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
rac1Pathway	Rac 1 cell motility signaling pathway	6
cb1rPathway	Metabolism of Anandamide, an Endogenous Cannabinoid	1
rasPathway	Ras Signaling Pathway	5

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

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

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