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	PARK2
Symbol Alias	PDJ, AR-JP, parkin
Approved Name	parkin RBR E3 ubiquitin protein ligase
Previous Name	Parkinson disease (autosomal recessive, juvenile) 2, parkin, "parkinson protein 2, E3 ubiquitin protein ligase (parkin)"
Name Alias	E3 ubiquitin ligase
Location	6q25.2-q27
Position	chr6:161347420-162727771, -1
External Links	HGNC: 8607 Entrez Gene: 5071 Ensembl: ENSG00000185345 UCSC: uc003qtx.4
No. of Studies	1 (Positive: 1; Negative: 0; trend: 0)
Overlap with SZ?	NO
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Noor A., 2014		Selected stringent CNV related to this gene is validated by qPCR from BD case data.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 112)

GO terms by PBA (count: 4)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0003779	actin binding	molecular function	IPI[21753002]	24
GO:0005634	nucleus	cellular component	IEA	283
GO:0030165	PDZ domain binding	molecular function	IPI[17512523]	16
GO:0007417	central nervous system development	biological process	TAS[9560156]	21

GO terms by database search (count: 108)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0031624	ubiquitin conjugating enzyme binding	molecular function	IPI[11439185]	2
GO:0004842	ubiquitin-protein transferase activity	molecular function	IDA[11078524]	12
GO:0042787	protein ubiquitination involved in ubiquitin-dependent protein catabolic process	biological process	IC[21376232]; IDA[17097639]; NAS[12628165]; TAS[10888878]	4
GO:0005783	endoplasmic reticulum	cellular component	IDA[12150907]	49
GO:0032368	regulation of lipid transport	biological process	TAS[23626584]	1
GO:0034620	cellular response to unfolded protein	biological process	TAS[18221368]	1
GO:0017124	SH3 domain binding	molecular function	TAS[23626584]	11
GO:0006351	transcription, DNA-templated	biological process	IEA	103
GO:1902236	negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	biological process	IDA[11439185]; IMP[21113145]	5
GO:0005515	protein binding	molecular function	IPI[10888878]	563
GO:0055069	zinc ion homeostasis	biological process	ISS	1
GO:0001964	startle response	biological process	IEA	7
GO:0010506	regulation of autophagy	biological process	IDA[20889974]	2
GO:0005829	cytosol	cellular component	IDA[19029340]; IMP[21508222]	223
GO:0097602	cullin family protein binding	molecular function	IDA[12628165]	1
GO:1901800	positive regulation of proteasomal protein catabolic process	biological process	IGI[23858059]	2
GO:0001933	negative regulation of protein phosphorylation	biological process	IDA[17512523]	3
GO:0000151	ubiquitin ligase complex	cellular component	IDA[12150907]	4
GO:0043005	neuron projection	cellular component	IEA	38
GO:1990444	F-box domain binding	molecular function	IPI[12628165]	1
GO:0010821	regulation of mitochondrion organization	biological process	IDA[21113145]; IGI[19279012]; NAS[20890124]	1
GO:0070050	neuron cellular homeostasis	biological process	ISS	2
GO:0071797	LUBAC complex	cellular component	IPI[23453807]	1
GO:1902530	positive regulation of protein linear polyubiquitination	biological process	IGI[23453807]	1
GO:0097237	cellular response to toxic substance	biological process	IMP[12628165]	1
GO:1990452	Parkin-FBXW7-Cul1 ubiquitin ligase complex	cellular component	IPI[12628165]	2
GO:1903265	positive regulation of tumor necrosis factor-mediated signaling pathway	biological process	IDA[23453807]	1
GO:0000266	mitochondrial fission	biological process	ISS	4
GO:0060548	negative regulation of cell death	biological process	IDA[12150907]	5
GO:0098779	activation of mitophagy in response to mitochondrial depolarization	biological process	IDA[19029340]; IMP[20871098]	1
GO:0014059	regulation of dopamine secretion	biological process	TAS[21563316]	8
GO:0051583	dopamine uptake involved in synaptic transmission	biological process	IEA	1
GO:0070842	aggresome assembly	biological process	IMP[14645198]	1
GO:0005794	Golgi apparatus	cellular component	IDA[17097639]	60
GO:0033132	negative regulation of glucokinase activity	biological process	IDA[24187134]	1
GO:0031072	heat shock protein binding	molecular function	IPI[12150907]	6
GO:0044257	cellular protein catabolic process	biological process	IMP[21376232]	1
GO:0090141	positive regulation of mitochondrial fission	biological process	ISS	1
GO:2000378	negative regulation of reactive oxygen species metabolic process	biological process	IGI[18541373]	1
GO:0008344	adult locomotory behavior	biological process	ISS	15
GO:0008270	zinc ion binding	molecular function	TAS[23626584]	77
GO:0043388	positive regulation of DNA binding	biological process	IDA[17314283]	4
GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	biological process	IEA	7
GO:0097413	Lewy body	cellular component	TAS[24522549]	1
GO:0019901	protein kinase binding	molecular function	IPI[20798600]	29
GO:0000422	mitochondrion degradation	biological process	IDA[25621951]; IMP[19029340]; ISS	2
GO:0061630	ubiquitin protein ligase activity	molecular function	IDA[11439185]; NAS[18221368]	2
GO:0042826	histone deacetylase binding	molecular function	IPI[21753002]	13
GO:0046928	regulation of neurotransmitter secretion	biological process	IEA	7
GO:0046329	negative regulation of JNK cascade	biological process	ISS	3
GO:1900407	regulation of cellular response to oxidative stress	biological process	ISS	1
GO:0043130	ubiquitin binding	molecular function	IDA[24784582]	5
GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	biological process	IDA[17314283]; IMP[23453807]	14
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	biological process	IDA[23453807]	91
GO:0031625	ubiquitin protein ligase binding	molecular function	IPI[12150907]	25
GO:0016235	aggresome	cellular component	IDA[14645198]	3
GO:2000377	regulation of reactive oxygen species metabolic process	biological process	IMP[18541373]	2
GO:1903382	negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway	biological process	IEA	1
GO:0007005	mitochondrion organization	biological process	ISS	8
GO:0019900	kinase binding	molecular function	IPI[17512523]	8
GO:0015631	tubulin binding	molecular function	IPI[21753002]	5
GO:1903146	regulation of mitochondrion degradation	biological process	TAS[21563316]	5
GO:0085020	protein K6-linked ubiquitination	biological process	IDA[25621951]; TAS[23626584]	2
GO:0090201	negative regulation of release of cytochrome c from mitochondria	biological process	IDA[19880420]	5
GO:0042802	identical protein binding	molecular function	IPI[21694720]	44
GO:0043524	negative regulation of neuron apoptotic process	biological process	IDA[12628165]	26
GO:0005739	mitochondrion	cellular component	IDA[19229105]; IGI[20457763]; IMP[19029340]; IMP[21508222]	75
GO:1903202	negative regulation of oxidative stress-induced cell death	biological process	NAS[24522549]; TAS[24252804]	1
GO:0032232	negative regulation of actin filament bundle assembly	biological process	IDA[17512523]	1
GO:0000209	protein polyubiquitination	biological process	IDA[12150907]	7
GO:0042417	dopamine metabolic process	biological process	TAS[23626584]	7
GO:0070936	protein K48-linked ubiquitination	biological process	IDA[21376232]	3
GO:1901215	negative regulation of neuron death	biological process	IGI[21376232]	6
GO:0051865	protein autoubiquitination	biological process	IDA[12628165]	2
GO:0019005	SCF ubiquitin ligase complex	cellular component	IDA[12628165]	2
GO:0010636	positive regulation of mitochondrial fusion	biological process	IMP[23453807]	1
GO:0070534	protein K63-linked ubiquitination	biological process	IDA[15728840]; NAS[20890124]; TAS[18221368]	4
GO:0001664	G-protein coupled receptor binding	molecular function	IPI[12150907]	9
GO:0016567	protein ubiquitination	biological process	IDA[11439185]; IMP[23933751]	18
GO:0034976	response to endoplasmic reticulum stress	biological process	IMP[21113145]	9
GO:0050821	protein stabilization	biological process	IMP[19229105]	12
GO:1903214	regulation of protein targeting to mitochondrion	biological process	NAS[20890124]	2
GO:0006979	response to oxidative stress	biological process	ISS	11
GO:0016874	ligase activity	molecular function	IEA	16
GO:1903378	positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway	biological process	IEA	1
GO:0044314	protein K27-linked ubiquitination	biological process	TAS[20098416]	1
GO:0010906	regulation of glucose metabolic process	biological process	TAS[23626584]	3
GO:0051087	chaperone binding	molecular function	IPI[15603737]	10
GO:1903377	negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway	biological process	IDA[17314283]	1
GO:0042415	norepinephrine metabolic process	biological process	IEA	2
GO:0010637	negative regulation of mitochondrial fusion	biological process	ISS	1
GO:1903351	cellular response to dopamine	biological process	TAS[23626584]	1
GO:0070979	protein K11-linked ubiquitination	biological process	IDA[25621951]	4
GO:0048471	perinuclear region of cytoplasm	cellular component	IDA[17097639]	50
GO:0044828	negative regulation by host of viral genome replication	biological process	IDA[25244949]	2
GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	biological process	IDA[11439185]	13
GO:0046676	negative regulation of insulin secretion	biological process	IDA[24187134]	4
GO:0007612	learning	biological process	IEA	18
GO:0031396	regulation of protein ubiquitination	biological process	IGI[23212910]; IMP[20871098]	1
GO:0035519	protein K29-linked ubiquitination	biological process	TAS[23626584]	1
GO:0030544	Hsp70 protein binding	molecular function	IPI[12150907]	3
GO:0006513	protein monoubiquitination	biological process	IDA[20889974]	2
GO:0035249	synaptic transmission, glutamatergic	biological process	IEA	14
GO:0005737	cytoplasm	cellular component	IDA[17512523]	322
GO:1902803	regulation of synaptic vesicle transport	biological process	NAS[21563316]	1
GO:0071287	cellular response to manganese ion	biological process	TAS[23628791]	3
GO:0070585	protein localization to mitochondrion	biological process	IEA	1
GO:1990381	ubiquitin-specific protease binding	molecular function	IPI[24063750]	1

Gene related KEGG pathways (count: 3)

KEGG pathways by PBA (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04120	Ubiquitin mediated proteolysis	4

KEGG pathways by database search (count: 2)

ID	Name	No. of Genes in BDgene	Brief Description
hsa01510	Neurodegenerative Diseases	10
hsa05020	Parkinson's disease	3

Gene related BioCarta pathways (count: 2)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 2)

ID	Name	No. of Genes in BDgene	Brief Description
parkinPathway	Role of Parkin in the Ubiquitin-Proteasomal Pathway	3
ParkinsonsPathway	Alpha-synuclein and Parkin-mediated proteolysis in Parkinson's disease	1

Gene related interactors from protein-protein interactions data in HPRD (count: 26)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
PARK2	PSMA7	NO	in vivo;yeast 2-hybrid	15987638
PARK2	TUBA4A	NO	in vivo	12716939
PARK2	PAFAH1B2	NO	yeast 2-hybrid	16169070
PARK2	SIM2	NO	in vivo	15963499
PARK2	CASP8	NO	in vitro	12692130
PARK2	TRIP13	NO	yeast 2-hybrid	16189514
PARK2	RAC1	YES	yeast 2-hybrid	16169070
PARK2	RAD1	NO	yeast 2-hybrid	16169070
PARK2	RANBP2	NO	in vitro;in vivo	16332688
PARK2	GRIN2B	YES	in vitro;in vivo	11679592
PARK2	RGS3	NO	in vitro	16637659
PARK2	NDUFA4L2	NO	yeast 2-hybrid	16169070
PARK2	TUBB	YES	in vivo	12716939
PARK2	RGS2	NO	yeast 2-hybrid	16169070
PARK2	UBE2G1	NO	in vitro	11439185
PARK2	HEXDC	NO	yeast 2-hybrid	16169070
PARK2	UBB	NO	in vitro	15105460
PARK2	FBXW7	NO	in vitro;in vivo	12628165
PARK2	UBE2L6	NO	in vitro;in vivo;yeast 2-hybrid	11078524
PARK2	SNCA	NO	in vivo	11588587
PARK2	SYT11	NO	in vitro;yeast 2-hybrid	12925569
PARK2	AIMP2	NO	in vitro;yeast 2-hybrid	12783850
PARK2	SEPT5	NO	in vitro;in vivo;yeast 2-hybrid	11078524
PARK2	SEPT4	NO	in vitro;in vivo;yeast 2-hybrid	14559152
PARK2	CASK	NO	in vitro;in vivo	11679592
PARK2	GPR37	NO	in vitro;in vivo	12150907 , 11439185

Related other genetic factors

Gene related SNPs (count: 0)

Gene related CNVs (count: 5)

ID	Location	Size	Band	Type
CNV_Zhang[2009]_127	chr6:162035802-162238195 (Affymetrix SNP 6.0 array reference genome)	202393		Singleton deletions
CNV_Zhang[2009]_135	chr6:162768919-162951431 (Affymetrix SNP 6.0 array reference genome)	182512		Singleton deletions
CNV_Zhang[2009]_131	chr6:162297547-162466706 (Affymetrix SNP 6.0 array reference genome)	169159		Singleton deletions
CNV_Kember[2015]_15	chr6:163041460-163139315 (UCSC build 37, hg19)	99376		deletion
CNV_Abdul Noor[2014]_9	chr6:162504743-162738093 (NCBI Build 36/hg18)	233000	7q31.1	deletion

Gene related other variants (count: 0)

Gene related regions (count: 2)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 6	chr6:0-170805979	3 (0/3/0)
6q26	chr6:160600000-164100000	1 (0/1/0)

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

Gene relationship with SZ

Gene relationship with MDD

View in gBrowse

Region: chr6:161347420..162727771 View in gBrowse