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 (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
100
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Acute lymphoid leukemia Likely pathogenic rs2489277337, rs2489276701 RCV003444128
RCV003444129
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
CDKN2A-related disorder Likely pathogenic; Pathogenic rs587780668, rs730881674, rs1800586, rs104894094, rs104894095, rs141798398 RCV004754304
RCV003895073
RCV004754323
RCV004754252
RCV004754253
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Embryonal rhabdomyosarcoma Likely pathogenic rs1819713922 RCV006254253
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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
View all (101 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Alveolar rhabdomyosarcoma Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Atypical endometrial hyperplasia Uncertain significance ClinVar
Disgenet
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
B-CELL ACUTE LYMPHOBLASTIC LEUKEMIA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
B-LYMPHOBLASTIC LEUKEMIA/LYMPHOMA WITH T Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acoustic Neuroma Acoustic Neuroma BEFREE 24964769
★☆☆☆☆
Found in Text Mining only
Acral Lentiginous Malignant Melanoma Acral Lentiginous Malignant Melanoma BEFREE 29537991, 30778854
★☆☆☆☆
Found in Text Mining only
Acromegaly Acromegaly BEFREE 30975543, 31828584
★☆☆☆☆
Found in Text Mining only
ACTH-Secreting Pituitary Adenoma Pituitary adenoma BEFREE 11276008, 15014032, 20616110
★☆☆☆☆
Found in Text Mining only
Actinic keratosis Actinic keratosis BEFREE 10498902, 11804749, 12485439, 13679450, 15008871, 17488404, 18331779, 28796927
★☆☆☆☆
Found in Text Mining only
Actinic keratosis Actinic keratosis LHGDN 12429789, 17488404, 18331779
★☆☆☆☆
Found in Text Mining only
Acute leukemia Leukemia BEFREE 10073286, 10634644, 11413509, 14513284, 16949174, 21681782, 25784651, 8555068, 8616035, 8652384, 9447829
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 10025891, 10090949, 10430092, 10512159, 11118035, 11168496, 11301189, 11380395, 11380466, 11413509, 11441822, 11455973, 12032783, 12036898, 12127556
View all (67 more)
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia GENOMICS_ENGLAND_DG 27756164
★☆☆☆☆
Found in Text Mining only
Acute monocytic leukemia Monocytic Leukemia BEFREE 10634644, 19667402, 20699639, 29432785
★☆☆☆☆
Found in Text Mining only