Regulation
  • G1-S Phase Transition
  • IL-10 Pathway
  • Molecular Mechanisms of Cancer
  • Pancreatic Adenocarcinoma
1 GeneTex pathway for CDKN2D Gene

SIGNOR curated interactions for CDKN2D Gene

Is activated by:

Gene Ontology (GO) - Biological Process for CDKN2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity IDA 8741839
GO:0000082 G1/S transition of mitotic cell cycle IDA 10208428
GO:0000731 DNA synthesis involved in DNA repair IMP 15750620
GO:0007049 cell cycle IEA --
GO:0007050 cell cycle arrest IDA 10208428
genes like me logo Genes that share ontologies with CDKN2D: view

Drugs & Compounds for CDKN2D Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for CDKN2D Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for CDKN2D Gene

2 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDKN2D

Alternative Splicing Database (ASD) splice patterns (SP) for CDKN2D Gene

No ASD Table

Relevant External Links for CDKN2D Gene

GeneLoc Exon Structure for
CDKN2D

Expression for CDKN2D Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CDKN2D Gene

mRNA expression in normal human tissues for CDKN2D Gene
mRNA expression by BioGPS for CDKN2D GenemRNA expression by GTEx for CDKN2D Gene

mRNA differential expression in normal tissues according to GTEx for CDKN2D Gene

This gene is overexpressed in Whole Blood (x13.3).

Protein differential expression in normal tissues from HIPED for CDKN2D Gene

This gene is overexpressed in Peripheral blood mononuclear cells (58.8) and Platelet (10.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CDKN2D Gene



Protein tissue co-expression partners for CDKN2D Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CDKN2D

SOURCE GeneReport for Unigene cluster for CDKN2D Gene:

Hs.435051

Evidence on tissue expression from TISSUES for CDKN2D Gene

  • Blood(4.6)
  • Bone marrow(4.6)
  • Muscle(4.4)
  • Nervous system(3.3)
  • Skin(2.4)
  • Intestine(2.3)
  • Kidney(2.2)
  • Lung(2.1)
  • Lymph node(2.1)
  • Pancreas(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CDKN2D Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • lymphatic
  • nervous
Regions:
Head and neck:
  • brain
  • eye
  • head
General:
  • skin
genes like me logo Genes that share expression patterns with CDKN2D: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for CDKN2D Gene

Orthologs for CDKN2D Gene

This gene was present in the common ancestor of chordates.

Orthologs for CDKN2D Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia CDKN2D 30 31
  • 99.6 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CDKN2D 30
  • 87.93 (n)
Cow
(Bos Taurus)
 Mammalia CDKN2D 30 31
  • 85.34 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Cdkn2d 30 17 31
  • 81.73 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia CDKN2D 31
  • 81 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia CDKN2D 31
  • 59 (a)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia CDKN2D 31
  • 67 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia cdkn2d 30
  • 65.07 (n)
Zebrafish
(Danio rerio)
 Actinopterygii LOC100333252 30
  • 64.01 (n)
cdkn2d 31
  • 56 (a)
 OneToOne
Species where no ortholog for CDKN2D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Chicken (Gallus gallus)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CDKN2D Gene

ENSEMBL:
Gene Tree for CDKN2D (if available)
TreeFam:
Gene Tree for CDKN2D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CDKN2D: view image

Paralogs for CDKN2D Gene

Paralogs for CDKN2D Gene

(24) SIMAP similar genes for CDKN2D Gene using alignment to 1 proteins:

  • CDN2D_HUMAN
genes like me logo Genes that share paralogs with CDKN2D: view

Variants for CDKN2D Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Additional dbSNP identifiers (rs#s) for CDKN2D Gene

Structural Variations from Database of Genomic Variants (DGV) for CDKN2D Gene

Variant ID Type Subtype PubMed ID
nsv833744 CNV loss 17160897
nsv833745 CNV loss 17160897

Variation tolerance for CDKN2D Gene

Residual Variation Intolerance Score: 54.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.22; 4.96% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDKN2D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CDKN2D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CDKN2D Gene

Disorders for CDKN2D Gene

MalaCards: The human disease database

(7) MalaCards diseases for CDKN2D Gene - From: DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CDKN2D

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Tumor Gene Database
(TGDB)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with CDKN2D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CDKN2D Gene

Publications for CDKN2D Gene

  1. Molecular cloning, expression pattern, and chromosomal localization of human CDKN2D/INK4d, an inhibitor of cyclin D-dependent kinases. (PMID: 8575754) Okuda T … Downing JR (Genomics 1995) 2 3 4 23
  2. Effects of common germline genetic variation in cell cycle control genes on breast cancer survival: results from a population-based cohort. (PMID: 18507837) Azzato EM … Pharoah PD (Breast cancer research : BCR 2008) 3 23 41
  3. Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population. (PMID: 18174243) Driver KE … Studies in Epidemiology and Risks of Cancer Heredity (SEARCH) Team (Carcinogenesis 2008) 3 23 41
  4. Mutation testing in melanoma families: INK4A, CDK4 and INK4D. (PMID: 10390011) Newton Bishop JA … Bishop DT (British journal of cancer 1999) 3 4 23
  5. Structure of human cyclin-dependent kinase inhibitor p19INK4d: comparison to known ankyrin-repeat-containing structures and implications for the dysfunction of tumor suppressor p16INK4a. (PMID: 9782052) Baumgartner R … Holak TA (Structure (London, England : 1993) 1998) 3 4 23

ExternalLinks

View latest publications for CDKN2D gene in Mastermind

Products for CDKN2D Gene

  • Signalway Proteins for CDKN2D

Sources for CDKN2D Gene