Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	23646
Gene name	Phospholipase D family member 3
Gene symbol	PLD3
Synonyms (NCBI Gene)	AD19HU-K4HUK4SCA46
Chromosome	19
Chromosome location	19q13.2
Summary	This gene encodes a member of the phospholipase D (PLD) family of enzymes that catalyze the hydrolysis of membrane phospholipids. The encoded protein is a single-pass type II membrane protein and contains two PLD phosphodiesterase domains. This protein in

163

Show/Hide all (163)

miRTarBase ID	miRNA	Experiments	Reference
MIRT017099	hsa-miR-335-5p	Microarray	18185580
MIRT051205	hsa-miR-16-5p	CLASH	23622248
MIRT044846	hsa-miR-320a	CLASH	23622248
MIRT044846	hsa-miR-320a	CLASH	23622248
MIRT042303	hsa-miR-484	CLASH	23622248
MIRT037314	hsa-miR-877-5p	CLASH	23622248
MIRT1240283	hsa-let-7a	CLIP-seq
MIRT1240284	hsa-let-7b	CLIP-seq
MIRT1240285	hsa-let-7c	CLIP-seq
MIRT1240286	hsa-let-7d	CLIP-seq
MIRT1240287	hsa-let-7e	CLIP-seq
MIRT1240288	hsa-let-7f	CLIP-seq
MIRT1240289	hsa-let-7g	CLIP-seq
MIRT1240290	hsa-let-7i	CLIP-seq
MIRT1240291	hsa-miR-129-5p	CLIP-seq
MIRT1240292	hsa-miR-146b-3p	CLIP-seq
MIRT1240293	hsa-miR-3157-3p	CLIP-seq
MIRT1240294	hsa-miR-3173-5p	CLIP-seq
MIRT1240295	hsa-miR-3927	CLIP-seq
MIRT1240296	hsa-miR-3978	CLIP-seq
MIRT1240297	hsa-miR-4281	CLIP-seq
MIRT1240298	hsa-miR-4308	CLIP-seq
MIRT1240299	hsa-miR-4449	CLIP-seq
MIRT1240300	hsa-miR-4532	CLIP-seq
MIRT1240301	hsa-miR-4731-5p	CLIP-seq
MIRT1240302	hsa-miR-4796-3p	CLIP-seq
MIRT1240303	hsa-miR-874	CLIP-seq
MIRT1240304	hsa-miR-875-3p	CLIP-seq
MIRT1240305	hsa-miR-98	CLIP-seq
MIRT1552341	hsa-miR-1324	CLIP-seq
MIRT1552342	hsa-miR-185	CLIP-seq
MIRT1552343	hsa-miR-1909	CLIP-seq
MIRT1552344	hsa-miR-3166	CLIP-seq
MIRT1552345	hsa-miR-3675-5p	CLIP-seq
MIRT1552346	hsa-miR-486-3p	CLIP-seq
MIRT1922316	hsa-miR-4640-5p	CLIP-seq
MIRT1922317	hsa-miR-4726-5p	CLIP-seq
MIRT1240283	hsa-let-7a	CLIP-seq
MIRT1240284	hsa-let-7b	CLIP-seq
MIRT1240285	hsa-let-7c	CLIP-seq
MIRT1240286	hsa-let-7d	CLIP-seq
MIRT1240287	hsa-let-7e	CLIP-seq
MIRT1240288	hsa-let-7f	CLIP-seq
MIRT1240289	hsa-let-7g	CLIP-seq
MIRT1240290	hsa-let-7i	CLIP-seq
MIRT1240295	hsa-miR-3927	CLIP-seq
MIRT1240305	hsa-miR-98	CLIP-seq
MIRT1240283	hsa-let-7a	CLIP-seq
MIRT1240284	hsa-let-7b	CLIP-seq
MIRT1240285	hsa-let-7c	CLIP-seq
MIRT1240286	hsa-let-7d	CLIP-seq
MIRT1240287	hsa-let-7e	CLIP-seq
MIRT1240288	hsa-let-7f	CLIP-seq
MIRT1240289	hsa-let-7g	CLIP-seq
MIRT1240290	hsa-let-7i	CLIP-seq
MIRT1552342	hsa-miR-185	CLIP-seq
MIRT1552343	hsa-miR-1909	CLIP-seq
MIRT1240295	hsa-miR-3927	CLIP-seq
MIRT1240305	hsa-miR-98	CLIP-seq
MIRT1240283	hsa-let-7a	CLIP-seq
MIRT1240284	hsa-let-7b	CLIP-seq
MIRT1240285	hsa-let-7c	CLIP-seq
MIRT1240286	hsa-let-7d	CLIP-seq
MIRT1240287	hsa-let-7e	CLIP-seq
MIRT1240288	hsa-let-7f	CLIP-seq
MIRT1240289	hsa-let-7g	CLIP-seq
MIRT1240290	hsa-let-7i	CLIP-seq
MIRT1240295	hsa-miR-3927	CLIP-seq
MIRT1240305	hsa-miR-98	CLIP-seq
MIRT2439541	hsa-miR-1243	CLIP-seq
MIRT2439542	hsa-miR-1245b-5p	CLIP-seq
MIRT2439543	hsa-miR-1470	CLIP-seq
MIRT2439544	hsa-miR-1912	CLIP-seq
MIRT2439545	hsa-miR-214	CLIP-seq
MIRT2439546	hsa-miR-3142	CLIP-seq
MIRT2439547	hsa-miR-3194-3p	CLIP-seq
MIRT2439548	hsa-miR-338-3p	CLIP-seq
MIRT2439549	hsa-miR-361-3p	CLIP-seq
MIRT2439550	hsa-miR-3619-5p	CLIP-seq
MIRT2439551	hsa-miR-3663-3p	CLIP-seq
MIRT1240296	hsa-miR-3978	CLIP-seq
MIRT2439552	hsa-miR-4267	CLIP-seq
MIRT1240298	hsa-miR-4308	CLIP-seq
MIRT2439553	hsa-miR-4530	CLIP-seq
MIRT1922316	hsa-miR-4640-5p	CLIP-seq
MIRT2439554	hsa-miR-4656	CLIP-seq
MIRT2439555	hsa-miR-4667-3p	CLIP-seq
MIRT2439556	hsa-miR-4690-5p	CLIP-seq
MIRT1922317	hsa-miR-4726-5p	CLIP-seq
MIRT1240301	hsa-miR-4731-5p	CLIP-seq
MIRT2439557	hsa-miR-4755-3p	CLIP-seq
MIRT2439558	hsa-miR-4763-5p	CLIP-seq
MIRT1240302	hsa-miR-4796-3p	CLIP-seq
MIRT2439559	hsa-miR-501-3p	CLIP-seq
MIRT2439560	hsa-miR-502-3p	CLIP-seq
MIRT2439561	hsa-miR-541	CLIP-seq
MIRT2439562	hsa-miR-654-5p	CLIP-seq
MIRT2439563	hsa-miR-761	CLIP-seq
MIRT1240304	hsa-miR-875-3p	CLIP-seq
MIRT2439542	hsa-miR-1245b-5p	CLIP-seq
MIRT1240291	hsa-miR-129-5p	CLIP-seq
MIRT1240292	hsa-miR-146b-3p	CLIP-seq
MIRT2439544	hsa-miR-1912	CLIP-seq
MIRT2439545	hsa-miR-214	CLIP-seq
MIRT2595343	hsa-miR-296-5p	CLIP-seq
MIRT2439546	hsa-miR-3142	CLIP-seq
MIRT1240293	hsa-miR-3157-3p	CLIP-seq
MIRT1240294	hsa-miR-3173-5p	CLIP-seq
MIRT2439548	hsa-miR-338-3p	CLIP-seq
MIRT2439550	hsa-miR-3619-5p	CLIP-seq
MIRT2439551	hsa-miR-3663-3p	CLIP-seq
MIRT1240296	hsa-miR-3978	CLIP-seq
MIRT2595344	hsa-miR-4292	CLIP-seq
MIRT1240298	hsa-miR-4308	CLIP-seq
MIRT2439553	hsa-miR-4530	CLIP-seq
MIRT1922316	hsa-miR-4640-5p	CLIP-seq
MIRT2439556	hsa-miR-4690-5p	CLIP-seq
MIRT2595345	hsa-miR-4699-3p	CLIP-seq
MIRT1922317	hsa-miR-4726-5p	CLIP-seq
MIRT2439557	hsa-miR-4755-3p	CLIP-seq
MIRT2439558	hsa-miR-4763-5p	CLIP-seq
MIRT2595346	hsa-miR-4795-3p	CLIP-seq
MIRT1240302	hsa-miR-4796-3p	CLIP-seq
MIRT2439559	hsa-miR-501-3p	CLIP-seq
MIRT2439560	hsa-miR-502-3p	CLIP-seq
MIRT2439561	hsa-miR-541	CLIP-seq
MIRT2439562	hsa-miR-654-5p	CLIP-seq
MIRT2439563	hsa-miR-761	CLIP-seq
MIRT1240303	hsa-miR-874	CLIP-seq
MIRT1240304	hsa-miR-875-3p	CLIP-seq
MIRT2595347	hsa-miR-9	CLIP-seq
MIRT1922316	hsa-miR-4640-5p	CLIP-seq
MIRT1922317	hsa-miR-4726-5p	CLIP-seq
MIRT2439541	hsa-miR-1243	CLIP-seq
MIRT2439542	hsa-miR-1245b-5p	CLIP-seq
MIRT1240291	hsa-miR-129-5p	CLIP-seq
MIRT1240292	hsa-miR-146b-3p	CLIP-seq
MIRT2439544	hsa-miR-1912	CLIP-seq
MIRT2439545	hsa-miR-214	CLIP-seq
MIRT2595343	hsa-miR-296-5p	CLIP-seq
MIRT2439546	hsa-miR-3142	CLIP-seq
MIRT1240293	hsa-miR-3157-3p	CLIP-seq
MIRT1240294	hsa-miR-3173-5p	CLIP-seq
MIRT2439548	hsa-miR-338-3p	CLIP-seq
MIRT2439550	hsa-miR-3619-5p	CLIP-seq
MIRT2439551	hsa-miR-3663-3p	CLIP-seq
MIRT1240296	hsa-miR-3978	CLIP-seq
MIRT2595344	hsa-miR-4292	CLIP-seq
MIRT1240298	hsa-miR-4308	CLIP-seq
MIRT2439553	hsa-miR-4530	CLIP-seq
MIRT1922316	hsa-miR-4640-5p	CLIP-seq
MIRT2439556	hsa-miR-4690-5p	CLIP-seq
MIRT2595345	hsa-miR-4699-3p	CLIP-seq
MIRT1922317	hsa-miR-4726-5p	CLIP-seq
MIRT2439557	hsa-miR-4755-3p	CLIP-seq
MIRT2439558	hsa-miR-4763-5p	CLIP-seq
MIRT2595346	hsa-miR-4795-3p	CLIP-seq
MIRT1240302	hsa-miR-4796-3p	CLIP-seq
MIRT2439561	hsa-miR-541	CLIP-seq
MIRT2439562	hsa-miR-654-5p	CLIP-seq
MIRT2439563	hsa-miR-761	CLIP-seq
MIRT1240303	hsa-miR-874	CLIP-seq
MIRT1240304	hsa-miR-875-3p	CLIP-seq

Show/Hide all (34)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IDA	29368044
GO:0000139	Component	Golgi membrane	IEA
GO:0002376	Process	Immune system process	IEA
GO:0003824	Function	Catalytic activity	IEA
GO:0004518	Function	Nuclease activity	IEA
GO:0004527	Function	Exonuclease activity	IEA
GO:0004630	Function	Phospholipase D activity	TAS	9140189
GO:0005515	Function	Protein binding	IPI	20195357, 24336208, 32296183
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005768	Component	Endosome	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	15794758, 22428023
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005794	Component	Golgi apparatus	IEA
GO:0006259	Process	DNA metabolic process	IEA
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006954	Process	Inflammatory response	IEA
GO:0010008	Component	Endosome membrane	IEA
GO:0012505	Component	Endomembrane system	IBA
GO:0014902	Process	Myotube differentiation	IDA	22428023
GO:0016020	Component	Membrane	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0031901	Component	Early endosome membrane	IDA	29386126
GO:0031901	Component	Early endosome membrane	IEA
GO:0031902	Component	Late endosome membrane	IDA	29386126
GO:0031902	Component	Late endosome membrane	IEA
GO:0043202	Component	Lysosomal lumen	IDA	30312375
GO:0043202	Component	Lysosomal lumen	IEA
GO:0045145	Function	Single-stranded DNA 5'-3' DNA exonuclease activity	IDA	30312375
GO:0045145	Function	Single-stranded DNA 5'-3' DNA exonuclease activity	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867, 19199708, 23533145
GO:1900015	Process	Regulation of cytokine production involved in inflammatory response	IEA
GO:1900015	Process	Regulation of cytokine production involved in inflammatory response	ISS

MIM	HGNC	e!Ensembl
615698	17158	ENSG00000105223

Q8IV08

Protein name

5'-3' exonuclease PLD3 (EC 3.1.16.1) ((S,S)-bis(monoacylglycero)phosphate synthase PLD3) (EC 3.1.4.-) (HindIII K4L homolog) (Hu-K4) (Phospholipase D3)

Protein function

5'->3' exonuclease that hydrolyzes the phosphodiester bond of single-stranded DNA (ssDNA) and RNA molecules to form nucleoside 3'-monophosphates and 5'-end 5'-hydroxy deoxyribonucleotide/ribonucleotide fragments (PubMed:30111894, PubMed:30312375

PDB

8Q1K , 8Q1X , 8S86 , 8V5T

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13918	PLDc_3	226 → 403	PLD-like domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed. In the brain, high levels of expression are detected in the frontal, temporal and occipital cortices and hippocampus. Expressed at low level in corpus callosum. Expressed in plasmacytoid dendritic cells and monocytes

Sequence

MKPKLMYQELKVPAEEPANELPMNEIEAWKAAEKKARWVLLVLILAVVGFGALMTQLFLW
EYGDLHLFGPNQRPAPCYDPCEAVLVESIPEGLDFPNASTGNPSTSQAWLGLLAGAHSSL
DIASFYWTLTNNDTHTQEPSAQQGEEVLRQLQTLAPKGVNVRIAVSKPSGPQPQADLQAL
LQSGAQVRMVDMQKLTHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNCSCL
ARDLTKIFEAYWFLGQAGSSIPSTWPRFYDTRYNQETPMEICLNGTPALAYLASAPPPLC
PSGRTPDLKALLNVVDNARSFIYVAVMNYLPTLEFSHPHRFWPAIDDGLRRATYERGVKV
RLLISCWGHSEPSMRAFLLSLAALRDNHTHSDIQVKLFVVPADEAQARIPYARVNHNKYM
VTERATYIGTSNWSGNYFTETAGTSLLVTQNGRGGLRSQLEAIFLRDWDSPYSHDLDTSA
DSVGNACRLL

Sequence length

490

Interactions

View interactions

	KEGG		Reactome
	Glycerophospholipid metabolism Ether lipid metabolism Metabolic pathways		Role of phospholipids in phagocytosis

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Spinocerebellar ataxia 46	Pathogenic	rs1317590341	RCV000990215

Show/Hide Unknown Diseases (11)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Alzheimer disease 19	Benign; Likely benign	rs145999145	RCV000106322
Cervical cancer	Likely benign	rs200368701	RCV005935061
Familial cancer of breast	Benign	rs3745198, rs3745199	RCV005926982 RCV005928578
Gastric cancer	Uncertain significance	rs752779193	RCV005932419
Hepatocellular carcinoma	Benign	rs3745198, rs3745199	RCV005926983 RCV005928579
Lung cancer	Uncertain significance	rs747934600	RCV005932085
Malignant tumor of urinary bladder	Uncertain significance	rs762406245	RCV005931457
Ovarian serous cystadenocarcinoma	Likely benign	rs200120635	RCV005932065
PLD3-related disorder	Likely benign; Benign; Uncertain significance	rs183821939, rs142070038, rs146083475, rs760407817, rs2079033716, rs200529365, rs139860064	RCV003963353 RCV003961188 RCV003943612 RCV003943889 RCV003939604 RCV003969487 RCV003903314
Thyroid cancer, nonmedullary, 1	Uncertain significance; Benign	rs747934600, rs3745199	RCV005932084 RCV005928580
Uterine corpus endometrial carcinoma	Likely benign	rs200120635	RCV005932066

Show/Hide Text Mining Associations (13)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Alzheimer Disease	Associate	24336208, 26402410, 26411346, 28199971, 29386126, 29395285, 29750252, 30208929, 32941707, 33288674, 36516243, 37925455
Alzheimer Disease	Inhibit	30208929
Breast Neoplasms	Inhibit	37978168
Carcinoma Pancreatic Ductal	Associate	35255936
Cognition Disorders	Associate	28199971
COVID 19	Associate	33971585
Dementia	Associate	29750252, 31836585
Infections	Associate	10074127
Lupus Erythematosus Systemic	Associate	33288674
Neoplasms	Associate	37978168
Otitis Media	Associate	27632927
Parkinson Disease	Associate	32941707
Spinocerebellar Ataxias	Associate	33288674

PLD3 (phospholipase D family member 3)