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CDKN2A cyclin-dependent kinase inhibitor 2A [ Homo sapiens (human) ]

Gene ID: 1029, updated on 23-Nov-2014
Official Symbol
CDKN2Aprovided by HGNC
Official Full Name
cyclin-dependent kinase inhibitor 2Aprovided by HGNC
Primary source
HGNC:HGNC:1787
See related
Ensembl:ENSG00000147889; HPRD:02542; MIM:600160; Vega:OTTHUMG00000019686
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
ARF; MLM; P14; P16; P19; CMM2; INK4; MTS1; TP16; CDK4I; CDKN2; INK4A; MTS-1; P14ARF; P19ARF; P16INK4; P16INK4A; P16-INK4A
Summary
This gene generates several transcript variants which differ in their first exons. At least three alternatively spliced variants encoding distinct proteins have been reported, two of which encode structurally related isoforms known to function as inhibitors of CDK4 kinase. The remaining transcript includes an alternate first exon located 20 Kb upstream of the remainder of the gene; this transcript contains an alternate open reading frame (ARF) that specifies a protein which is structurally unrelated to the products of the other variants. This ARF product functions as a stabilizer of the tumor suppressor protein p53 as it can interact with, and sequester, the E3 ubiquitin-protein ligase MDM2, a protein responsible for the degradation of p53. In spite of the structural and functional differences, the CDK inhibitor isoforms and the ARF product encoded by this gene, through the regulatory roles of CDK4 and p53 in cell cycle G1 progression, share a common functionality in cell cycle G1 control. This gene is frequently mutated or deleted in a wide variety of tumors, and is known to be an important tumor suppressor gene. [provided by RefSeq, Sep 2012]
See CDKN2A in Epigenomics, MapViewer
Location:
9p21
Exon count:
6
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 9 NC_000009.12 (21967752..21994491, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (21967751..21994490, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene tubulin beta 8 class VIII pseudogene 1 Neighboring gene methylthioadenosine phosphorylase Neighboring gene endogenous retrovirus group FRD, member 3 Neighboring gene CDKN2A antisense RNA 1 (head to head) Neighboring gene CDKN2B antisense RNA 1 Neighboring gene cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4) Neighboring gene ubiquitin A-52 residue ribosomal protein fusion product 1 pseudogene 6

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Cutaneous malignant melanoma 2
MedGen: C1835044 OMIM: 155601 GeneReviews: Not available
Compare labs
Melanoma astrocytoma syndrome
MedGen: C1835042 OMIM: 155755 GeneReviews: Not available
Compare labs
Melanoma-pancreatic cancer syndrome
MedGen: C1838547 OMIM: 606719 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A common variant on chromosome 9p21 affects the risk of myocardial infarction.
NHGRI GWA Catalog
A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.
NHGRI GWA Catalog
Chromosome 7p11.2 (EGFR) variation influences glioma risk.
NHGRI GWA Catalog
Confirmation of multiple risk Loci and genetic impacts by a genome-wide association study of type 2 diabetes in the Japanese population.
NHGRI GWA Catalog
Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels.
NHGRI GWA Catalog
Genome-wide association meta-analysis identifies new endometriosis risk loci.
NHGRI GWA Catalog
Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants.
NHGRI GWA Catalog
Genome-wide association study for type 2 diabetes in Indians identifies a new susceptibility locus at 2q21.
NHGRI GWA Catalog
Genome-wide association study identifies a sequence variant within the DAB2IP gene conferring susceptibility to abdominal aortic aneurysm.
NHGRI GWA Catalog
Genome-wide association study identifies five new breast cancer susceptibility loci.
NHGRI GWA Catalog
Genome-wide association study identifies five susceptibility loci for glioma.
NHGRI GWA Catalog
Genome-wide association study identifies three loci associated with melanoma risk.
NHGRI GWA Catalog
Genome-wide association study identifies three new melanoma susceptibility loci.
NHGRI GWA Catalog
Genome-wide association study identifies three novel loci for type 2 diabetes.
NHGRI GWA Catalog
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
NHGRI GWA Catalog
Genome-wide association study of coronary and aortic calcification implicates risk loci for coronary artery disease and myocardial infarction.
NHGRI GWA Catalog
Genome-wide association study of coronary artery disease in the Japanese.
NHGRI GWA Catalog
Genome-wide association study of intracranial aneurysm identifies three new risk loci.
NHGRI GWA Catalog
Genome-wide association study of type 2 diabetes in a sample from Mexico City and a meta-analysis of a Mexican-American sample from Starr County, Texas.
NHGRI GWA Catalog
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
NHGRI GWA Catalog
Germline sequence variants in TGM3 and RGS22 confer risk of basal cell carcinoma.
NHGRI GWA Catalog
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
NHGRI GWA Catalog
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
NHGRI GWA Catalog
Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
NHGRI GWA Catalog
New gene functions in megakaryopoiesis and platelet formation.
NHGRI GWA Catalog
Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes.
NHGRI GWA Catalog
Susceptibility loci for intracranial aneurysm in European and Japanese populations.
NHGRI GWA Catalog
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
NHGRI GWA Catalog
Variation at 10p12.2 and 10p14 influences risk of childhood B-cell acute lymphoblastic leukemia and phenotype.
NHGRI GWA Catalog

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 upregulates the expression of cyclin-dependent kinase inhibitor 2A (CDKN2A) in human B cells PubMed
Nef nef HIV-1 Nef is identified to have a physical interaction with cyclin-dependent kinase inhibitor 2A (CDKN2A) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
Tat tat p14(ARF) inhibits transcription activation of the HIV-1 LTR by Tat protein; the ARF-mediated inhibition of the HIV-1 LTR occurs by promoting Tat degradation via an ubiquitin-independent pathway PubMed
reverse transcriptase gag-pol RT activity of latently HIV-1-infected cells decreases in the presence of exogenous p16INK4A PubMed

Go to the HIV-1, Human Interaction Database

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Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
MDM2/MDM4 family protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
NF-kappaB binding IDA
Inferred from Direct Assay
more info
PubMed 
cyclin-dependent protein serine/threonine kinase inhibitor activity IDA
Inferred from Direct Assay
more info
PubMed 
p53 binding IPI
Inferred from Physical Interaction
more info
PubMed 
poly(A) RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin-protein transferase inhibitor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
G1/S transition of mitotic cell cycle IDA
Inferred from Direct Assay
more info
PubMed 
Ras protein signal transduction IEP
Inferred from Expression Pattern
more info
PubMed 
activation of cysteine-type endopeptidase activity involved in apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
apoptotic mitochondrial changes IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell cycle arrest IDA
Inferred from Direct Assay
more info
PubMed 
cell cycle arrest IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular senescence IMP
Inferred from Mutant Phenotype
more info
PubMed 
mitotic cell cycle TAS
Traceable Author Statement
more info
 
negative regulation of B cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of NF-kappaB transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell growth IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell-matrix adhesion IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cyclin-dependent protein serine/threonine kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of immature T cell proliferation in thymus ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of protein kinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of ubiquitin-protein transferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of DNA damage response, signal transduction by p53 class mediator IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell cycle arrest IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cellular senescence IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of macrophage apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of protein sumoylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of smooth muscle cell apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
protein K63-linked ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein destabilization IDA
Inferred from Direct Assay
more info
PubMed 
protein polyubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein stabilization IDA
Inferred from Direct Assay
more info
PubMed 
rRNA processing IEA
Inferred from Electronic Annotation
more info
 
regulation of G2/M transition of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of apoptotic DNA fragmentation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein export from nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein stability ISS
Inferred from Sequence or Structural Similarity
more info
 
replicative senescence IMP
Inferred from Mutant Phenotype
more info
PubMed 
senescence-associated heterochromatin focus assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
somatic stem cell division ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with nuclear body IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein complex IDA
Inferred from Direct Assay
more info
PubMed 
senescence-associated heterochromatin focus IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
cyclin-dependent kinase inhibitor 2A
Names
cyclin-dependent kinase inhibitor 2A
CDKN2A
CDK4 inhibitor p16-INK4
multiple tumor suppressor 1
cell cycle negative regulator beta
cyclin-dependent kinase 4 inhibitor A
cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)

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_007485.1 

    Range
    5001..31740
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_11

mRNA and Protein(s)

  1. NM_000077.4NP_000068.1  cyclin-dependent kinase inhibitor 2A isoform p16INK4a

    See proteins identical to NP_000068.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is also known as alpha. Transcripts 1 and 4, encoding p16INK4a and p14ARF, have distinct first exons which contain the translation start codon, and share a common second exon, which is translated in different reading frames. Thus, the p16INK4a protein encoded by this variant (1) lacks sequence similarity to the protein product of variant 4 (p14ARF).
    Source sequence(s)
    AL449423, BI258230, BQ012762, BX099567, L27211
    Consensus CDS
    CCDS6510.1
    UniProtKB/TrEMBL
    K7PML8
    UniProtKB/Swiss-Prot
    P42771
    Related
    ENSP00000307101, OTTHUMP00000021147, ENST00000304494, OTTHUMT00000051915
    Conserved Domains (2) summary
    cd00204
    Location:19130
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    pfam12796
    Location:16108
    Ank_2; Ankyrin repeats (3 copies)
  2. NM_001195132.1NP_001182061.1  cyclin-dependent kinase inhibitor 2A isoform p16gamma

    See proteins identical to NP_001182061.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) includes an additional exon that causes a frameshift in the 3' coding region, compared to variant 1 (encoding p16INK4a). The resulting isoform (p16gamma) has a distinct C-terminus and is longer than p16INK4a. This variant has been described in PMID:17486064. It is a candidate for nonsense-mediated mRNA decay (NMD), but it is not known if the endogenous protein is expressed in vivo.
    Source sequence(s)
    AL449423, BX099567, DQ318021
    Consensus CDS
    CCDS56565.1
    UniProtKB/Swiss-Prot
    P42771
    Conserved Domains (2) summary
    cd00204
    Location:19130
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    pfam12796
    Location:16108
    Ank_2; Ankyrin repeats (3 copies)
  3. NM_058195.3NP_478102.2  cyclin-dependent kinase inhibitor 2A isoform p14ARF

    See proteins identical to NP_478102.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), also known as beta, encodes isoform p14ARF. Transcripts 1 and 4, encoding p16INK4a and p14ARF have distinct first exons which contain the translation start codon, and share a common second exon, which is translated in different reading frames. Thus, the p16INK4a protein encoded by this variant (1) lacks sequence similarity to the protein product of variant 4 (p14ARF). Note that this variant may use an alternative upstream start codon, which would produce an isoform that is 41 aa longer at the N-terminus, or an alternative downstream start codon, which would produce an isoform (smARF, described in PMID:16713577) that is 47 aa shorter at the N-terminus; it is unclear if the isoforms derived from the alternative start codons are present in vivo. The p14ARF isoform is known to be nucleoplasmic but may also be recruited to mitochondria, as described in PMID:20107316.
    Source sequence(s)
    BQ012762, BX099567, S78535, U38945
    Consensus CDS
    CCDS6511.2
    UniProtKB/Swiss-Prot
    Q8N726
    Related
    ENSP00000462950, OTTHUMP00000215053, ENST00000579755, OTTHUMT00000051918
    Conserved Domains (1) summary
    pfam07392
    Location:454
    P19Arf_N; Cyclin-dependent kinase inhibitor 2a p19Arf N-terminus
  4. NM_058197.4NP_478104.2  cyclin-dependent kinase inhibitor 2A isoform p12

    See proteins identical to NP_478104.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate open reading frame (ARF), when compared to variants 1 or 4. The ARF results from an alternative splicing between a distinct first exon, which contains the translation start codon, and the common second exon. Thus, the protein encoded by this variant (p12) lacks sequence similarity to the protein product of variant 4. This variant is specifically expressed in pancreas, and has been described in PMID:10445844. It is a candidate for nonsense-mediated mRNA decay (NMD), but it is not known if the endogenous protein is expressed in vivo.
    Source sequence(s)
    AF115544, AL449423, BQ012762, BX099567
    UniProtKB/TrEMBL
    G3XAG3
    UniProtKB/Swiss-Prot
    P42771
    Conserved Domains (2) summary
    pfam13637
    Location:1650
    Ank_4; Ankyrin repeats (many copies)
    pfam13857
    Location:1650
    Ank_5; Ankyrin repeats (many copies)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Alternate HuRef

Genomic

  1. AC_000141.1 

    Range
    21930969..21957759
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000009.12 

    Range
    21967752..21994491
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005251343.1XP_005251400.1  

    See proteins identical to XP_005251400.1

    UniProtKB/Swiss-Prot
    P42771
    Conserved Domains (2) summary
    cd00204
    Location:279
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    pfam13637
    Location:2879
    Ank_4; Ankyrin repeats (many copies)

Alternate CHM1_1.1

Genomic

  1. NC_018920.2 

    Range
    21967646..21994319
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_058196.1: Suppressed sequence

    Description
    NM_058196.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.