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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	5352
Gene name	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2
Gene symbol	PLOD2
Synonyms (NCBI Gene)	BRKS2LH2TLH
Chromosome	3
Chromosome location	3q24
Summary	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 (10)

SNP ID	Visualize variation	Clinical significance	Consequence
rs115199093	A>G	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, missense variant, coding sequence variant
rs121434459	G>A	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs121434460	C>A	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs121434461	C>T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs145809663	T>C	Conflicting-interpretations-of-pathogenicity, benign	Missense variant, coding sequence variant, non coding transcript variant
rs749709000	G>-,GG	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant, intron variant
rs778360818	C>A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs893004444	T>C	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs1057524250	A>G	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1057524251	A>G	Pathogenic	Splice donor variant

112

Show/Hide all (112)

miRTarBase ID	miRNA	Experiments	Reference
MIRT024186	hsa-miR-221-3p	Sequencing	20371350
MIRT027724	hsa-miR-98-5p	Microarray	19088304
MIRT029832	hsa-miR-26b-5p	Microarray	19088304
MIRT047089	hsa-miR-183-5p	CLASH	23622248
MIRT040384	hsa-miR-615-3p	CLASH	23622248
MIRT039306	hsa-miR-425-5p	CLASH	23622248
MIRT052752	hsa-miR-1260b	CLASH	23622248
MIRT439946	hsa-miR-136-5p	HITS-CLIP	24374217
MIRT439946	hsa-miR-136-5p	HITS-CLIP	24374217
MIRT029832	hsa-miR-26b-5p	Luciferase reporter assay	27310702
MIRT029832	hsa-miR-26b-5p	Luciferase reporter assay	27310702
MIRT029832	hsa-miR-26b-5p	Luciferase reporter assay	27310702
MIRT029832	hsa-miR-26b-5p	Luciferase reporter assay	27310702
MIRT1243030	hsa-miR-1197	CLIP-seq
MIRT1243031	hsa-miR-4474-5p	CLIP-seq
MIRT1243032	hsa-miR-4477b	CLIP-seq
MIRT1243033	hsa-miR-548ac	CLIP-seq
MIRT1243034	hsa-miR-548d-3p	CLIP-seq
MIRT1243035	hsa-miR-548z	CLIP-seq
MIRT1243036	hsa-miR-649	CLIP-seq
MIRT1243037	hsa-miR-3685	CLIP-seq
MIRT1243038	hsa-miR-384	CLIP-seq
MIRT1243039	hsa-miR-4720-3p	CLIP-seq
MIRT1243040	hsa-miR-4804-3p	CLIP-seq
MIRT1243041	hsa-miR-889	CLIP-seq
MIRT1552359	hsa-miR-1297	CLIP-seq
MIRT1552360	hsa-miR-1305	CLIP-seq
MIRT1552361	hsa-miR-2278	CLIP-seq
MIRT1552362	hsa-miR-24	CLIP-seq
MIRT1552363	hsa-miR-26a	CLIP-seq
MIRT1552364	hsa-miR-26b	CLIP-seq
MIRT1552365	hsa-miR-3065-5p	CLIP-seq
MIRT1552366	hsa-miR-3136-3p	CLIP-seq
MIRT1552367	hsa-miR-3145-3p	CLIP-seq
MIRT1552368	hsa-miR-3166	CLIP-seq
MIRT1552369	hsa-miR-323-3p	CLIP-seq
MIRT1552370	hsa-miR-328	CLIP-seq
MIRT1552371	hsa-miR-338-5p	CLIP-seq
MIRT1552372	hsa-miR-3609	CLIP-seq
MIRT1552373	hsa-miR-3653	CLIP-seq
MIRT1552374	hsa-miR-3658	CLIP-seq
MIRT1552375	hsa-miR-382	CLIP-seq
MIRT1552376	hsa-miR-4436b-5p	CLIP-seq
MIRT1552377	hsa-miR-4465	CLIP-seq
MIRT1552378	hsa-miR-4468	CLIP-seq
MIRT1243032	hsa-miR-4477b	CLIP-seq
MIRT1552379	hsa-miR-4670-3p	CLIP-seq
MIRT1552380	hsa-miR-4714-3p	CLIP-seq
MIRT1243039	hsa-miR-4720-3p	CLIP-seq
MIRT1243040	hsa-miR-4804-3p	CLIP-seq
MIRT1552381	hsa-miR-498	CLIP-seq
MIRT1552382	hsa-miR-520g	CLIP-seq
MIRT1552383	hsa-miR-520h	CLIP-seq
MIRT1243033	hsa-miR-548ac	CLIP-seq
MIRT1552384	hsa-miR-548ae	CLIP-seq
MIRT1552385	hsa-miR-548ah	CLIP-seq
MIRT1552386	hsa-miR-548aj	CLIP-seq
MIRT1552387	hsa-miR-548am	CLIP-seq
MIRT1243034	hsa-miR-548d-3p	CLIP-seq
MIRT1552388	hsa-miR-548x	CLIP-seq
MIRT1243035	hsa-miR-548z	CLIP-seq
MIRT1243041	hsa-miR-889	CLIP-seq
MIRT2071826	hsa-miR-3163	CLIP-seq
MIRT2071827	hsa-miR-3978	CLIP-seq
MIRT1552373	hsa-miR-3653	CLIP-seq
MIRT1552374	hsa-miR-3658	CLIP-seq
MIRT1552359	hsa-miR-1297	CLIP-seq
MIRT1552360	hsa-miR-1305	CLIP-seq
MIRT1552363	hsa-miR-26a	CLIP-seq
MIRT1552364	hsa-miR-26b	CLIP-seq
MIRT1552373	hsa-miR-3653	CLIP-seq
MIRT1552374	hsa-miR-3658	CLIP-seq
MIRT1552377	hsa-miR-4465	CLIP-seq
MIRT1552381	hsa-miR-498	CLIP-seq
MIRT2595762	hsa-miR-200b	CLIP-seq
MIRT2595763	hsa-miR-200c	CLIP-seq
MIRT2595764	hsa-miR-3117-5p	CLIP-seq
MIRT2595765	hsa-miR-3161	CLIP-seq
MIRT1552373	hsa-miR-3653	CLIP-seq
MIRT1552374	hsa-miR-3658	CLIP-seq
MIRT1243037	hsa-miR-3685	CLIP-seq
MIRT2595766	hsa-miR-3688-3p	CLIP-seq
MIRT2595767	hsa-miR-369-3p	CLIP-seq
MIRT1243038	hsa-miR-384	CLIP-seq
MIRT2071827	hsa-miR-3978	CLIP-seq
MIRT2595768	hsa-miR-429	CLIP-seq
MIRT1552376	hsa-miR-4436b-5p	CLIP-seq
MIRT2595769	hsa-miR-4694-3p	CLIP-seq
MIRT2595770	hsa-miR-4699-5p	CLIP-seq
MIRT1243039	hsa-miR-4720-3p	CLIP-seq
MIRT1243040	hsa-miR-4804-3p	CLIP-seq
MIRT2595771	hsa-miR-7	CLIP-seq
MIRT1243041	hsa-miR-889	CLIP-seq
MIRT2595762	hsa-miR-200b	CLIP-seq
MIRT2595763	hsa-miR-200c	CLIP-seq
MIRT2595764	hsa-miR-3117-5p	CLIP-seq
MIRT2595765	hsa-miR-3161	CLIP-seq
MIRT1552373	hsa-miR-3653	CLIP-seq
MIRT1552374	hsa-miR-3658	CLIP-seq
MIRT1243037	hsa-miR-3685	CLIP-seq
MIRT2595766	hsa-miR-3688-3p	CLIP-seq
MIRT2595767	hsa-miR-369-3p	CLIP-seq
MIRT1243038	hsa-miR-384	CLIP-seq
MIRT2071827	hsa-miR-3978	CLIP-seq
MIRT2595768	hsa-miR-429	CLIP-seq
MIRT1552376	hsa-miR-4436b-5p	CLIP-seq
MIRT2595769	hsa-miR-4694-3p	CLIP-seq
MIRT2595770	hsa-miR-4699-5p	CLIP-seq
MIRT1243039	hsa-miR-4720-3p	CLIP-seq
MIRT1243040	hsa-miR-4804-3p	CLIP-seq
MIRT2595771	hsa-miR-7	CLIP-seq
MIRT1243041	hsa-miR-889	CLIP-seq

Show/Hide all (29)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001666	Process	Response to hypoxia	IEP	15174142
GO:0005506	Function	Iron ion binding	IEA
GO:0005615	Component	Extracellular space	IBA
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005783	Component	Endoplasmic reticulum	TAS	9054364
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0005794	Component	Golgi apparatus	IBA
GO:0006493	Process	Protein O-linked glycosylation	IDA	10934207
GO:0008475	Function	Procollagen-lysine 5-dioxygenase activity	IBA
GO:0008475	Function	Procollagen-lysine 5-dioxygenase activity	IDA	10934207
GO:0008475	Function	Procollagen-lysine 5-dioxygenase activity	IEA
GO:0008475	Function	Procollagen-lysine 5-dioxygenase activity	ISS	9582318
GO:0008475	Function	Procollagen-lysine 5-dioxygenase activity	TAS	9054364
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:0017185	Process	Peptidyl-lysine hydroxylation	IDA	10934207
GO:0017185	Process	Peptidyl-lysine hydroxylation	ISS	9582318
GO:0030199	Process	Collagen fibril organization	IBA
GO:0030867	Component	Rough endoplasmic reticulum membrane	IEA
GO:0031012	Component	Extracellular matrix	IBA
GO:0031418	Function	L-ascorbic acid binding	IEA
GO:0033823	Function	Procollagen glucosyltransferase activity	IDA	10934207
GO:0036211	Process	Protein modification process	TAS	9054364
GO:0046872	Function	Metal ion binding	IEA
GO:0046947	Process	Hydroxylysine biosynthetic process	IDA	10934207
GO:0051213	Function	Dioxygenase activity	IEA
GO:0070062	Component	Extracellular exosome	HDA	19199708

MIM	HGNC	e!Ensembl
601865	9082	ENSG00000152952

O00469

Protein name

Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 (EC 1.14.11.4) (Lysyl hydroxylase 2) (LH2)

Protein function

Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links. {ECO:0000250|UniProtKB

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03171	2OG-FeII_Oxy	645 → 737	2OG-Fe(II) oxygenase superfamily	Domain

Tissue specificity

TISSUE SPECIFICITY: Highly expressed in pancreas and muscle. Isoform 1 and isoform 2 are expressed in the majority of the examined cell types. Isoform 2 is specifically expressed in skin, lung, dura and aorta. {ECO:0000269|PubMed:10372558}.

Sequence

MGGCTVKPQLLLLALVLHPWNPCLGADSEKPSSIPTDKLLVITVATKESDGFHRFMQSAK
YFNYTVKVLGQGEEWRGGDGINSIGGGQKVRLMKEVMEHYADQDDLVVMFTECFDVIFAG
GPEEVLKKFQKANHKVVFAADGILWPDKRLADKYPVVHIGKRYLNSGGFIGYAPYVNRIV
QQWNLQDNDDDQLFYTKVYIDPLKREAINITLDHKCKIFQTLNGAVDEVVLKFENGKARA
KNTFYETLPVAINGNGPTKILLNYFGNYVPNSWTQDNGCTLCEFDTVDLSAVDVHPNVSI
GVFIEQPTPFLPRFLDILLTLDYPKEALKLFIHNKEVYHEKDIKVFFDKAKHEIKTIKIV
GPEENLSQAEARNMGMDFCRQDEKCDYYFSVDADVVLTNPRTLKILIEQNRKIIAPLVTR
HGKLWSNFWGALSPDGYYARSEDYVDIVQGNRVGVWNVPYMANVYLIKGKTLRSEMNERN
YFVRDKLDPDMALCRNAREMGVFMYISNRHEFGRLLSTANYNTSHYNNDLWQIFENPVDW
KEKYINRDYSKIFTENIVEQPCPDVFWFPIFSEKACDELVEEMEHYGKWSGGKHHDSRIS
GGYENVPTDDIHMKQVDLENVWLHFIREFIAPVTLKVFAGYYTKGFALLNFVVKYSPERQ
RSLRPHHDASTFTINIALNNVGEDFQGGGCKFLRYNCSIESPRKGWSFMHPGRLTHLHEG
LPVKNGTRYIAVSFIDP

Sequence length

737

Interactions

View interactions

	KEGG		Reactome
	Lysine degradation Metabolic pathways		Collagen biosynthesis and modifying enzymes

168

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Bruck syndrome 2	Pathogenic; Likely pathogenic	rs2108157679, rs1436930576, rs1353563172, rs2108057452, rs121434459, rs121434460, rs121434461, rs778254905, rs1248510301, rs2473220795, rs780770356, rs749709000, rs1937608887	RCV001784855 RCV001782659 RCV005025531 RCV002267184 RCV000008080 RCV000008081 RCV000008082 RCV005036735 RCV003330303 RCV003990202 RCV001782894 RCV000034323 RCV001196592
Osteogenesis imperfecta	Likely pathogenic; Pathogenic	rs1353563172, rs749709000	RCV002266071 RCV004799755

Show/Hide Unknown Diseases (11)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cervical cancer	Conflicting classifications of pathogenicity	rs149019740	RCV005897610
Cholangiocarcinoma	Benign	rs9289713	RCV005902377
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity	rs140613062	RCV005902985
Familial cancer of breast	Conflicting classifications of pathogenicity	rs140613062	RCV005902982
Gastric cancer	Benign	rs9836725	RCV005906902
Hepatocellular carcinoma	Conflicting classifications of pathogenicity	rs149019740, rs140613062	RCV005897609 RCV005902983
Lung cancer	Benign	rs9289713	RCV005902378
Malignant tumor of esophagus	Benign; Conflicting classifications of pathogenicity	rs9289713, rs140613062	RCV005902375 RCV005902984
Ovarian serous cystadenocarcinoma	Conflicting classifications of pathogenicity	rs140613062	RCV005902986
PLOD2-related disorder	Likely benign; Conflicting classifications of pathogenicity; Benign; Uncertain significance	rs1176368109, rs79161810, rs115199093, rs145809663, rs762644377, rs766060544, rs142554555, rs148118826, rs147402171, rs150981193, rs147665692, rs557891596	RCV003951253 RCV003947464 RCV003955034 RCV003920035 RCV003420657 RCV003973798 RCV003419172 RCV003915677 RCV003905622 RCV003930492 RCV003895441 RCV003973108
Uterine carcinosarcoma	Benign	rs9836725, rs9289713	RCV005906903 RCV005902376

Show/Hide Text Mining Associations (47)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenocarcinoma of Lung	Associate	29072684
Breast Neoplasms	Associate	33257795, 37155842
Bruck syndrome 1	Associate	25238597, 27298363, 29178448, 31472299, 39769143, 9927692
Bruck syndrome 1	Inhibit	31472299
Bruck syndrome 2	Associate	20839288, 29178448, 31472299
Bruck syndrome 2	Stimulate	31472299
Calcinosis Cutis	Associate	37146419
Camptodactyly 1	Associate	29178448
Carcinogenesis	Associate	21338529, 34258263, 36071678
Carcinoma Hepatocellular	Associate	35560794, 38052560
Carcinoma Non Small Cell Lung	Associate	29072684
Carcinoma Pancreatic Ductal	Associate	32958051
Carcinoma Renal Cell	Associate	26983694, 31446433, 32986937, 33287763, 33836688, 34388114, 36901940, 37328520, 38008826
Carcinoma Squamous Cell	Associate	33887877
Cleft Palate	Associate	29178448
Colorectal Neoplasms	Associate	29453334, 36071678
Colorectal Neoplasms	Stimulate	37227305
Endometrial Neoplasms	Associate	37227305
Esophageal Squamous Cell Carcinoma	Associate	36042592
Fibrosis	Associate	30303512, 9927692
Fractures Bone	Associate	29178448
Glioblastoma	Associate	16254489, 35682709
Glioma	Associate	28410212
Haspeslagh Fryns Muelenaere syndrome	Associate	29178448
Hypoxia	Associate	23423382, 37452322, 40500522
Hypoxia	Stimulate	28410212, 37146419, 38008826
Hypoxia Brain	Associate	23423382
Hypoxia Brain	Stimulate	37246768, 38008826
Kidney Neoplasms	Associate	33287763
Kyphomelic dysplasia	Associate	29178448
Laryngeal Neoplasms	Associate	32432748
Lymphatic Metastasis	Associate	34944486, 36042592
Neoplasm Invasiveness	Associate	34944486
Neoplasm Metastasis	Associate	26983694, 29072684, 33887877, 34944486, 36042592, 38171245
Neoplasm Metastasis	Stimulate	37227305
Neoplasms	Stimulate	21338529, 34257533
Neoplasms	Associate	23319410, 26983694, 27310702, 29072684, 31446433, 33887877, 34258263, 34944486, 35682709, 36042592, 36901940, 37155842, 37227305
Osteogenesis Imperfecta	Associate	21829228, 29178448
Osteosarcoma	Associate	37227305
Protein S Deficiency	Associate	38052560
Scleroderma Systemic	Stimulate	37246768
Soft Tissue Injuries	Associate	35627171
Squamous Cell Carcinoma of Head and Neck	Associate	33887877, 34257533, 34565301, 34944486, 37452322
Stomach Neoplasms	Associate	34281542, 35789544, 37227305
Thrombosis	Associate	37328520
Urinary Bladder Neoplasms	Associate	27310702
Uterine Cervical Neoplasms	Associate	21338529, 32258155, 34116656, 34258263, 36281082

PLOD2 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 2)