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

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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

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Spinocerebellar ataxia 46	Pathogenic	rs1317590341	RCV000990215	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (17)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Alzheimer disease 19	Benign; Likely benign	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Cervical cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHARCOT-MARIE-TOOTH DISEASE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHARCOT-MARIE-TOOTH DISEASE TYPE 4	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHARCOT-MARIE-TOOTH DISEASE, DEMYELINATING, TYPE 4F	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY MOTOR AND SENSORY NEUROPATHY TYPE 5	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY MOTOR AND SENSORY NEUROPATHY TYPE I	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PLD3-related disorder	Likely benign; Benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA TYPE 46	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (25)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Alzheimer Disease	Alzheimer disease	Pubtator	24336208, 26402410, 26411346, 28199971, 29386126, 29395285, 29750252, 30208929, 32941707, 33288674, 36516243, 37925455	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Alzheimer disease	Pubtator	30208929	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Alzheimer Disease, Early Onset	Alzheimer disease	BEFREE	26411346		★★★★★ ★☆☆☆☆ Found in Text Mining only
Alzheimer Disease, Late Onset	Alzheimer disease	BEFREE	24336208, 24935720, 24951455, 26411346, 29386126, 30208929, 31121321, 31159836		★★★★★ ★☆☆☆☆ Found in Text Mining only
Amyloidosis	Amyloidosis	BEFREE	26402410, 29704008, 31121321		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	37978168	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	35255936	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognition disorder	Pubtator	28199971	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Conjunctivitis	Conjunctivitis	BEFREE	2846769		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dementia	Dementia	Pubtator	29750252, 31836585	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dermatitis, Atopic	Dermatitis	BEFREE	31260080		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Eczema	Eczema	BEFREE	31260080		★★★★★ ★☆☆☆☆ Found in Text Mining only
Henoch-Schoenlein Purpura	Henoch-Schonlein Nephritis	BEFREE	29847346		★★★★★ ★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	31121321		★★★★★ ★☆☆☆☆ Found in Text Mining only
Keratoconjunctivitis	Keratoconjunctivitis	BEFREE	11322419		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus Systemic	Systemic lupus erythematosus	Pubtator	33288674	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Mild cognitive disorder	Cognitive disorder	BEFREE	30103332		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	Pubtator	32941707	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	BEFREE	30111894		★★★★★ ★☆☆☆☆ Found in Text Mining only
SPINOCEREBELLAR ATAXIA 46	Spinocerebellar Ataxia	UNIPROT_DG	29053796, 30312375		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spinocerebellar Ataxias	Spinocerebellar ataxia	Pubtator	33288674	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Systemic Scleroderma	Scleroderma	BEFREE	30111894		★★★★★ ★☆☆☆☆ Found in Text Mining only

PLD3 (phospholipase D family member 3)