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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	8985
Gene name Gene Name - the full gene name approved by the HGNC.	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PLOD3
Synonyms (NCBI Gene) Gene synonyms aliases	BCARD, LH3
Chromosome Chromosome number	7
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	7q22.1
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene is a membrane-bound homodimeric enzyme that is localized to the cisternae of the rough endoplasmic reticulum. The enzyme (cofactors iron and ascorbate) catalyzes the hydroxylation of lysyl residues in collagen-like peptide

Show/Hide all(5)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121434414	T>C	Pathogenic	Missense variant, coding sequence variant
rs377320080	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs748105435	A>C	Likely-pathogenic	Stop gained, coding sequence variant
rs786205872	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs1562894320	G>A	Likely-pathogenic	Coding sequence variant, missense variant

Show/Hide all(92)

miRTarBase ID	miRNA	Experiments	Reference
MIRT000169	hsa-miR-21-5p	Luciferase reporter assay, Quantitative proteomic approach	19253296
MIRT002723	hsa-miR-124-3p	Microarray	15685193
MIRT002723	hsa-miR-124-3p	Proteomics;Microarray	18668037
MIRT002723	hsa-miR-124-3p	Microarray	15685193
MIRT036230	hsa-miR-320b	CLASH	23622248
MIRT1243042	hsa-miR-1200	CLIP-seq
MIRT1243043	hsa-miR-1207-5p	CLIP-seq
MIRT1243044	hsa-miR-124	CLIP-seq
MIRT1243045	hsa-miR-1271	CLIP-seq
MIRT1243046	hsa-miR-1273g	CLIP-seq
MIRT1243047	hsa-miR-1289	CLIP-seq
MIRT1243048	hsa-miR-140-5p	CLIP-seq
MIRT1243049	hsa-miR-182	CLIP-seq
MIRT1243050	hsa-miR-187	CLIP-seq
MIRT1243051	hsa-miR-2355-5p	CLIP-seq
MIRT1243052	hsa-miR-3186-3p	CLIP-seq
MIRT1243053	hsa-miR-3622a-5p	CLIP-seq
MIRT1243054	hsa-miR-3664-3p	CLIP-seq
MIRT1243055	hsa-miR-3672	CLIP-seq
MIRT1243056	hsa-miR-3689a-3p	CLIP-seq
MIRT1243057	hsa-miR-3689c	CLIP-seq
MIRT1243058	hsa-miR-4269	CLIP-seq
MIRT1243059	hsa-miR-4277	CLIP-seq
MIRT1243060	hsa-miR-4300	CLIP-seq
MIRT1243061	hsa-miR-431	CLIP-seq
MIRT1243062	hsa-miR-4313	CLIP-seq
MIRT1243063	hsa-miR-4324	CLIP-seq
MIRT1243064	hsa-miR-4436b-3p	CLIP-seq
MIRT1243065	hsa-miR-4464	CLIP-seq
MIRT1243066	hsa-miR-4514	CLIP-seq
MIRT1243067	hsa-miR-4640-5p	CLIP-seq
MIRT1243068	hsa-miR-4658	CLIP-seq
MIRT1243069	hsa-miR-4680-5p	CLIP-seq
MIRT1243070	hsa-miR-4692	CLIP-seq
MIRT1243071	hsa-miR-4706	CLIP-seq
MIRT1243072	hsa-miR-4711-3p	CLIP-seq
MIRT1243073	hsa-miR-4726-5p	CLIP-seq
MIRT1243074	hsa-miR-4736	CLIP-seq
MIRT1243075	hsa-miR-4742-5p	CLIP-seq
MIRT1243076	hsa-miR-4748	CLIP-seq
MIRT1243077	hsa-miR-4749-5p	CLIP-seq
MIRT1243078	hsa-miR-4755-3p	CLIP-seq
MIRT1243079	hsa-miR-4758-5p	CLIP-seq
MIRT1243080	hsa-miR-4761-5p	CLIP-seq
MIRT1243081	hsa-miR-4763-3p	CLIP-seq
MIRT1243082	hsa-miR-4795-5p	CLIP-seq
MIRT1243083	hsa-miR-506	CLIP-seq
MIRT1243084	hsa-miR-510	CLIP-seq
MIRT1243085	hsa-miR-516a-3p	CLIP-seq
MIRT1243086	hsa-miR-544b	CLIP-seq
MIRT1243087	hsa-miR-548an	CLIP-seq
MIRT1243088	hsa-miR-563	CLIP-seq
MIRT1243089	hsa-miR-635	CLIP-seq
MIRT1243090	hsa-miR-657	CLIP-seq
MIRT1243091	hsa-miR-759	CLIP-seq
MIRT1243092	hsa-miR-873	CLIP-seq
MIRT1243093	hsa-miR-920	CLIP-seq
MIRT1243094	hsa-miR-96	CLIP-seq
MIRT1243067	hsa-miR-4640-5p	CLIP-seq
MIRT1243073	hsa-miR-4726-5p	CLIP-seq
MIRT1243078	hsa-miR-4755-3p	CLIP-seq
MIRT2456707	hsa-miR-1915	CLIP-seq
MIRT1243062	hsa-miR-4313	CLIP-seq
MIRT1243067	hsa-miR-4640-5p	CLIP-seq
MIRT2456708	hsa-miR-4726-3p	CLIP-seq
MIRT1243073	hsa-miR-4726-5p	CLIP-seq
MIRT1243078	hsa-miR-4755-3p	CLIP-seq
MIRT1243052	hsa-miR-3186-3p	CLIP-seq
MIRT1243055	hsa-miR-3672	CLIP-seq
MIRT1243047	hsa-miR-1289	CLIP-seq
MIRT2688144	hsa-miR-146b-3p	CLIP-seq
MIRT2688145	hsa-miR-1914	CLIP-seq
MIRT1243051	hsa-miR-2355-5p	CLIP-seq
MIRT2688146	hsa-miR-3150a-3p	CLIP-seq
MIRT2688147	hsa-miR-3175	CLIP-seq
MIRT1243052	hsa-miR-3186-3p	CLIP-seq
MIRT1243053	hsa-miR-3622a-5p	CLIP-seq
MIRT1243054	hsa-miR-3664-3p	CLIP-seq
MIRT1243055	hsa-miR-3672	CLIP-seq
MIRT1243058	hsa-miR-4269	CLIP-seq
MIRT1243059	hsa-miR-4277	CLIP-seq
MIRT1243066	hsa-miR-4514	CLIP-seq
MIRT1243069	hsa-miR-4680-5p	CLIP-seq
MIRT1243070	hsa-miR-4692	CLIP-seq
MIRT1243071	hsa-miR-4706	CLIP-seq
MIRT1243075	hsa-miR-4742-5p	CLIP-seq
MIRT1243077	hsa-miR-4749-5p	CLIP-seq
MIRT1243082	hsa-miR-4795-5p	CLIP-seq
MIRT2688148	hsa-miR-491-5p	CLIP-seq
MIRT1243084	hsa-miR-510	CLIP-seq
MIRT1243092	hsa-miR-873	CLIP-seq
MIRT2688149	hsa-miR-939	CLIP-seq

Show/Hide all(57)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001701	Process	In utero embryonic development	IEA
GO:0001886	Process	Endothelial cell morphogenesis	IEA
GO:0003824	Function	Catalytic activity	IEA
GO:0005506	Function	Iron ion binding	EXP	30089812
GO:0005506	Function	Iron ion binding	IEA
GO:0005515	Function	Protein binding	IPI	16189514, 25416956, 25910212, 26028330, 29892012, 31515488, 32296183
GO:0005576	Component	Extracellular region	IEA
GO:0005615	Component	Extracellular space	IBA
GO:0005615	Component	Extracellular space	IEA
GO:0005615	Component	Extracellular space	ISS
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005783	Component	Endoplasmic reticulum	IDA	10934207
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005783	Component	Endoplasmic reticulum	TAS	9724729
GO:0005788	Component	Endoplasmic reticulum lumen	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0005791	Component	Rough endoplasmic reticulum	IEA
GO:0005794	Component	Golgi apparatus	IBA
GO:0005794	Component	Golgi apparatus	IDA	10934207, 27435297
GO:0005802	Component	Trans-Golgi network	IEA
GO:0006493	Process	Protein O-linked glycosylation	IMP	10934207
GO:0008104	Process	Intracellular protein localization	IEA
GO:0008475	Function	Procollagen-lysine 5-dioxygenase activity	IBA
GO:0008475	Function	Procollagen-lysine 5-dioxygenase activity	IDA	9582318, 9724729
GO:0008475	Function	Procollagen-lysine 5-dioxygenase activity	IEA
GO:0008475	Function	Procollagen-lysine 5-dioxygenase activity	IMP	10934207, 18298658
GO:0016020	Component	Membrane	IEA
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0016705	Function	Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0017185	Process	Peptidyl-lysine hydroxylation	IDA	9582318, 9724729
GO:0017185	Process	Peptidyl-lysine hydroxylation	IMP	10934207, 18298658
GO:0021915	Process	Neural tube development	IEA
GO:0030199	Process	Collagen fibril organization	IBA
GO:0030199	Process	Collagen fibril organization	IEA
GO:0030199	Process	Collagen fibril organization	TAS
GO:0031012	Component	Extracellular matrix	IBA
GO:0031418	Function	L-ascorbic acid binding	IEA
GO:0032963	Process	Collagen metabolic process	IEA
GO:0033823	Function	Procollagen glucosyltransferase activity	IBA
GO:0033823	Function	Procollagen glucosyltransferase activity	IEA
GO:0033823	Function	Procollagen glucosyltransferase activity	IMP	10934207, 18298658
GO:0036094	Function	Small molecule binding	EXP	30089812
GO:0042311	Process	Vasodilation	IEA
GO:0046872	Function	Metal ion binding	EXP	30089812
GO:0046872	Function	Metal ion binding	IEA
GO:0046947	Process	Hydroxylysine biosynthetic process	IEA
GO:0048730	Process	Epidermis morphogenesis	IEA
GO:0050211	Function	Procollagen galactosyltransferase activity	IEA
GO:0050211	Function	Procollagen galactosyltransferase activity	IMP	18298658
GO:0050211	Function	Procollagen galactosyltransferase activity	TAS
GO:0051213	Function	Dioxygenase activity	IEA
GO:0060425	Process	Lung morphogenesis	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867, 19199708
GO:0070831	Process	Basement membrane assembly	IEA

MIM	HGNC	e!Ensembl
603066	9083	ENSG00000106397

Protein

UniProt ID

O60568

Protein name

Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 [Includes: Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 (EC 1.14.11.4) (Lysyl hydroxylase 3) (LH3); Procollagen glycosyltransferase (EC 2.4.1.50) (EC 2.4.1.66) (Galactosylhydr

Protein function

Multifunctional enzyme that catalyzes a series of essential post-translational modifications on Lys residues in procollagen (PubMed:11956192, PubMed:12475640, PubMed:18298658, PubMed:18834968, PubMed:30089812). Plays a redundant role in catalyzi

PDB

6FXK , 6FXM , 6FXR , 6FXT , 6FXX , 6FXY , 6TE3 , 6TEC , 6TES , 6TEU , 6TEX , 6TEZ , 6WFV , 8ONE

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03171	2OG-FeII_Oxy	648 → 738	2OG-Fe(II) oxygenase superfamily	Domain

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous (PubMed:9724729). Detected in heart, placenta and pancreas and at lower levels in lung, liver and skeletal muscle (PubMed:9582318, PubMed:9724729). {ECO:0000269|PubMed:9582318, ECO:0000269|PubMed:9724729}.

Sequence

MTSSGPGPRFLLLLPLLLPPAASASDRPRGRDPVNPEKLLVITVATAETEGYLRFLRSAE
FFNYTVRTLGLGEEWRGGDVARTVGGGQKVRWLKKEMEKYADREDMIIMFVDSYDVILAG
SPTELLKKFVQSGSRLLFSAESFCWPEWGLAEQYPEVGTGKRFLNSGGFIGFATTIHQIV
RQWKYKDDDDDQLFYTRLYLDPGLREKLSLNLDHKSRIFQNLNGALDEVVLKFDRNRVRI
RNVAYDTLPIVVHGNGPTKLQLNYLGNYVPNGWTPEGGCGFCNQDRRTLPGGQPPPRVFL
AVFVEQPTPFLPRFLQRLLLLDYPPDRVTLFLHNNEVFHEPHIADSWPQLQDHFSAVKLV
GPEEALSPGEARDMAMDLCRQDPECEFYFSLDADAVLTNLQTLRILIEENRKVIAPMLSR
HGKLWSNFWGALSPDEYYARSEDYVELVQRKRVGVWNVPYISQAYVIRGDTLRMELPQRD
VFSGSDTDPDMAFCKSFRDKGIFLHLSNQHEFGRLLATSRYDTEHLHPDLWQIFDNPVDW
KEQYIHENYSRALEGEGIVEQPCPDVYWFPLLSEQMCDELVAEMEHYGQWSGGRHEDSRL
AGGYENVPTVDIHMKQVGYEDQWLQLLRTYVGPMTESLFPGYHTKARAVMNFVVRYRPDE
QPSLRPHHDSSTFTLNVALNHKGLDYEGGGCRFLRYDCVISSPRKGWALLHPGRLTHYHE
GLPTTWGTRYIMVSFVDP

Sequence length

738

Interactions

View interactions

	KEGG		Reactome
	Lysine degradation Other types of O-glycan biosynthesis Metabolic pathways		Collagen biosynthesis and modifying enzymes

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Bone Fragility With Contractures, Arterial Rupture, And Deafness	bone fragility with contractures, arterial rupture, and deafness	rs786205872, rs748105435, rs1562894320	N/A

Show/Hide Text Mining Associations (33)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Blister	Associate	30463024
Carcinogenesis	Associate	34576068
Carcinoma Hepatocellular	Associate	29397868, 31811111
Carcinoma Non Small Cell Lung	Associate	35039611
Carcinoma Renal Cell	Associate	31446433, 33828127
Collagen Diseases	Associate	36403858
Colonic Neoplasms	Stimulate	34239923
Colonic Neoplasms	Associate	34576068
Colorectal Neoplasms	Associate	34646265
Connective Tissue Diseases	Associate	30463024, 36403858
Disease	Associate	30721533
Ectodermal Dysplasia Skin Fragility Syndrome	Associate	30463024
Endometrial Neoplasms	Associate	34576068
Epidermolysis Bullosa	Associate	30463024
Epidermolysis Bullosa Dystrophica	Inhibit	26380979
Epidermolysis Bullosa Dystrophica	Associate	30463024
Fibrosis	Associate	31811111
Glioblastoma	Associate	34576068, 35788194
Intracranial Aneurysm	Associate	34668355
Intracranial Hemorrhages	Associate	36403858
Kidney Neoplasms	Stimulate	33828127
Lung Neoplasms	Associate	35039611
Lymphoma	Associate	26700650
Neoplasms	Associate	31446433, 34121340, 34239923, 34304093, 34576068, 34646265, 35641481, 39174928
Neoplasms	Inhibit	35039611
Osteogenesis Imperfecta	Associate	30721533
Osteogenesis imperfecta type 1A	Associate	34668355
Osteogenesis Imperfecta Type VII	Associate	30463024
Prostatic Neoplasms	Associate	39174928
Sarcoma	Associate	34576068
Soft Tissue Injuries	Associate	35627171
Stomach Neoplasms	Associate	22559327, 30804389, 34576068
Uterine Cervical Neoplasms	Associate	40640353

PLOD3 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 3)