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

Summary

Official Symbol: CDKN2Aprovided by HGNC
Official Full Name: cyclin dependent kinase inhibitor 2Aprovided by HGNC
Primary source: HGNC:HGNC:1787
See related: Ensembl:ENSG00000147889 MIM:600160; AllianceGenome:HGNC:1787
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; CAI2; 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]
Expression: Low expression observed in reference dataset See more
Orthologs: all
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Genomic context

Location:: 9p21.3

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (21967752..21995324, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (21982052..22009697, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (21967751..21995323, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Impact of CDKN2A gene expression on colon adenocarcinoma via biosignature analysis.
Title: Impact of CDKN2A gene expression on colon adenocarcinoma via biosignature analysis.
Relationship between p16/ki67 immunoscores and PAX1/ZNF582 methylation status in precancerous and cancerous cervical lesions in high-risk HPV-positive women.
Title: Relationship between p16/ki67 immunoscores and PAX1/ZNF582 methylation status in precancerous and cancerous cervical lesions in high-risk HPV-positive women.
T2-FLAIR mismatch sign, an imaging biomarker for CDKN2A-intact in non-enhancing astrocytoma, IDH-mutant.
Title: T2-FLAIR mismatch sign, an imaging biomarker for CDKN2A-intact in non-enhancing astrocytoma, IDH-mutant.
Prognostic Impact of CDKN2A Mutations Associated With Smoking and Drinking History in Japanese Digestive Cancers.
Title: Prognostic Impact of CDKN2A Mutations Associated With Smoking and Drinking History in Japanese Digestive Cancers.
Cathepsin L induces cellular senescence by upregulating CUX1 and p16[INK4a].
Title: Cathepsin L induces cellular senescence by upregulating CUX1 and p16(INK4a).
A novel EZH2/NXPH4/CDKN2A axis is involved in regulating the proliferation and migration of non-small cell lung cancer cells.
Title: A novel EZH2/NXPH4/CDKN2A axis is involved in regulating the proliferation and migration of non-small cell lung cancer cells.
SATB1 and p16 Expression and Prognostic Value in Croatian Hodgkin Lymphoma Patients: A Unicentric Study.
Title: SATB1 and p16 Expression and Prognostic Value in Croatian Hodgkin Lymphoma Patients: A Unicentric Study.
The crosstalk role of CDKN2A between tumor progression and cuproptosis resistance in colorectal cancer.
Title: The crosstalk role of CDKN2A between tumor progression and cuproptosis resistance in colorectal cancer.
Expression of p16 protein in breast cancer.
Title: Expression of p16 protein in breast cancer.
Uterine Inflammatory Myofibroblastic Tumors: p16 as a Surrogate for CDKN2A Deletion and Predictor of Aggressive Behavior.
Title: Uterine Inflammatory Myofibroblastic Tumors: p16 as a Surrogate for CDKN2A Deletion and Predictor of Aggressive Behavior.

Submit: New GeneRIF Correction See all GeneRIFs (2267)

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

Associated conditions

Description	Tests
Melanoma and neural system tumor syndrome MedGen: C1835042 OMIM: 155755 GeneReviews: Not available	Compare labs
Melanoma, cutaneous malignant, susceptibility to, 2 MedGen: C1835044 OMIM: 155601 GeneReviews: Not available	Compare labs
Melanoma-pancreatic cancer syndrome MedGen: C1838547 OMIM: 606719 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2022-03-18) ClinGen Genome Curation PagePubMed Triplosensitivity No evidence available (Last evaluated 2022-03-18) ClinGen Genome Curation Page

EBI GWAS Catalog

Description
A common variant on chromosome 9p21 affects the risk of myocardial infarction. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. EBI GWAS Catalog EBI GWAS CatalogPubMed
Chromosome 7p11.2 (EGFR) variation influences glioma risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Confirmation of multiple risk Loci and genetic impacts by a genome-wide association study of type 2 diabetes in the Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association meta-analysis identifies new endometriosis risk loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study for type 2 diabetes in Indians identifies a new susceptibility locus at 2q21. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies a sequence variant within the DAB2IP gene conferring susceptibility to abdominal aortic aneurysm. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies five new breast cancer susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies five susceptibility loci for glioma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies three loci associated with melanoma risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies three new melanoma susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies three novel loci for type 2 diabetes. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of coronary and aortic calcification implicates risk loci for coronary artery disease and myocardial infarction. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of coronary artery disease in the Japanese. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of intracranial aneurysm identifies three new risk loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
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. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. EBI GWAS Catalog EBI GWAS CatalogPubMed
Germline sequence variants in TGM3 and RGS22 confer risk of basal cell carcinoma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of ADAMTS7 as a novel locus for coronary atherosclerosis and association of ABO with myocardial infarction in the presence of coronary atherosclerosis: two genome-wide association studies. EBI GWAS Catalog EBI GWAS CatalogPubMed
Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale genotyping identifies 41 new loci associated with breast cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. EBI GWAS Catalog EBI GWAS CatalogPubMed
New gene functions in megakaryopoiesis and platelet formation. EBI GWAS Catalog EBI GWAS CatalogPubMed
Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. EBI GWAS Catalog EBI GWAS CatalogPubMed
Susceptibility loci for intracranial aneurysm in European and Japanese populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Two-marker association tests yield new disease associations for coronary artery disease and hypertension. EBI GWAS Catalog EBI GWAS CatalogPubMed
Variation at 10p12.2 and 10p14 influences risk of childhood B-cell acute lymphoblastic leukemia and phenotype. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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	HIV-1 Tat downregulates the expression of INK4/p16 in Tat-positive cells	PubMed
	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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC33151P2 (e-PCR)
- UniSTS:273152

RH67869 (e-PCR)
- UniSTS:58120

GDB:434761 (e-PCR)
- UniSTS:157208

PMC99853P1 (e-PCR)
- UniSTS:273689

GDB:437702 (e-PCR)
- UniSTS:157253

GDB:437709 (e-PCR)
- UniSTS:157254

GDB:437717 (e-PCR)
- UniSTS:157255

GDB:572854 (e-PCR)
- UniSTS:157772

RH103023 (e-PCR)
- UniSTS:97357

GDB:572861 (e-PCR)
- UniSTS:157774

D9S2060 (e-PCR)
- UniSTS:27737

D9S974 (e-PCR)
- UniSTS:150377

PMC140684P1 (e-PCR)
- UniSTS:270960

PMC140684P2 (e-PCR)
- UniSTS:270961

GDB:679537 (e-PCR)
- UniSTS:158612

GDB:679538 (e-PCR)
- UniSTS:158613

PMC25103P3 (e-PCR)
- UniSTS:272283

D9S1748 (e-PCR)
- UniSTS:154017

GDB:626084 (e-PCR)
- UniSTS:158388

GDB:626104 (e-PCR)
- UniSTS:158391

GDB:626109 (e-PCR)
- UniSTS:158392

GDB:626123 (e-PCR)
- UniSTS:158393

GDB:626126 (e-PCR)
- UniSTS:158394

STS-S69824 (e-PCR)
- UniSTS:27844

PMC92514P2 (e-PCR)
- UniSTS:273616

PMC92514P3 (e-PCR)
- UniSTS:273617

PMC92514P4 (e-PCR)
- UniSTS:273618

D9S942 (e-PCR)
- UniSTS:149983

PMC33151P1 (e-PCR)
- UniSTS:273151

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables MDM2/MDM4 family protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables NF-kappaB binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA binding	HDA more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables SUMO transferase activity	EXP Inferred from Experiment more info	PubMed
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 cyclin-dependent protein serine/threonine kinase inhibitor activity	IEA Inferred from Electronic Annotation more info
enables cyclin-dependent protein serine/threonine kinase inhibitor activity	TAS Traceable Author Statement more info	PubMed
enables disordered domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables p53 binding	IPI Inferred from Physical Interaction 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
enables ubiquitin ligase inhibitor activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase inhibitor activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in Ras protein signal transduction	IEP Inferred from Expression Pattern more info	PubMed
involved_in amyloid fibril formation	IDA Inferred from Direct Assay more info	PubMed
involved_in amyloid fibril formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of apoptotic process involved in mammary gland involution	IEA Inferred from Electronic Annotation more info
involved_in apoptotic signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in autophagy of mitochondrion	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cellular response to hydrogen peroxide	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular senescence	IEA Inferred from Electronic Annotation more info
involved_in cellular senescence	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epidermis development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within glucose homeostasis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within keratinocyte differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within keratinocyte proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of mammary gland epithelial cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in mitochondrial depolarization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of B cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of cell cycle	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 cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell-matrix adhesion	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of cyclin-dependent protein serine/threonine kinase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of immature T cell proliferation in thymus	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within negative regulation of mammary gland epithelial cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein neddylation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of proteolysis involved in protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of proteolysis involved in protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of ubiquitin-dependent protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of ubiquitin-protein transferase activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in nuclear body organization	EXP Inferred from Experiment more info	PubMed
acts_upstream_of_or_within oncogene-induced cell senescence	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA damage response, signal transduction by p53 class mediator	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of apoptotic process involved in mammary gland involution	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of macrophage apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of macrophage apoptotic process	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of protein localization to nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein sumoylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of signal transduction by p53 class mediator	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of smooth muscle cell apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of smooth muscle cell apoptotic process	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in protein K63-linked ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein destabilization	IDA Inferred from Direct Assay more info	PubMed
involved_in protein localization to nucleolus	EXP Inferred from Experiment more info	PubMed
involved_in protein localization to nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in protein polyubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein stabilization	IDA Inferred from Direct Assay more info	PubMed
involved_in protein sumoylation	TAS Traceable Author Statement more info
involved_in rRNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within rRNA transcription	IEA Inferred from Electronic Annotation more info
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 cell cycle	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of cell cycle	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell cycle	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of nucleocytoplasmic transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of protein export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein stability	IEP Inferred from Expression Pattern more info	PubMed
involved_in regulation of protein stability	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of protein targeting to mitochondrion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in replicative senescence	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in somatic stem cell division	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within somatic stem cell population maintenance	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
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 cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytosol	TAS Traceable Author Statement more info
located_in mitochondrial matrix	TAS Traceable Author Statement more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	IMP Inferred from Mutant Phenotype more info	PubMed
colocalizes_with nuclear body	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	TAS Traceable Author Statement 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
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
located_in senescence-associated heterochromatin focus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: cyclin-dependent kinase inhibitor 2A

Names: CDK4 inhibitor p16-INK4; CDKN2A/ARF Intron 2 lncRNA; alternative reading frame; cell cycle negative regulator beta; cyclin-dependent kinase 4 inhibitor A; cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4); inhibitor of cdk4 A; multiple tumor suppressor 1; multiple tumour suppressor 1

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

NG_007485.1 RefSeqGene

Range

5001..31740

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_11

mRNA and Protein(s)

NM_000077.5 → NP_000068.1 cyclin-dependent kinase inhibitor 2A isoform p16INK4a

See identical proteins and their annotated locations for 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)

BI258230, BQ012762, BX099567, L27211

Consensus CDS

CCDS6510.1

UniProtKB/Swiss-Prot

A5X2G7, D3DRK1, G3XAG3, O95440, P42771, Q15191, Q5VVJ5, Q96B52, Q9NP05

UniProtKB/TrEMBL

J3QRG6, K7PML8

Related

ENSP00000307101.5, ENST00000304494.10

Conserved Domains (2) summary

COG0666
Location:16 → 151

ANKYR; Ankyrin repeat [Signal transduction mechanisms]

sd00045
Location:16 → 42

ANK; ANK repeat [structural motif]
NM_001195132.2 → NP_001182061.1 cyclin-dependent kinase inhibitor 2A isoform p16gamma

See identical proteins and their annotated locations for 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

Related

ENSP00000418915.1, ENST00000498124.1

Conserved Domains (3) summary

cd00204
Location:19 → 130

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:16 → 108

Ank_2; Ankyrin repeats (3 copies)

sd00045
Location:16 → 42

ANK; ANK repeat [structural motif]
NM_001363763.2 → NP_001350692.1 cyclin-dependent kinase inhibitor 2A isoform 6

Status: REVIEWED

Source sequence(s)

AL449423

Consensus CDS

CCDS87644.1

UniProtKB/TrEMBL

L8E941

Related

ENSP00000467857.1, ENST00000498628.6

Conserved Domains (2) summary

COG0666
Location:2 → 100

ANKYR; Ankyrin repeat [Signal transduction mechanisms]

sd00045
Location:25 → 57

ANK; ANK repeat [structural motif]
NM_058195.4 → NP_478102.2 cyclin-dependent kinase inhibitor 2A isoform p14ARF

See identical proteins and their annotated locations for NP_478102.2

Status: REVIEWED

Description

Transcript Variant: This variant (4), also known as beta, encodes 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 p14ARF protein encoded by this variant (4) lacks sequence similarity to the protein product of variant 1 (p16INK4a). 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 protein 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

D3DRK2, Q13195, Q13399, Q16360, Q7KZR9, Q8N726

Related

ENSP00000462950.1, ENST00000579755.2

Conserved Domains (1) summary

pfam07392
Location:4 → 54

P19Arf_N; Cyclin-dependent kinase inhibitor 2a p19Arf N-terminus
NM_058197.5 → NP_478104.2 cyclin-dependent kinase inhibitor 2A isoform p12

See identical proteins and their annotated locations for 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/Swiss-Prot

P42771

UniProtKB/TrEMBL

G3XAG3

Related

ENSP00000369496.3, ENST00000380151.3

Conserved Domains (2) summary

sd00045
Location:16 → 42

ANK; ANK repeat [structural motif]

cl02529
Location:19 → 49

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 ...

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

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

21967752..21995324 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047422597.1 → XP_047278553.1 cyclin-dependent kinase inhibitor 2A isoform X4

UniProtKB/TrEMBL

L8E941

Related

ENSP00000467390.1, ENST00000578845.2
XM_011517676.3 → XP_011515978.1 cyclin-dependent kinase inhibitor 2A isoform X2

Conserved Domains (3) summary

cd00204
Location:19 → 130

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:16 → 108

Ank_2; Ankyrin repeats (3 copies)

sd00045
Location:16 → 42

ANK; ANK repeat [structural motif]
XM_011517675.3 → XP_011515977.1 cyclin-dependent kinase inhibitor 2A isoform X1

Conserved Domains (3) summary

cd00204
Location:19 → 130

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:16 → 108

Ank_2; Ankyrin repeats (3 copies)

sd00045
Location:16 → 42

ANK; ANK repeat [structural motif]
XM_047422596.1 → XP_047278552.1 cyclin-dependent kinase inhibitor 2A isoform X3
XM_047422598.1 → XP_047278554.1 cyclin-dependent kinase inhibitor 2A isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

21982052..22009697 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054361703.1 → XP_054217678.1 cyclin-dependent kinase inhibitor 2A isoform X4

UniProtKB/TrEMBL

L8E941
XM_054361701.1 → XP_054217676.1 cyclin-dependent kinase inhibitor 2A isoform X2
XM_054361700.1 → XP_054217675.1 cyclin-dependent kinase inhibitor 2A isoform X1
XM_054361702.1 → XP_054217677.1 cyclin-dependent kinase inhibitor 2A isoform X3
XM_054361704.1 → XP_054217679.1 cyclin-dependent kinase inhibitor 2A isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.