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.	64175
Gene name Gene Name - the full gene name approved by the HGNC.	Prolyl 3-hydroxylase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	P3H1
Synonyms (NCBI Gene) Gene synonyms aliases	GROS1, LEPRE1, OI8
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1p34.2
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes an enzyme that is a member of the collagen prolyl hydroxylase family. These enzymes are localized to the endoplasmic reticulum and their activity is required for proper collagen synthesis and assembly. Mutations in this gene are associat

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SNP ID	Visualize variation	Clinical significance	Consequence
rs72659348	G>-	Pathogenic	5 prime UTR variant, non coding transcript variant, coding sequence variant, frameshift variant
rs72659351	C>A	Pathogenic	Splice donor variant
rs72659354	C>A	Pathogenic	Splice donor variant
rs72659355	G>T	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs72659356	G>A,C	Likely-pathogenic	Coding sequence variant, stop gained, missense variant, genic downstream transcript variant, downstream transcript variant
rs113593896	T>A,C	Conflicting-interpretations-of-pathogenicity, benign	Non coding transcript variant, missense variant, coding sequence variant
rs114044880	C>A,T	Conflicting-interpretations-of-pathogenicity, benign	Intron variant
rs118203996	G>A,C	Pathogenic, uncertain-significance	Stop gained, non coding transcript variant, missense variant, coding sequence variant
rs137853890	C>G,T	Likely-pathogenic	Genic downstream transcript variant, downstream transcript variant, synonymous variant, coding sequence variant, intron variant
rs137853952	CT>G	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs139259804	C>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Non coding transcript variant, missense variant, coding sequence variant
rs140468248	C>A,G	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant, missense variant
rs149894086	T>C	Conflicting-interpretations-of-pathogenicity, likely-benign	Missense variant, coding sequence variant, non coding transcript variant
rs200901466	G>A	Conflicting-interpretations-of-pathogenicity	Intron variant
rs369651701	C>T	Pathogenic	Splice donor variant
rs533729683	G>A,C	Likely-benign, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, missense variant, 3 prime UTR variant, coding sequence variant
rs762525651	C>A	Likely-pathogenic	Splice donor variant
rs770943260	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, coding sequence variant, 5 prime UTR variant
rs786205443	C>T	Likely-pathogenic	Intron variant
rs886042897	C>G	Pathogenic	Splice acceptor variant
rs1013320485	T>A,C	Likely-pathogenic	Splice acceptor variant
rs1229143002	G>A	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs1553143142	AGAGT>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant, 5 prime UTR variant
rs1553143741	CA>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant, 5 prime UTR variant
rs1557569037	T>A	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs1570452407	->G	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant, 3 prime UTR variant
rs1570453963	->T	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant, downstream transcript variant
rs1570454914	T>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1570472113	T>A	Pathogenic	Non coding transcript variant, synonymous variant, coding sequence variant, stop gained
rs1570479611	G>A	Pathogenic	5 prime UTR variant, stop gained, upstream transcript variant, genic upstream transcript variant, non coding transcript variant, coding sequence variant

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miRTarBase ID	miRNA	Experiments	Reference
MIRT474209	hsa-miR-29b-3p	PAR-CLIP	23592263
MIRT474208	hsa-miR-29c-3p	PAR-CLIP	23592263
MIRT474207	hsa-miR-29a-3p	PAR-CLIP	23592263
MIRT474206	hsa-miR-3154	PAR-CLIP	23592263
MIRT474205	hsa-miR-2278	PAR-CLIP	23592263
MIRT474203	hsa-miR-6871-3p	PAR-CLIP	23592263
MIRT474204	hsa-miR-6510-5p	PAR-CLIP	23592263
MIRT474202	hsa-miR-3668	PAR-CLIP	23592263
MIRT474201	hsa-miR-335-5p	PAR-CLIP	23592263
MIRT474200	hsa-miR-6887-3p	PAR-CLIP	23592263
MIRT474199	hsa-miR-6795-3p	PAR-CLIP	23592263
MIRT474198	hsa-miR-4677-3p	PAR-CLIP	23592263
MIRT474197	hsa-miR-4468	PAR-CLIP	23592263
MIRT474196	hsa-miR-767-5p	PAR-CLIP	23592263
MIRT474194	hsa-miR-7974	PAR-CLIP	23592263
MIRT474195	hsa-miR-5682	PAR-CLIP	23592263
MIRT474193	hsa-miR-6826-3p	PAR-CLIP	23592263
MIRT440333	hsa-miR-432-5p	HITS-CLIP	24374217
MIRT440333	hsa-miR-432-5p	HITS-CLIP	24374217
MIRT755093	hsa-miR-29b-3p	PAR-CLIP	23592263
MIRT755094	hsa-miR-29c-3p	PAR-CLIP	23592263
MIRT755095	hsa-miR-29a-3p	PAR-CLIP	23592263
MIRT755096	hsa-miR-3154	PAR-CLIP	23592263
MIRT755097	hsa-miR-2278	PAR-CLIP	23592263
MIRT755098	hsa-miR-6871-3p	PAR-CLIP	23592263
MIRT755099	hsa-miR-6510-5p	PAR-CLIP	23592263
MIRT755100	hsa-miR-3668	PAR-CLIP	23592263
MIRT755101	hsa-miR-335-5p	PAR-CLIP	23592263
MIRT755102	hsa-miR-6887-3p	PAR-CLIP	23592263
MIRT755103	hsa-miR-6795-3p	PAR-CLIP	23592263
MIRT755104	hsa-miR-4677-3p	PAR-CLIP	23592263
MIRT755105	hsa-miR-4468	PAR-CLIP	23592263
MIRT755106	hsa-miR-767-5p	PAR-CLIP	23592263
MIRT755107	hsa-miR-7974	PAR-CLIP	23592263
MIRT755108	hsa-miR-5682	PAR-CLIP	23592263
MIRT755109	hsa-miR-6826-3p	PAR-CLIP	23592263

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GO ID	Ontology	Definition	Evidence	Reference
GO:0005506	Function	Iron ion binding	IEA
GO:0005515	Function	Protein binding	IPI	30021884, 33961781
GO:0005515	Function	Protein binding	ISS	15044469
GO:0005518	Function	Collagen binding	ISS	15044469
GO:0005576	Component	Extracellular region	IEA
GO:0005634	Component	Nucleus	IDA	1095156
GO:0005737	Component	Cytoplasm	IDA	1095156
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005783	Component	Endoplasmic reticulum	IDA	19846465, 20089953
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0006457	Process	Protein folding	IMP	17277775
GO:0006457	Process	Protein folding	ISS	15044469
GO:0008285	Process	Negative regulation of cell population proliferation	NAS	10951563
GO:0010976	Process	Positive regulation of neuron projection development	ISS
GO:0016020	Component	Membrane	HDA	19946888
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0016705	Function	Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	IEA
GO:0018126	Process	Protein hydroxylation	IMP	17277775
GO:0019797	Function	Procollagen-proline 3-dioxygenase activity	IBA
GO:0019797	Function	Procollagen-proline 3-dioxygenase activity	IEA
GO:0019797	Function	Procollagen-proline 3-dioxygenase activity	ISS	15044469
GO:0030199	Process	Collagen fibril organization	IEA
GO:0030278	Process	Regulation of ossification	IEA
GO:0030308	Process	Negative regulation of cell growth	IEA
GO:0031012	Component	Extracellular matrix	HDA	28327460
GO:0031418	Function	L-ascorbic acid binding	IEA
GO:0032963	Process	Collagen metabolic process	IBA
GO:0032963	Process	Collagen metabolic process	IEA
GO:0032963	Process	Collagen metabolic process	ISS	15044469
GO:0032991	Component	Protein-containing complex	ISS	15044469
GO:0046872	Function	Metal ion binding	IEA
GO:0050708	Process	Regulation of protein secretion	IMP	17277775
GO:0050821	Process	Protein stabilization	IMP	19846465, 22615817
GO:0051213	Function	Dioxygenase activity	IEA
GO:0060348	Process	Bone development	IMP	17277775, 22615817
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:1901874	Process	Negative regulation of post-translational protein modification	IMP	17277775, 22615817

MIM	HGNC	e!Ensembl
610339	19316	ENSG00000117385

Protein

UniProt ID

Q32P28

Protein name

Prolyl 3-hydroxylase 1 (EC 1.14.11.7) (Growth suppressor 1) (Leucine- and proline-enriched proteoglycan 1) (Leprecan-1)

Protein function

Basement membrane-associated chondroitin sulfate proteoglycan (CSPG). Has prolyl 3-hydroxylase activity catalyzing the post-translational formation of 3-hydroxyproline in -Xaa-Pro-Gly- sequences in collagens, especially types IV and V. May be in

PDB

8K0E , 8K0F , 8K0I , 8K0M , 8K17 , 8KC9

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13640	2OG-FeII_Oxy_3	575 → 677	2OG-Fe(II) oxygenase superfamily	Domain

Sequence

MAVRALKLLTTLLAVVAAASQAEVESEAGWGMVTPDLLFAEGTAAYARGDWPGVVLSMER
ALRSRAALRALRLRCRTQCAADFPWELDPDWSPSPAQASGAAALRDLSFFGGLLRRAACL
RRCLGPPAAHSLSEEMELEFRKRSPYNYLQVAYFKINKLEKAVAAAHTFFVGNPEHMEMQ
QNLDYYQTMSGVKEADFKDLETQPHMQEFRLGVRLYSEEQPQEAVPHLEAALQEYFVAYE
ECRALCEGPYDYDGYNYLEYNADLFQAITDHYIQVLNCKQNCVTELASHPSREKPFEDFL
PSHYNYLQFAYYNIGNYTQAVECAKTYLLFFPNDEVMNQNLAYYAAMLGEEHTRSIGPRE
SAKEYRQRSLLEKELLFFAYDVFGIPFVDPDSWTPEEVIPKRLQEKQKSERETAVRISQE
IGNLMKEIETLVEEKTKESLDVSRLTREGGPLLYEGISLTMNSKLLNGSQRVVMDGVISD
HECQELQRLTNVAATSGDGYRGQTSPHTPNEKFYGVTVFKALKLGQEGKVPLQSAHLYYN
VTEKVRRIMESYFRLDTPLYFSYSHLVCRTAIEEVQAERKDDSHPVHVDNCILNAETLVC
VKEPPAYTFRDYSAILYLNGDFDGGNFYFTELDAKTVTAEVQPQCGRAVGFSSGTENPHG
VKAVTRGQRCAIALWFTLDPRHSERDRVQADDLVKMLFSPEEMDLSQEQPLDAQQGPPEP
AQESLSGSESKPKDEL

Sequence length

736

Interactions

View interactions

	Reactome
			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
Osteogenesis Imperfecta	Osteogenesis imperfecta type 8, Osteogenesis Imperfecta, Recessive, Osteogenesis imperfecta type III, osteogenesis imperfecta	rs762525651, rs1570452407, rs118203996, rs72659356, rs1570453963, rs137853890, rs72659347, rs773269078, rs137853948, rs369651701, rs1570479611, rs1652311421, rs886042897, rs1330779100, rs72659351 View all (13 more)	N/A

Show/Hide Text Mining Associations (34)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Bone Diseases	Associate	17277775
Breast Neoplasms	Inhibit	19436308
Breast Neoplasms	Associate	35937944
Campomelia Cumming type	Associate	35327962
Carcinoma Hepatocellular	Associate	32951492, 37081465
Cartilage Diseases	Associate	19550437, 19781681
Collagen Diseases	Associate	39245686
Craniosynostoses	Associate	35327962
Esophageal Squamous Cell Carcinoma	Associate	26330293
Fetal Growth Retardation	Associate	35327962
Fractures Bone	Associate	36963805
Fractures Multiple	Associate	18566967
Hypophosphatasia	Associate	39276275
Leukemia	Associate	35190588
Leukemia Myeloid Acute	Associate	35190588
Lung Neoplasms	Associate	35190588
Lymphedema Congenital Recessive	Associate	18566967
Musculoskeletal Diseases	Associate	35327962
Neoplasms	Associate	35190588
Neoplasms Bone Tissue	Associate	36963805
Non Muscle Invasive Bladder Neoplasms	Associate	22724020
Osteogenesis Imperfecta	Associate	17277775, 18566967, 18996919, 19550437, 19781681, 20089953, 20188343, 20839288, 21282188, 21829228, 22281939, 22615817, 23301918, 25742658, 26634552 View all (6 more)
Osteogenesis imperfecta type 2A	Associate	18996919
Osteogenesis imperfecta type 2B	Inhibit	19550437
Osteogenesis imperfecta type 3	Associate	18566967, 35327962
Osteogenesis Imperfecta Type IV	Associate	29329516
Osteogenesis Imperfecta Type IX	Associate	19781681, 28802583
Osteogenesis imperfecta type VIII	Associate	23301918, 27383115, 28802583, 36833249, 36963805, 37437959
Osteoporosis pseudoglioma syndrome	Associate	20839288
Retinal Detachment	Associate	29329516
Retinal Perforations	Associate	29329516
Sillence syndrome	Associate	35327962
Vitamin D Hydroxylation Deficient Rickets Type 1A	Associate	22281939
Vitreous Detachment	Associate	29329516

P3H1 (prolyl 3-hydroxylase 1)