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	PLD1
Approved Name	phospholipase D1, phosphatidylcholine-specific
Name Alias	choline phosphatase 1
Location	3q26
Position	chr3:171600405-171810950, -1
External Links	HGNC: 9067 Entrez Gene: 5337 Ensembl: ENSG00000075651 UCSC: uc003fhs.3
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
Gratacos, M.,2009	SNP: rs4256166	Nominal associations with bipolar disorder was observed.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 25)

GO terms by PBA (count: 1)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0016020	membrane	cellular component	IDA[19946888]	137

GO terms by database search (count: 24)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007265	Ras protein signal transduction	biological process	TAS[10848592]	7
GO:0006655	phosphatidylglycerol biosynthetic process	biological process	TAS	1
GO:0005768	endosome	cellular component	IDA[14718562]	27
GO:0030139	endocytic vesicle	cellular component	IDA[22797597]	8
GO:0006935	chemotaxis	biological process	TAS[10848592]	7
GO:0005515	protein binding	molecular function	IPI[17853892]	563
GO:0031902	late endosome membrane	cellular component	IEA	5
GO:0006644	phospholipid metabolic process	biological process	TAS	18
GO:0050830	defense response to Gram-positive bacterium	biological process	IEA	7
GO:0070290	N-acylphosphatidylethanolamine-specific phospholipase D activity	molecular function	IEA	2
GO:0032534	regulation of microvillus assembly	biological process	IMP[22797597]	1
GO:0016042	lipid catabolic process	biological process	IEA	4
GO:0000139	Golgi membrane	cellular component	IEA	36
GO:0004630	phospholipase D activity	molecular function	IEA	1
GO:0006654	phosphatidic acid biosynthetic process	biological process	TAS	2
GO:0035091	phosphatidylinositol binding	molecular function	IEA	5
GO:0048471	perinuclear region of cytoplasm	cellular component	IEA	50
GO:0007264	small GTPase mediated signal transduction	biological process	TAS[8530346]	18
GO:0005794	Golgi apparatus	cellular component	IDA[14718562]	60
GO:0016324	apical plasma membrane	cellular component	IDA[22797597]	24
GO:0046474	glycerophospholipid biosynthetic process	biological process	TAS	5
GO:0044281	small molecule metabolic process	biological process	TAS	117
GO:0005765	lysosomal membrane	cellular component	IDA[17897319]	14
GO:0005789	endoplasmic reticulum membrane	cellular component	TAS	52

Gene related KEGG pathways (count: 4)

KEGG pathways by PBA (count: 0)

KEGG pathways by database search (count: 4)

ID	Name	No. of Genes in BDgene
hsa05212	Pancreatic cancer	10
hsa00564	Glycerophospholipid metabolism	7
hsa00565	Ether lipid metabolism	3
hsa04912	GnRH signaling pathway	17

Gene related BioCarta pathways (count: 3)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 3)

ID	Name	No. of Genes in BDgene
rasPathway	Ras Signaling Pathway	5
cb1rPathway	Metabolism of Anandamide, an Endogenous Cannabinoid	1
rac1Pathway	Rac 1 cell motility signaling pathway	6

Gene related interactors from protein-protein interactions data in HPRD (count: 20)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
PLD1	ARF6	NO	in vivo	12379803
PLD1	CDC42	NO	in vitro;in vivo	10747870
PLD1	STXBP1	NO	in vitro;in vivo	14744865
PLD1	CAV1	NO	in vivo	12429840 , 10090765
PLD1	RALA	NO	in vitro;in vivo	9207251
PLD1	RHOG	NO	in vitro	12376551
PLD1	PEA15	NO	in vitro;in vitro;in vivo;in vivo;yeast 2-hybrid	10926929 , 18541525
PLD1	ARIH1	NO	yeast 2-hybrid	10926929
PLD1	PIP5K1A	NO	in vivo	11032811
PLD1	ACTA1	NO	in vivo	12388543
PLD1	PRKCA	NO	in vitro;in vivo	12839565 , 10441128
PLD1	RHOA	NO	in vitro;in vivo	11311142 , 12593858 , 9565577
PLD1	ARF1	NO	in vitro;in vivo	9688545
PLD1	EGFR	YES	in vivo	11459228
PLD1	PKN3	NO	in vitro;in vivo	11259428
PLD1	PKN1	NO	in vitro;in vivo	11259428
PLD1	SNCA	NO	in vitro;in vivo	11821392
PLD1	ACTG1	NO	in vitro;in vivo	12388543
PLD1	ACTB	NO	in vitro;in vivo	11373276
PLD1	RAC1	YES	in vivo	11950936

Related other genetic factors

Gene related SNPs (count: 48)

Literature-origin SNPs (count: 1)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs4256166	chr3:171737087 - 171737087(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(1/0/0)

LD-proxies (count: 47)

rs_ID	Location	Functional Annotation
rs4894496	chr3:171700241 - 171700241(1)	intron_variant; non_coding_transcript_variant
rs13321742	chr3:171802003 - 171802003(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs12632766	chr3:171793565 - 171793565(1)	5_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs9872581	chr3:171793108 - 171793108(1)	5_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs9831169	chr3:171793051 - 171793051(1)	5_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs3934620	chr3:171792448 - 171792448(1)	intron_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_variant
rs9839909	chr3:171790673 - 171790673(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs9815321	chr3:171789940 - 171789940(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs4586847	chr3:171789773 - 171789773(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs4473582	chr3:171755086 - 171755086(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs6801138	chr3:171745482 - 171745482(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs7635962	chr3:171742676 - 171742676(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs4894760	chr3:171734646 - 171734646(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs4894504	chr3:171734609 - 171734609(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs1882256	chr3:171733037 - 171733037(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs1882257	chr3:171732962 - 171732962(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs1921345	chr3:171732358 - 171732358(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs1921344	chr3:171732390 - 171732390(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs6445024	chr3:171730503 - 171730503(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs6773632	chr3:171731409 - 171731409(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs7638344	chr3:171729609 - 171729609(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs7616441	chr3:171729802 - 171729802(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs9879513	chr3:171729153 - 171729153(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs7638141	chr3:171729356 - 171729356(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs7631451	chr3:171726955 - 171726955(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs9831491	chr3:171727454 - 171727454(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs4131284	chr3:171725817 - 171725817(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs7631356	chr3:171726863 - 171726863(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs4894750	chr3:171724115 - 171724115(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs7647840	chr3:171724845 - 171724845(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs6764285	chr3:171723330 - 171723330(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs4894747	chr3:171723974 - 171723974(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs6445018	chr3:171721447 - 171721447(1)	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs6790634	chr3:171720879 - 171720879(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs9832431	chr3:171722108 - 171722108(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs9828579	chr3:171722020 - 171722020(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs6809647	chr3:171722666 - 171722666(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs9870809	chr3:171722268 - 171722268(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs6763933	chr3:171723011 - 171723011(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs6807121	chr3:171722733 - 171722733(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs7618276	chr3:171710646 - 171710646(1)	downstream_gene_variant; intron_variant; upstream_gene_variant
rs16856586	chr3:171718934 - 171718934(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs4894503	chr3:171716191 - 171716191(1)	intron_variant; non_coding_transcript_variant
rs12632647	chr3:171701419 - 171701419(1)	intron_variant; non_coding_transcript_variant
rs4894497	chr3:171702078 - 171702078(1)	intron_variant; non_coding_transcript_variant
rs6806023	chr3:171708339 - 171708339(1)	intron_variant; non_coding_transcript_variant
rs1869648	chr3:171708971 - 171708971(1)	downstream_gene_variant; intron_variant; upstream_gene_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 2)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 3	chr3:0-198295559	2 (0/2/0)
3q26	chr3:161000000-183000000	1 (0/0/1)

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

Gene relationship with SZ

Gene relationship with MDD

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Region: chr3:171600405..171810950 View in gBrowse