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
cellcyclePathway	Cyclins and Cell Cycle Regulation	1
ctcfPathway	CTCF: First Multivalent Nuclear Factor	3
g1Pathway	Cell Cycle: G1/S Check Point	2
arfPathway	Tumor Suppressor Arf Inhibits Ribosomal Biogenesis	4

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

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

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