Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

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Basic Info

Approved Symbol	CDKN2A
Previous Symbol	CDKN2, MLM
Symbol Alias	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf, p14ARF
Approved Name	cyclin-dependent kinase inhibitor 2A
Previous Name	cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)
Location	9p21
Position	chr9:21967753-21995301, -1
External Links	HGNC: 1787 Entrez Gene: 1029 Ensembl: ENSG00000147889 UCSC: uc003zpk.3
No. of Studies	1 (Positive: 1; Negative: 0; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Moskvina, V.,2009		In BD:Smallest P-value per gene=0.0063, Product of P truncation <=0.01=0.0063, Product of P truncation <=0.001=NA. It showed evidence for association with BD.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 66)

GO terms by PBA (count: 2)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0003677	DNA binding	molecular function	IEA	83
GO:0005634	nucleus	cellular component	IDA[16243918]	283

GO terms by database search (count: 64)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0000209	protein polyubiquitination	biological process	IDA[18305112]	7
GO:0030889	negative regulation of B cell proliferation	biological process	ISS	5
GO:1903051	negative regulation of proteolysis involved in cellular protein catabolic process	biological process	IMP[25217637]	1
GO:0044822	poly(A) RNA binding	molecular function	IDA[22681889]	44
GO:0008637	apoptotic mitochondrial changes	biological process	IMP[12082630]	4
GO:0055105	ubiquitin-protein transferase inhibitor activity	molecular function	ISS	1
GO:0090399	replicative senescence	biological process	IMP[14720514]	2
GO:0005730	nucleolus	cellular component	IDA	28
GO:0010389	regulation of G2/M transition of mitotic cell cycle	biological process	IMP[15582998]	2
GO:2000111	positive regulation of macrophage apoptotic process	biological process	ISS[20381282]	2
GO:0007265	Ras protein signal transduction	biological process	IEP[9054499]	7
GO:0051882	mitochondrial depolarization	biological process	IMP[25217637]	2
GO:0033088	negative regulation of immature T cell proliferation in thymus	biological process	ISS	1
GO:0051059	NF-kappaB binding	molecular function	IDA[10353611]	3
GO:0035985	senescence-associated heterochromatin focus	cellular component	IDA[16901784]	1
GO:0050821	protein stabilization	biological process	IDA[10360174]	12
GO:0048103	somatic stem cell division	biological process	ISS	1
GO:0070534	protein K63-linked ubiquitination	biological process	IDA[18305112]	4
GO:0033235	positive regulation of protein sumoylation	biological process	IMP[19057511]	2
GO:0051444	negative regulation of ubiquitin-protein transferase activity	biological process	ISS	1
GO:0002039	p53 binding	molecular function	IPI[9529249]	7
GO:0043234	protein complex	cellular component	IDA[9529249]	27
GO:0005737	cytoplasm	cellular component	IDA[16243918]	322
GO:0032088	negative regulation of NF-kappaB transcription factor activity	biological process	IDA[10353611]	6
GO:0090398	cellular senescence	biological process	IMP[16243918]	2
GO:0042326	negative regulation of phosphorylation	biological process	IDA[10208428]	3
GO:0001953	negative regulation of cell-matrix adhesion	biological process	IMP[10205165]	3
GO:0097371	MDM2/MDM4 family protein binding	molecular function	IPI[16173922]	1
GO:0030308	negative regulation of cell growth	biological process	IDA[10208428]	11
GO:1903214	regulation of protein targeting to mitochondrion	biological process	IMP[25217637]	2
GO:0006469	negative regulation of protein kinase activity	biological process	IMP[15582998]	7
GO:0019901	protein kinase binding	molecular function	IPI[8259215]	29
GO:0071158	positive regulation of cell cycle arrest	biological process	IDA[9529249]	1
GO:0043065	positive regulation of apoptotic process	biological process	IMP[22094112]	25
GO:0006919	activation of cysteine-type endopeptidase activity involved in apoptotic process	biological process	IMP[12082630]	7
GO:0007050	cell cycle arrest	biological process	IDA[15149599]; IMP[16243918]	10
GO:0006351	transcription, DNA-templated	biological process	IEA	103
GO:0016604	nuclear body	cellular component	IDA[10360174]	3
GO:0046825	regulation of protein export from nucleus	biological process	IMP[10360174]	1
GO:0031648	protein destabilization	biological process	IDA[9529249]	5
GO:1901798	positive regulation of signal transduction by p53 class mediator	biological process	IDA[16173922]	1
GO:0000082	G1/S transition of mitotic cell cycle	biological process	IDA[10208428]	9
GO:0008285	negative regulation of cell proliferation	biological process	IDA[15149599]; IMP[16243918]	41
GO:0000278	mitotic cell cycle	biological process	TAS	33
GO:0005654	nucleoplasm	cellular component	IDA[10360174]; TAS	163
GO:0045736	negative regulation of cyclin-dependent protein serine/threonine kinase activity	biological process	IDA[8259215]	1
GO:0000422	mitochondrion degradation	biological process	IMP[25217637]	2
GO:0045892	negative regulation of transcription, DNA-templated	biological process	IMP[16901784]	43
GO:0006364	rRNA processing	biological process	IEA	2
GO:2000059	negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process	biological process	IDA[16173922]	1
GO:1902510	regulation of apoptotic DNA fragmentation	biological process	IMP[12082630]	2
GO:0005515	protein binding	molecular function	IPI[11278317]	563
GO:0008134	transcription factor binding	molecular function	IPI[19057511]	28
GO:0005739	mitochondrion	cellular component	IEA; IMP[25217637]	75
GO:0031647	regulation of protein stability	biological process	ISS	5
GO:0034393	positive regulation of smooth muscle cell apoptotic process	biological process	ISS[20381282]	2
GO:1900182	positive regulation of protein localization to nucleus	biological process	IDA[16173922]	3
GO:0035986	senescence-associated heterochromatin focus assembly	biological process	IMP[16901784]	1
GO:0043517	positive regulation of DNA damage response, signal transduction by p53 class mediator	biological process	IDA[9529249]	3
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	biological process	IDA[17569660]	91
GO:0005829	cytosol	cellular component	TAS	223
GO:0004861	cyclin-dependent protein serine/threonine kinase inhibitor activity	molecular function	IDA[8259215]	1
GO:2000774	positive regulation of cellular senescence	biological process	IMP[16901784]	2
GO:0045893	positive regulation of transcription, DNA-templated	biological process	IDA[17569660]	58

Gene related KEGG pathways (count: 8)

KEGG pathways by PBA (count: 4)

ID	Name	No. of Genes in BDgene
hsa04110	Cell cycle	8
hsa04115	p53 signaling pathway	4
hsa05214	Glioma	9
hsa05219	Bladder cancer	3

KEGG pathways by database search (count: 4)

ID	Name	No. of Genes in BDgene
hsa05212	Pancreatic cancer	10
hsa05218	Melanoma	7
hsa05220	Chronic myeloid leukemia	6
hsa05223	Non-small cell lung cancer	8

Gene related BioCarta pathways (count: 4)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 4)

ID	Name	No. of Genes in BDgene
ctcfPathway	CTCF: First Multivalent Nuclear Factor	3
g1Pathway	Cell Cycle: G1/S Check Point	2
arfPathway	Tumor Suppressor Arf Inhibits Ribosomal Biogenesis	4
cellcyclePathway	Cyclins and Cell Cycle Regulation	1

Gene related interactors from protein-protein interactions data in HPRD (count: 39)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
CDKN2A	MDM2	NO	in vitro;in vivo;yeast 2-hybrid	12085228 , 9529248 , 9529249
CDKN2A	RPS7	NO	yeast 2-hybrid	16582619
CDKN2A	ANKRD12	YES	in vitro;yeast 2-hybrid	16582619
CDKN2A	NCL	YES	in vitro;in vivo;yeast 2-hybrid	16582619
CDKN2A	WRN	NO	in vitro;in vivo	15355988
CDKN2A	MCM2	NO	in vitro	15232106
CDKN2A	ZFP91	NO	in vitro;yeast 2-hybrid	16582619
CDKN2A	KIAA1984	NO	in vitro;in vivo;yeast 2-hybrid	16582619
CDKN2A	E2F1	NO	in vitro	11314038
CDKN2A	CCNG1	NO	in vitro;in vivo	12556559
CDKN2A	HSP90AB1	NO	in vitro;yeast 2-hybrid	16582619
CDKN2A	ZNF227	NO	yeast 2-hybrid	16582619
CDKN2A	PSMC3	NO	in vitro;in vivo;yeast 2-hybrid	14665636
CDKN2A	E4F1	NO	in vivo	12446718
CDKN2A	SLC4A1	NO	in vitro;in vivo;yeast 2-hybrid	15811326
CDKN2A	CDKN2AIP	NO	in vivo	12154087
CDKN2A	CDK6	NO	in vitro	9751050
CDKN2A	CDC45L	NO	in vitro	15232106
CDKN2A	CDC7	NO	in vitro	15232106
CDKN2A	GMNN	NO	in vitro	15232106
CDKN2A	HIF1A	NO	in vivo	11382768
CDKN2A	PEX19	NO	yeast 2-hybrid	16582619
CDKN2A	UBE2A	NO	in vivo	12640129
CDKN2A	TBRG1	NO	in vitro;in vivo;yeast 2-hybrid	16582619
CDKN2A	CDC5L	NO	in vitro	15232106
CDKN2A	CDKN2C	NO	in vitro	8259215
CDKN2A	CDK4	NO	in vitro;in vivo	9228064 , 15232106 , 17517622
CDKN2A	AHNAK	NO	yeast 2-hybrid	16582619
CDKN2A	TPI1	NO	yeast 2-hybrid	16582619
CDKN2A	HUWE1	NO	in vitro	15989956
CDKN2A	PPP1R9B	NO	in vitro;in vivo;yeast 2-hybrid	11278317
CDKN2A	ORC4L	NO	in vitro	15232106
CDKN2A	MCM5	NO	in vitro	15232106
CDKN2A	ZNF410	NO	in vitro;yeast 2-hybrid	12370286
CDKN2A	CDC6	NO	in vitro	15232106
CDKN2A	MYC	NO	in vivo	15361884
CDKN2A	MCM10	NO	in vitro	15232106
CDKN2A	SERTAD1	NO	in vitro;in vivo;yeast 2-hybrid	10580009 , 15065884
CDKN2A	ALS2CR8	NO	in vivo;yeast 2-hybrid	12154087

Related other genetic factors

Gene related SNPs (count: 0)

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 5)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
9p22.3-p21.1	chr9:14200000-33200000	1 (0/0/1)
Chr 9	chr9:0-138394717	3 (0/3/0)
9p21	chr9:19900000-33200000	2 (0/1/1)
9p21-p12	chr9:19900000-40000000	1 (0/0/1)
9p21.3	chr9:19900000-25600000	1 (0/1/0)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Overlap with SZ from cross-disorder studies (count: 1)

Reference	Description	Result Category
19065143	In SZ:Smallest P-value per gene=0.00132, Product of P truncation <=0.01=0.00132, Product of P truncation <=0.001=NA It showed evidence for association with SZ.	Positive

Overlap with SZ from candidate gene intersection analysis (count: 0)

Gene relationship with MDD

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Region: chr9:21967753..21995301 View in gBrowse