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    CDKN2B cyclin dependent kinase inhibitor 2B [ Homo sapiens (human) ]

    Gene ID: 1030, updated on 2-Nov-2024

    Summary

    Official Symbol
    CDKN2Bprovided by HGNC
    Official Full Name
    cyclin dependent kinase inhibitor 2Bprovided by HGNC
    Primary source
    HGNC:HGNC:1788
    See related
    Ensembl:ENSG00000147883 MIM:600431; AllianceGenome:HGNC:1788
    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
    P15; MTS2; TP15; CDK4I; INK4B; p15INK4b
    Summary
    This gene lies adjacent to the tumor suppressor gene CDKN2A in a region that is frequently mutated and deleted in a wide variety of tumors. This gene encodes a cyclin-dependent kinase inhibitor, which forms a complex with CDK4 or CDK6, and prevents the activation of the CDK kinases, thus the encoded protein functions as a cell growth regulator that controls cell cycle G1 progression. The expression of this gene was found to be dramatically induced by TGF beta, which suggested its role in the TGF beta induced growth inhibition. Two alternatively spliced transcript variants of this gene, which encode distinct proteins, have been reported. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in colon (RPKM 20.3), small intestine (RPKM 17.6) and 17 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CDKN2B in Genome Data Viewer
    Location:
    9p21.3
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (22002903..22009313, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (22017276..22023690, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (22002902..22009312, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:21968891-21969804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19811 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28244 Neighboring gene CDKN2A antisense RNA 1 Neighboring gene uncharacterized LOC124902130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:21989455-21990037 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19814 Neighboring gene cyclin dependent kinase inhibitor 2A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19815 Neighboring gene CDKN2B antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 15403 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:22026023-22027222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28245 Neighboring gene ubiquitin A-52 residue ribosomal protein fusion product 1 pseudogene 6 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 9:22068931 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:22102887-22104086 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:22117311-22118510 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28246 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:22363678-22364189 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:22446999-22447498 Neighboring gene DMRT like family A1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data.
    EBI GWAS Catalog
    A common variant on chromosome 9p21 affects the risk of myocardial infarction.
    EBI GWAS Catalog
    A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
    EBI GWAS Catalog
    A genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans.
    EBI GWAS Catalog
    A genome-wide association study in the Japanese population confirms 9p21 and 14q23 as susceptibility loci for primary open angle glaucoma.
    EBI GWAS Catalog
    A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci.
    EBI GWAS Catalog
    A genome-wide association study of optic disc parameters.
    EBI GWAS Catalog
    A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.
    EBI GWAS Catalog
    Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data.
    EBI GWAS Catalog
    Association between chromosome 9p21 variants and the ankle-brachial index identified by a meta-analysis of 21 genome-wide association studies.
    EBI GWAS Catalog
    Chromosome 7p11.2 (EGFR) variation influences glioma risk.
    EBI GWAS Catalog
    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
    Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels.
    EBI GWAS Catalog
    Genome-wide association meta-analysis identifies new endometriosis risk loci.
    EBI GWAS Catalog
    Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
    EBI GWAS Catalog
    Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants.
    EBI GWAS Catalog
    Genome-wide association study for coronary artery calcification with follow-up in myocardial infarction.
    EBI GWAS Catalog
    Genome-wide association study identifies five new breast cancer susceptibility loci.
    EBI GWAS Catalog
    Genome-wide association study identifies five susceptibility loci for glioma.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia.
    EBI GWAS Catalog
    Genome-wide association study identifies three novel loci for type 2 diabetes.
    EBI GWAS Catalog
    Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
    EBI GWAS Catalog
    Genome-wide association study of coronary and aortic calcification implicates risk loci for coronary artery disease and myocardial infarction.
    EBI GWAS Catalog
    Genome-wide association study of coronary artery disease in the Japanese.
    EBI GWAS Catalog
    Genome-wide association study of intracranial aneurysm identifies three new risk loci.
    EBI GWAS 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.
    EBI GWAS Catalog
    Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
    EBI GWAS Catalog
    Germline sequence variants in TGM3 and RGS22 confer risk of basal cell carcinoma.
    EBI GWAS Catalog
    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
    Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations.
    EBI GWAS Catalog
    Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
    EBI GWAS Catalog
    Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
    EBI GWAS Catalog
    Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes.
    EBI GWAS Catalog
    Susceptibility loci for intracranial aneurysm in European and Japanese populations.
    EBI GWAS Catalog
    Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
    EBI GWAS Catalog
    Two-marker association tests yield new disease associations for coronary artery disease and hypertension.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cellular response to cell-matrix adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to nutrient IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to transforming growth factor beta stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of cellular senescence IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in liver development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in megakaryocyte differentiation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in negative regulation of G1/S transition of mitotic cell cycle IEA
    Inferred from Electronic Annotation
    more info
     
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of epithelial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of glial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of epithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transforming growth factor beta receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of G0 to G1 transition IMP
    Inferred from Mutant Phenotype
    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 cyclin-dependent protein serine/threonine kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to cytokine IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to organic cyclic compound IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spleen development 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 cytosol 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 

    General protein information

    Preferred Names
    cyclin-dependent kinase 4 inhibitor B
    Names
    CDK inhibitory protein
    CDK4B inhibitor
    MTS-2
    cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)
    cyclin-dependent kinases 4 and 6 binding protein
    multiple tumor suppressor 2
    p14-INK4b
    p14_CDK inhibitor
    p14_INK4B
    p15 CDK inhibitor
    p15-INK4b
    p15_INK4B

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_023297.1 RefSeqGene

      Range
      5009..11411
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_004936.4NP_004927.2  cyclin-dependent kinase 4 inhibitor B isoform 1

      See identical proteins and their annotated locations for NP_004927.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AF488731, BC014469, BC018984, BI560960
      Consensus CDS
      CCDS6512.1
      UniProtKB/Swiss-Prot
      O15125, P42772, Q6FI09
      UniProtKB/TrEMBL
      K7PPU3
      Related
      ENSP00000276925.6, ENST00000276925.7
      Conserved Domains (2) summary
      cd00204
      Location:21132
      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 ...
      sd00045
      Location:4676
      ANK; ANK repeat [structural motif]
    2. NM_078487.2NP_511042.1  cyclin-dependent kinase 4 inhibitor B isoform 2

      See identical proteins and their annotated locations for NP_511042.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses a different splice site, which leads to a translation frame shift, when compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus when compared to isoform 1.
      Source sequence(s)
      AF004819, AF488731, BC014469, BC018984, BI560960
      Consensus CDS
      CCDS6513.1
      UniProtKB/TrEMBL
      Q5ZEY8
      Related
      ENSP00000369487.4, ENST00000380142.5
      Conserved Domains (1) summary
      cl02529
      Location:2154
      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

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      22002903..22009313 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      22017276..22023690 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)