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    CDKN2D cyclin dependent kinase inhibitor 2D [ Homo sapiens (human) ]

    Gene ID: 1032, updated on 28-Oct-2024

    Summary

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    Official Symbol
    CDKN2Dprovided by HGNC
    Official Full Name
    cyclin dependent kinase inhibitor 2Dprovided by HGNC
    Primary source
    HGNC:HGNC:1790
    See related
    Ensembl:ENSG00000129355 MIM:600927; AllianceGenome:HGNC:1790
    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
    p19; INK4D; p19-INK4D
    Summary
    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]
    Expression
    Biased expression in bone marrow (RPKM 80.4), brain (RPKM 18.7) and 5 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CDKN2D in Genome Data Viewer
    Location:
    19p13.2
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (10566460..10568979, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (10692920..10695436, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10677136..10679655, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene autophagy related 4D cysteine peptidase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13975 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13976 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13977 Neighboring gene microRNA 1238 Neighboring gene KRI1 homolog Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10675791-10676358 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10676359-10676926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10677875-10678382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13979 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10083 Neighboring gene adaptor related protein complex 1 subunit mu 2 Neighboring gene MPRA-validated peak3354 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10703269-10703793 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10704320-10704844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13980 Neighboring gene LSM2 pseudogene 1

    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 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. p19(INK4d) mRNA and protein expression as new prognostic factors in ovarian cancer patients. Felisiak-Golabek A, et al. Cancer Biol Ther, 2013 Oct 1. PMID 24022213, Free PMC Article
    2. Induction of p19INK4d in response to ultraviolet light improves DNA repair and confers resistance to apoptosis in neuroblastoma cells. Ceruti JM, et al. Oncogene, 2005 Jun 9. PMID 15750620
    3. Convergence of vitamin D and retinoic acid signalling at a common hormone response element. Tavera-Mendoza L, et al. EMBO Rep, 2006 Feb. PMID 16322758, Free PMC Article
    4. Folding mechanism of an ankyrin repeat protein: scaffold and active site formation of human CDK inhibitor p19(INK4d). Löw C, et al. J Mol Biol, 2007 Oct 12. PMID 17804013
    5. Conformational switch upon phosphorylation: human CDK inhibitor p19INK4d between the native and partially folded state. Löw C, et al. ACS Chem Biol, 2009 Jan 16. PMID 19063602

    See all (79) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Deregulation of the p19/CDK4/CDK6 axis in Jak2[V617F] megakaryocytes accelerates the development of myelofibrosis.
      Title: Deregulation of the p19/CDK4/CDK6 axis in Jak2(V617F) megakaryocytes accelerates the development of myelofibrosis.
    2. Identification of <i>Cdk8</i> and <i>Cdkn2d</i> as New Prame-Target Genes in 2C-like Embryonic Stem Cells.
      Title: Identification of Cdk8 and Cdkn2d as New Prame-Target Genes in 2C-like Embryonic Stem Cells.
    3. p19(INK4d) inhibits proliferation and enhances imatinib efficacy through BCR-ABL signaling pathway in chronic myeloid leukemia.
      Title: p19(INK4d) inhibits proliferation and enhances imatinib efficacy through BCR-ABL signaling pathway in chronic myeloid leukemia.
    4. p19INK4d: More than Just a Cyclin-Dependent Kinase Inhibitor.
      Title: p19INK4d: More than Just a Cyclin-Dependent Kinase Inhibitor.
    5. he results support the concept that P19ink4d may play an important role in the pathogenesis and development of noise induced hearing loss.
      Title: [The expression of P19ink4d in the pathogenesis and development of hearing loss].
    6. p19(INK4d) plays an active role during human tooth development along with MSX1 and MSX2
      Title: Regulation of proliferation in developing human tooth germs by MSX homeodomain proteins and cyclin-dependent kinase inhibitor p19(INK4d).
    7. We unexpectedly found that p19INK4d plays an important role in human terminal erythropoiesis
      Title: Unexpected role for p19INK4d in posttranscriptional regulation of GATA1 and modulation of human terminal erythropoiesis.
    8. p19(INK4D) is one of the key mediators of miR-125b activity during the onset of megakaryocyte polyploidization.
      Title: miR-125b modulates megakaryocyte maturation by targeting the cell-cycle inhibitor p19(INK4D).
    9. p19 may play an important role in the ototoxic effects of cisplatin and is probably involved in the pathogenesis of hearing loss.
      Title: Role of p19ink4d in the pathogenesis of hearing loss.
    10. MiR-451 inhibited the proliferation of esophageal squamous cell carcinoma cells by targeting CDKN2D and MAP3K1 expression.
      Title: MiR-451 inhibits proliferation of esophageal carcinoma cell line EC9706 by targeting CDKN2D and MAP3K1.
    Submit: New GeneRIF Correction See all GeneRIFs (33)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cyclin-dependent protein serine/threonine kinase inhibitor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cyclin-dependent protein serine/threonine kinase inhibitor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA synthesis involved in DNA repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in autophagic cell death IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of cell cycle G1/S phase transition IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cell growth IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of cell population proliferation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of cysteine-type endopeptidase activity involved in apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of phosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of G1/S transition of mitotic cell cycle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of G1/S transition of mitotic cell cycle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of cyclin-dependent protein serine/threonine kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to UV IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to retinoic acid IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to vitamin D IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of cyclin D2-CDK4 complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    cyclin-dependent kinase 4 inhibitor D
    Names
    CDK inhibitor p19INK4d
    cell cycle inhibitor, Nur77 associating protein
    cyclin-dependent kinase 4 inhibitor D p19
    cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)
    inhibitor of cyclin-dependent kinase 4d

    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.

    mRNA and Protein(s)

    1. NM_001800.4 → NP_001791.1  cyclin-dependent kinase 4 inhibitor D

      See identical proteins and their annotated locations for NP_001791.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) contains a different 5' UTR region, and encodes an identical protein, as compared to variant 2.
      Source sequence(s)
      AC011475
      Consensus CDS
      CCDS12244.1
      UniProtKB/Swiss-Prot
      P55273, Q13102, Q6FGE9
      Related
      ENSP00000377224.1, ENST00000393599.3
      Conserved Domains (3) summary
      COG0666
      Location:16 → 131
      ANKYR; Ankyrin repeat [Signal transduction mechanisms]
      sd00045
      Location:41 → 71
      ANK; ANK repeat [structural motif]
      pfam12796
      Location:79 → 158
      Ank_2; Ankyrin repeats (3 copies)

    2. NM_079421.3 → NP_524145.1  cyclin-dependent kinase 4 inhibitor D

      See identical proteins and their annotated locations for NP_524145.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains a different 5' UTR region, and encodes an identical protein, as compared to variant 1.
      Source sequence(s)
      AC011475
      Consensus CDS
      CCDS12244.1
      UniProtKB/Swiss-Prot
      P55273, Q13102, Q6FGE9
      Related
      ENSP00000337056.1, ENST00000335766.2
      Conserved Domains (3) summary
      COG0666
      Location:16 → 131
      ANKYR; Ankyrin repeat [Signal transduction mechanisms]
      sd00045
      Location:41 → 71
      ANK; ANK repeat [structural motif]
      pfam12796
      Location:79 → 158
      Ank_2; Ankyrin repeats (3 copies)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      10566460..10568979 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      10692920..10695436 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P55273.1 GenPept UniProtKB/Swiss-Prot:P55273

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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