Gene Gene information from NCBI Gene database.
Entrez ID 1029
Gene name Cyclin dependent kinase inhibitor 2A
Gene symbol CDKN2A
Synonyms (NCBI Gene)
ARFCAI2CDK4ICDKN2CMM2INK4INK4AMLMMTS-1MTS1P14P14ARFP16P16-INK4AP16INK4P16INK4AP19P19ARFTP16
Chromosome 9
Chromosome location 9p21.3
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 inhibito
SNPs SNP information provided by dbSNP.
101
SNP ID Visualize variation Clinical significance Consequence
rs1800586 C>A,G,T Conflicting-interpretations-of-pathogenicity, likely-benign, pathogenic, uncertain-significance 5 prime UTR variant, upstream transcript variant, intron variant, genic upstream transcript variant, non coding transcript variant
rs4987127 C>T Conflicting-interpretations-of-pathogenicity, likely-benign, benign Missense variant, 3 prime UTR variant, coding sequence variant, non coding transcript variant, synonymous variant
rs6413463 A>G,T Conflicting-interpretations-of-pathogenicity, likely-benign, benign Missense variant, 3 prime UTR variant, coding sequence variant, non coding transcript variant, synonymous variant
rs6413464 C>A,G Likely-pathogenic, benign-likely-benign, uncertain-significance, benign Missense variant, 3 prime UTR variant, coding sequence variant, non coding transcript variant
rs11552822 C>A,T Likely-pathogenic, conflicting-interpretations-of-pathogenicity, uncertain-significance Missense variant, 3 prime UTR variant, non coding transcript variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
33
miRTarBase ID miRNA Experiments Reference
MIRT004362 hsa-miR-24-3p qRT-PCRWestern blot 18365017
MIRT004362 hsa-miR-24-3p qRT-PCRWestern blot 18365017
MIRT004489 hsa-let-7g-5p qRT-PCRLuciferase reporter assayWestern blot 20309945
MIRT004709 hsa-miR-125b-5p Western blot 20347935
MIRT006071 hsa-miR-492 MicroarrayqRT-PCR 21319197
Transcription factors Transcription factors information provided by TRRUST V2 database.
28
Transcription factor Regulation Reference
DDB1 Unknown 19208841
DNMT1 Repression 17934516
DNMT1 Unknown 17490527
DNMT3A Unknown 17490527
E2F1 Activation 11705881;12695664;12766778;15716352;22621932
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
110
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 10353611
GO:0000209 Process Protein polyubiquitination IDA 18305112
GO:0000422 Process Autophagy of mitochondrion IMP 25217637
GO:0001953 Process Negative regulation of cell-matrix adhesion IMP 10205165
GO:0002039 Function P53 binding IPI 9529249
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
600160 1787 ENSG00000147889
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P42771
Protein name Cyclin-dependent kinase inhibitor 2A (Cyclin-dependent kinase 4 inhibitor A) (CDK4I) (Multiple tumor suppressor 1) (MTS-1) (p16-INK4a) (p16-INK4) (p16INK4A)
Protein function Acts as a negative regulator of the proliferation of normal cells by interacting strongly with CDK4 and CDK6. This inhibits their ability to interact with cyclins D and to phosphorylate the retinoblastoma protein. {ECO:0000269|PubMed:16782892, E
PDB 1A5E , 1BI7 , 1DC2 , 2A5E , 7OZT
Family and domains
Tissue specificity TISSUE SPECIFICITY: Widely expressed but not detected in brain or skeletal muscle. Isoform 3 is pancreas-specific. {ECO:0000269|PubMed:10445844}.
Sequence
MEPAAGSSMEPSADWLATAAARGRVEEVRALLEAGALPNAPNSYGRRPIQVMMMGSARVA
ELLLLHGAEPNCADPATLTRPVHDAAREGFLDTLVVLHRAGARLDVRDAWGRLPVDLAEE
LGHRDVARYLRAAAGGTRGSNHARIDAAEGPSDIPD
Sequence length 156
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q8N726
Protein name Tumor suppressor ARF (Alternative reading frame) (ARF) (Cyclin-dependent kinase inhibitor 2A) (p14ARF)
Protein function Capable of inducing cell cycle arrest in G1 and G2 phases. Acts as a tumor suppressor. Binds to MDM2 and blocks its nucleocytoplasmic shuttling by sequestering it in the nucleolus. This inhibits the oncogenic action of MDM2 by blocking MDM2-indu
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF07392 P19Arf_N 4 54 Cyclin-dependent kinase inhibitor 2a p19Arf N-terminus Family
Sequence
MVRRFLVTLRIRRACGPPRVRVFVVHIPRLTGEWAAPGAPAAVALVLMLLRSQRLGQQPL
PRRPGHDDGQRPSGGAAAAPRRGAQLRRPRHSHPTRARRCPGGLPGHAGGAAPGRGAAGR
ARCLGPSARGPG
Sequence length 132
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Endocrine resistance
Platinum drug resistance
Cell cycle
p53 signaling pathway
Cellular senescence
Cushing syndrome
Human cytomegalovirus infection
Human T-cell leukemia virus 1 infection
Pathways in cancer
Viral carcinogenesis
MicroRNAs in cancer
Pancreatic cancer
Glioma
Melanoma
Bladder cancer
Chronic myeloid leukemia
Non-small cell lung cancer
Hepatocellular carcinoma
  Apoptotic factor-mediated response
Oxidative Stress Induced Senescence
Senescence-Associated Secretory Phenotype (SASP)
Oncogene Induced Senescence
SUMOylation of DNA damage response and repair proteins
SUMOylation of transcription factors
Regulation of TP53 Degradation
Cyclin D associated events in G1
Stabilization of p53
Transcriptional Regulation by VENTX
Regulation of RUNX3 expression and activity
Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4
Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6
Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4
Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6
Defective Intrinsic Pathway for Apoptosis Due to p14ARF Loss of Function
Evasion of Oncogene Induced Senescence Due to p14ARF Defects
Evasion of Oxidative Stress Induced Senescence Due to p14ARF Defects
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
2848
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Acute lymphoid leukemia Likely pathogenic rs2489277337, rs2489276701 RCV003444128
RCV003444129
CDKN2A-related disorder Likely pathogenic; Pathogenic rs587780668, rs730881674, rs1800586, rs104894094, rs104894095, rs141798398 RCV004754304
RCV003895073
RCV004754323
RCV004754252
RCV004754253
RCV003396344
Embryonal rhabdomyosarcoma Likely pathogenic rs1819713922 RCV006254253
Familial melanoma Likely pathogenic; Pathogenic rs2131148082, rs2131095862, rs2131112280, rs2131113797, rs2131148302, rs2131147969, rs2131148812, rs587780668, rs1819949737, rs1317637377, rs2131148531, rs2131096682, rs2131147945, rs587782083, rs587782206
View all (82 more)
RCV001368663
RCV001389216
RCV001380818
RCV001380650
RCV001385044
RCV002026032
RCV001992217
RCV000122949
RCV001916136
RCV001942064
RCV002041568
RCV001966514
RCV001986397
RCV000638995
RCV000458116
RCV000687345
RCV001239877
RCV000458351
RCV000161946
RCV001850264
RCV001225200
RCV000168189
RCV000232355
RCV001220072
RCV003746642
RCV000168272
RCV003074637
RCV003058215
RCV002824664
RCV002810716
RCV002938678
RCV000198192
RCV000206296
RCV000206427
RCV000554207
RCV000472170
RCV000471227
RCV000685369
RCV000229122
RCV000234329
RCV000234305
RCV005101031
RCV002512955
RCV000196633
RCV000205342
RCV000472219
RCV000227154
RCV000545232
RCV000471463
RCV000122946
RCV001239756
RCV003585387
RCV003585423
RCV003585616
RCV003584334
RCV003584386
RCV003746843
RCV003747360
RCV003746085
RCV003746237
RCV002524693
RCV003584593
RCV001239759
RCV000638957
RCV000460188
RCV000465157
RCV000466313
RCV000457482
RCV000459258
RCV000692301
RCV000807478
RCV000638987
RCV000638989
RCV002527070
RCV000528787
RCV000549066
RCV000541791
RCV000525976
RCV000543773
RCV000532665
RCV001382593
RCV001377736
RCV000698266
RCV000687200
RCV000638996
RCV000702250
RCV000686351
RCV000705257
RCV000694543
RCV000693768
RCV000692157
RCV000817300
RCV002535739
RCV000798145
RCV000811410
RCV000804158
RCV000817019
RCV001034206
RCV001034096
RCV001034207
RCV001055189
RCV001062903
RCV001378150
RCV001245432
RCV000525168
RCV005094344
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Alveolar rhabdomyosarcoma Conflicting classifications of pathogenicity rs11552822 RCV006253912
Atypical endometrial hyperplasia Uncertain significance rs1819723898 RCV003327300
Cervical cancer Uncertain significance; Benign; Likely benign rs2131079543, rs144481587 RCV005911368
RCV005887901
Clear cell carcinoma of kidney Conflicting classifications of pathogenicity rs45476696 RCV005900187
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
3 Hydroxy 3 Methylglutaryl CoA Lyase Deficiency Associate 14982841
Abdominal Injuries Associate 23154831
Aberrant Crypt Foci Associate 12000733
Abnormalities Drug Induced Associate 19131428, 24399002, 27568665
Abortion Habitual Associate 39941094
Acrospiroma Associate 27159948
Acute Disease Associate 7742529
Adenocarcinoma Associate 10601379, 12149142, 15098254, 15612080, 15785933, 16163549, 16598757, 16731604, 17072968, 17326708, 18410530, 18663352, 18831746, 19043591, 19366452
View all (31 more)
Adenocarcinoma Inhibit 18296270, 21857254, 22908062, 26192918, 30375264
Adenocarcinoma Stimulate 24258618, 26910219, 30946937