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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	5351
Gene name	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1
Gene symbol	PLOD1
Synonyms (NCBI Gene)	EDS6EDSKCL1LHLH1LLHPLOD
Chromosome	1
Chromosome location	1p36.22
Summary	Lysyl hydroxylase is a membrane-bound homodimeric protein localized to the cisternae of the endoplasmic reticulum. The enzyme (cofactors iron and ascorbate) catalyzes the hydroxylation of lysyl residues in collagen-like peptides. The resultant hydroxylysy

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SNP ID	Visualize variation	Clinical significance	Consequence
rs112460511	G>C,T	Likely-pathogenic	Splice acceptor variant
rs121913550	C>T	Pathogenic	Stop gained, coding sequence variant
rs121913551	G>A	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs121913552	C>G	Pathogenic	Stop gained, coding sequence variant
rs121913553	G>A,C	Pathogenic	Stop gained, missense variant, coding sequence variant
rs121913554	C>T	Pathogenic	Stop gained, coding sequence variant
rs138490756	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance, benign, likely-benign	Missense variant, coding sequence variant
rs138698098	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs140758113	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, synonymous variant
rs142710681	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs149425237	G>A	Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs377406897	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs557317492	C>T	Uncertain-significance, likely-benign, likely-pathogenic	Coding sequence variant, missense variant
rs565513365	A>C,G	Pathogenic	Splice acceptor variant
rs745409628	ACCGCAGGCTGGAGACCAAG>-	Pathogenic	Coding sequence variant, frameshift variant
rs763409574	A>G	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs771186398	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs797044446	GAG>-	Pathogenic	Coding sequence variant, inframe deletion
rs797044447	A>-	Pathogenic	Splice acceptor variant
rs797044448	G>A	Pathogenic	Splice donor variant
rs886042976	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs886043926	A>-	Pathogenic	Frameshift variant, coding sequence variant
rs886043927	T>C	Pathogenic	Splice donor variant
rs1057518879	G>A	Pathogenic	Stop gained, coding sequence variant
rs1224538282	C>T	Pathogenic	Stop gained, coding sequence variant
rs1389548210	G>A,C	Pathogenic	Splice donor variant
rs1401035675	A>G	Likely-pathogenic	Splice acceptor variant
rs1433428588	C>T	Pathogenic	Coding sequence variant, stop gained
rs1439043436	C>T	Pathogenic	Coding sequence variant, stop gained
rs1471557079	->CAGCGGCTCCTGC	Pathogenic	Coding sequence variant, frameshift variant
rs1553134578	C>T	Pathogenic	Coding sequence variant, stop gained
rs1553137486	A>G	Likely-pathogenic	Splice acceptor variant
rs1557500194	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs1569713366	C>T	Pathogenic	Stop gained, coding sequence variant
rs1569724692	->C	Pathogenic	Frameshift variant, coding sequence variant

100

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miRTarBase ID	miRNA	Experiments	Reference
MIRT022239	hsa-miR-124-3p	Proteomics;Microarray	18668037
MIRT024504	hsa-miR-215-5p	Microarray	19074876
MIRT026202	hsa-miR-192-5p	Microarray	19074876
MIRT052618	hsa-let-7a-5p	CLASH	23622248
MIRT046301	hsa-miR-23b-3p	CLASH	23622248
MIRT045528	hsa-miR-149-5p	CLASH	23622248
MIRT041701	hsa-miR-484	CLASH	23622248
MIRT1242998	hsa-miR-1229	CLIP-seq
MIRT1242999	hsa-miR-1257	CLIP-seq
MIRT1243000	hsa-miR-1283	CLIP-seq
MIRT1243001	hsa-miR-1289	CLIP-seq
MIRT1243002	hsa-miR-1324	CLIP-seq
MIRT1243003	hsa-miR-135a	CLIP-seq
MIRT1243004	hsa-miR-135b	CLIP-seq
MIRT1243005	hsa-miR-150	CLIP-seq
MIRT1243006	hsa-miR-1912	CLIP-seq
MIRT1243007	hsa-miR-2117	CLIP-seq
MIRT1243008	hsa-miR-3120-5p	CLIP-seq
MIRT1243009	hsa-miR-3182	CLIP-seq
MIRT1243010	hsa-miR-3198	CLIP-seq
MIRT1243011	hsa-miR-326	CLIP-seq
MIRT1243012	hsa-miR-330-3p	CLIP-seq
MIRT1243013	hsa-miR-330-5p	CLIP-seq
MIRT1243014	hsa-miR-3609	CLIP-seq
MIRT1243015	hsa-miR-3925-3p	CLIP-seq
MIRT1243016	hsa-miR-4294	CLIP-seq
MIRT1243017	hsa-miR-4309	CLIP-seq
MIRT1243018	hsa-miR-4652-5p	CLIP-seq
MIRT1243019	hsa-miR-4685-5p	CLIP-seq
MIRT1243020	hsa-miR-4713-5p	CLIP-seq
MIRT1243021	hsa-miR-516b	CLIP-seq
MIRT1243022	hsa-miR-520d-5p	CLIP-seq
MIRT1243023	hsa-miR-524-5p	CLIP-seq
MIRT1243024	hsa-miR-532-3p	CLIP-seq
MIRT1243025	hsa-miR-548ah	CLIP-seq
MIRT1243026	hsa-miR-548n	CLIP-seq
MIRT1243027	hsa-miR-548t	CLIP-seq
MIRT1243028	hsa-miR-626	CLIP-seq
MIRT1243029	hsa-miR-766	CLIP-seq
MIRT2071807	hsa-miR-3612	CLIP-seq
MIRT2071808	hsa-miR-3652	CLIP-seq
MIRT2071809	hsa-miR-378	CLIP-seq
MIRT2071810	hsa-miR-378b	CLIP-seq
MIRT2071811	hsa-miR-378c	CLIP-seq
MIRT2071812	hsa-miR-378d	CLIP-seq
MIRT2071813	hsa-miR-378e	CLIP-seq
MIRT2071814	hsa-miR-378f	CLIP-seq
MIRT2071815	hsa-miR-378h	CLIP-seq
MIRT2071816	hsa-miR-378i	CLIP-seq
MIRT2071817	hsa-miR-422a	CLIP-seq
MIRT2071818	hsa-miR-4292	CLIP-seq
MIRT2071819	hsa-miR-4308	CLIP-seq
MIRT2071820	hsa-miR-4430	CLIP-seq
MIRT2071821	hsa-miR-4443	CLIP-seq
MIRT2071822	hsa-miR-4802-5p	CLIP-seq
MIRT2071823	hsa-miR-483-3p	CLIP-seq
MIRT2071824	hsa-miR-650	CLIP-seq
MIRT2071825	hsa-miR-668	CLIP-seq
MIRT2298953	hsa-miR-198	CLIP-seq
MIRT2298954	hsa-miR-3591-3p	CLIP-seq
MIRT1243015	hsa-miR-3925-3p	CLIP-seq
MIRT1243019	hsa-miR-4685-5p	CLIP-seq
MIRT1243029	hsa-miR-766	CLIP-seq
MIRT1242998	hsa-miR-1229	CLIP-seq
MIRT1243009	hsa-miR-3182	CLIP-seq
MIRT2595760	hsa-miR-4286	CLIP-seq
MIRT2595761	hsa-miR-4742-5p	CLIP-seq
MIRT2071823	hsa-miR-483-3p	CLIP-seq
MIRT2071825	hsa-miR-668	CLIP-seq
MIRT1242998	hsa-miR-1229	CLIP-seq
MIRT1243001	hsa-miR-1289	CLIP-seq
MIRT1243003	hsa-miR-135a	CLIP-seq
MIRT1243004	hsa-miR-135b	CLIP-seq
MIRT1243005	hsa-miR-150	CLIP-seq
MIRT2298953	hsa-miR-198	CLIP-seq
MIRT1243007	hsa-miR-2117	CLIP-seq
MIRT1243008	hsa-miR-3120-5p	CLIP-seq
MIRT2688136	hsa-miR-3176	CLIP-seq
MIRT1243009	hsa-miR-3182	CLIP-seq
MIRT2688137	hsa-miR-3187-3p	CLIP-seq
MIRT1243010	hsa-miR-3198	CLIP-seq
MIRT1243011	hsa-miR-326	CLIP-seq
MIRT1243013	hsa-miR-330-5p	CLIP-seq
MIRT2298954	hsa-miR-3591-3p	CLIP-seq
MIRT2688138	hsa-miR-3922-3p	CLIP-seq
MIRT2595760	hsa-miR-4286	CLIP-seq
MIRT1243016	hsa-miR-4294	CLIP-seq
MIRT1243017	hsa-miR-4309	CLIP-seq
MIRT2688139	hsa-miR-4492	CLIP-seq
MIRT2688140	hsa-miR-4498	CLIP-seq
MIRT2688141	hsa-miR-4505	CLIP-seq
MIRT2688142	hsa-miR-4529-5p	CLIP-seq
MIRT1243019	hsa-miR-4685-5p	CLIP-seq
MIRT1243020	hsa-miR-4713-5p	CLIP-seq
MIRT2595761	hsa-miR-4742-5p	CLIP-seq
MIRT2071823	hsa-miR-483-3p	CLIP-seq
MIRT1243021	hsa-miR-516b	CLIP-seq
MIRT1243024	hsa-miR-532-3p	CLIP-seq
MIRT2071825	hsa-miR-668	CLIP-seq
MIRT2688143	hsa-miR-762	CLIP-seq

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Transcription factor	Regulation	Reference
PITX2	Unknown	21837767

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GO ID	Ontology	Definition	Evidence	Reference
GO:0001666	Process	Response to hypoxia	IEP	15174142
GO:0005506	Function	Iron ion binding	IEA
GO:0005515	Function	Protein binding	IPI	26496610, 28514442, 33961781
GO:0005615	Component	Extracellular space	IBA
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005783	Component	Endoplasmic reticulum	IEA
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	9724729, 10934207
GO:0008475	Function	Procollagen-lysine 5-dioxygenase activity	IEA
GO:0008475	Function	Procollagen-lysine 5-dioxygenase activity	IMP	8621606
GO:0008475	Function	Procollagen-lysine 5-dioxygenase activity	ISS	9582318
GO:0008544	Process	Epidermis development	IMP	8449506
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	8621606, 9724729, 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:0046872	Function	Metal ion binding	IEA
GO:0051213	Function	Dioxygenase activity	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:1902494	Component	Catalytic complex	IEA

MIM	HGNC	e!Ensembl
153454	9081	ENSG00000083444

Q02809

Protein name

Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (EC 1.14.11.4) (Lysyl hydroxylase 1) (LH1)

Protein function

Part of a complex composed of PLOD1, P3H3 and P3H4 that catalyzes hydroxylation of lysine residues in collagen alpha chains and is required for normal assembly and cross-linkling of collagen fibrils (By similarity). Forms hydroxylysine residues

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03171	2OG-FeII_Oxy	637 → 727	2OG-Fe(II) oxygenase superfamily	Domain

Sequence

MRPLLLLALLGWLLLAEAKGDAKPEDNLLVLTVATKETEGFRRFKRSAQFFNYKIQALGL
GEDWNVEKGTSAGGGQKVRLLKKALEKHADKEDLVILFADSYDVLFASGPRELLKKFRQA
RSQVVFSAEELIYPDRRLETKYPVVSDGKRFLGSGGFIGYAPNLSKLVAEWEGQDSDSDQ
LFYTKIFLDPEKREQINITLDHRCRIFQNLDGALDEVVLKFEMGHVRARNLAYDTLPVLI
HGNGPTKLQLNYLGNYIPRFWTFETGCTVCDEGLRSLKGIGDEALPTVLVGVFIEQPTPF
VSLFFQRLLRLHYPQKHMRLFIHNHEQHHKAQVEEFLAQHGSEYQSVKLVGPEVRMANAD
ARNMGADLCRQDRSCTYYFSVDADVALTEPNSLRLLIQQNKNVIAPLMTRHGRLWSNFWG
ALSADGYYARSEDYVDIVQGRRVGVWNVPYISNIYLIKGSALRGELQSSDLFHHSKLDPD
MAFCANIRQQDVFMFLTNRHTLGHLLSLDSYRTTHLHNDLWEVFSNPEDWKEKYIHQNYT
KALAGKLVETPCPDVYWFPIFTEVACDELVEEMEHFGQWSLGNNKDNRIQGGYENVPTID
IHMNQIGFEREWHKFLLEYIAPMTEKLYPGYYTRAQFDLAFVVRYKPDEQPSLMPHHDAS
TFTINIALNRVGVDYEGGGCRFLRYNCSIRAPRKGWTLMHPGRLTHYHEGLPTTRGTRYI
AVSFVDP

Sequence length

727

Interactions

View interactions

	KEGG		Reactome
	Lysine degradation Metabolic pathways		Collagen biosynthesis and modifying enzymes

1507

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Ehlers-Danlos syndrome	Pathogenic; Likely pathogenic	rs2100758252, rs2100754171, rs121913550, rs121913552, rs1439043436	RCV002278046 RCV002278053 RCV004798730 RCV002276550 RCV002279546
Ehlers-Danlos syndrome, kyphoscoliotic type 1	Pathogenic; Likely pathogenic	rs1189324317, rs1645691337, rs746930362, rs2100764790, rs2100760068, rs2100756997, rs2100743480, rs1440249864, rs1434924385, rs1375808651, rs199730384, rs1362343873, rs776398739, rs571824470, rs2522862314 View all (52 more)	RCV001386992 RCV001382370 RCV001979458 RCV001966442 RCV001960636 RCV002007501 RCV001946668 RCV001880899 RCV001899020 RCV002009040 RCV003514548 RCV003104293 RCV002780144 RCV002903718 RCV003005478 RCV003034261 RCV003046167 RCV003226125 RCV001387123 RCV001002397 RCV003236406 RCV000819031 RCV003629111 RCV001038850 RCV003330284 RCV003515423 RCV003514763 RCV003515652 RCV003516132 RCV003516284 RCV003516285 RCV003516308 RCV003514976 RCV003515777 RCV003516019 RCV000015438 RCV000015442 RCV000015443 RCV000015444 RCV000015447 RCV000015448 RCV000015449 RCV000015440 RCV003629385 RCV003630260 RCV003630200 RCV003630447 RCV003630541 RCV003630704 RCV003630779 RCV003630829 RCV003630854 RCV003630796 RCV003628622 RCV003628628 RCV003628843 RCV003628992 RCV003811599 RCV004577205 RCV001865680 RCV001853637 RCV003767816 RCV001855284 RCV000680071 RCV000680070 RCV000803703 RCV000816388 RCV000800852 RCV000986239 RCV001045967
Familial thoracic aortic aneurysm and aortic dissection	Likely pathogenic; Pathogenic	rs1440249864, rs199730384, rs571824470, rs2522874923, rs745409628, rs565513365, rs121913552, rs1433428588, rs1401035675	RCV004651770 RCV005704894 RCV004661498 RCV003176797 RCV002311073 RCV002401967 RCV002313712 RCV002315149 RCV002315161
PLOD1-related disorder	Likely pathogenic; Pathogenic	rs2522850390, rs761014653, rs121913552	RCV003404199 RCV003399575 RCV003904842

Show/Hide Unknown Diseases (19)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cardiovascular phenotype	Conflicting classifications of pathogenicity	rs149425237	RCV005404465
Cholangiocarcinoma	Benign	rs41307745	RCV005896739
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Benign	rs41307745	RCV005897941
Familial pancreatic carcinoma	Benign	rs41307745	RCV005896734
Hepatocellular carcinoma	Benign	rs41307745	RCV005896730
Keratoconus	Conflicting classifications of pathogenicity	rs369263247	RCV003324532
Lymphoma	Benign	rs41307745	RCV005896736
Malignant lymphoma, large B-cell, diffuse	Benign	rs41307745	RCV005896735
Melanoma	Uncertain significance	rs1553134266	RCV005901332
Myopathy	Uncertain significance	rs2100768765	RCV002052430
Nonpapillary renal cell carcinoma	Benign	rs41307745	RCV005896731
Ovarian cancer	Benign	rs41307745	RCV005896732
Sarcoma	Likely benign	rs765270896	RCV005928394
Squamous cell carcinoma of the head and neck	Benign	rs41307745	RCV005896729
Thymoma	Benign	rs41307745	RCV005896738
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	rs576907642	RCV005898670
Uterine carcinosarcoma	Benign	rs41307745	RCV005896737
Uterine corpus endometrial carcinoma	Benign; Uncertain significance	rs41307745, rs1553135489	RCV005897940 RCV005901193
Uveal melanoma	Benign; Likely benign	rs41307745, rs376476977	RCV005896733 RCV005903760

Show/Hide Text Mining Associations (34)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Aortic Aneurysm Familial Thoracic 1	Associate	34400365
Bicuspid Aortic Valve Disease	Associate	23525417
Bone Fragility with Contractures Arterial Rupture and Deafness	Inhibit	21699693
Bone Fragility with Contractures Arterial Rupture and Deafness	Associate	25277362, 33129265
Bruck syndrome 1	Associate	30721533
Carcinoma Renal Cell	Associate	31446433, 33287763
Cicatrix	Associate	32174067
Disease	Associate	30721533
Ehlers Danlos Syndrome	Associate	25277362, 29982180, 31063316
Ehlers Danlos syndrome type 6	Associate	11286629, 15854030, 21699693, 25277362, 28667723, 29982180, 31063316, 31288483, 32174067, 33129265, 33579342, 8981946
Epstein Barr Virus Infections	Associate	34304093
Gastroschisis	Associate	32163230
Hepatolenticular Degeneration	Associate	39809184
Hereditary Motor And Sensory Neuropathy VI	Associate	21699693, 28667723
Hypoxia	Associate	30257451
Hypoxia Brain	Associate	30257451, 31940282
Joint Instability	Associate	32174067
Kidney Neoplasms	Associate	33287763
Lujan Fryns syndrome	Associate	32174067
Lymphoma Non Hodgkin	Associate	33503035
Muscle Hypotonia	Associate	32174067
Myopia	Associate	21527992, 32174067
Neoplasm Metastasis	Associate	33134376
Neoplasms	Associate	31199049, 31446433, 33441653, 34304093, 34455762, 35627171
Osteoporotic Fractures	Associate	17320498
Osteosarcoma	Associate	33134376, 34455762
Plagiocephaly and X linked mental retardation	Associate	25277362
Prostatic Neoplasms	Associate	31940282
Rhabdoid Tumor	Associate	20212451
Sarcoma	Associate	35627171
Soft Tissue Injuries	Associate	35627171
Stomach Neoplasms	Associate	34304093, 34455762
Urinary Bladder Neoplasms	Associate	31199049, 34455762
Vascular Diseases	Associate	34400365

PLOD1 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 1)