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	64175
Gene name	Prolyl 3-hydroxylase 1
Gene symbol	P3H1
Synonyms (NCBI Gene)	GROS1LEPRE1OI8
Chromosome	1
Chromosome location	1p34.2
Summary	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

Show/Hide all (30)

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

Show/Hide all (38)

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

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

962

Show/Hide Causal Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Familial cancer of breast	Likely pathogenic; Pathogenic	rs72659353	RCV005912558
Osteogenesis imperfecta	Pathogenic; Likely pathogenic	rs72659351, rs752575140, rs2124093521, rs1570479611, rs1330779100, rs1570453963	RCV002276526 RCV002277816 RCV002277819 RCV000790419 RCV004579563 RCV004800610
Osteogenesis imperfecta type 8	Pathogenic; Likely pathogenic	rs137853950, rs72659353, rs1652551021, rs773832238, rs757634052, rs2124079876, rs2124076122, rs780595278, rs778110583, rs2124142972, rs752671524, rs2124174456, rs72659349, rs778209371, rs72659350 View all (92 more)	RCV003497294 RCV001371301 RCV001390265 RCV003600830 RCV003820402 RCV002264825 RCV001838974 RCV002024402 RCV001889484 RCV001933024 RCV001907474 RCV001953879 RCV001940990 RCV001990923 RCV001895766 RCV002030594 RCV001951372 RCV001930947 RCV002029243 RCV002026744 RCV002052197 RCV002052276 RCV000001315 RCV000001316 RCV000001317 RCV000001318 RCV000001319 RCV000001320 RCV000001321 RCV002254405 RCV003096240 RCV003134415 RCV002286562 RCV002302845 RCV003091843 RCV002637016 RCV002833105 RCV002889981 RCV003046752 RCV003123572 RCV003123573 RCV003142301 RCV003495125 RCV003600372 RCV003232058 RCV001036322 RCV003322940 RCV003454835 RCV003388691 RCV003496184 RCV003495464 RCV003496220 RCV003496375 RCV003496500 RCV003496976 RCV003495083 RCV003494624 RCV003494625 RCV003494626 RCV003494627 RCV003494628 RCV003494956 RCV003494808 RCV003495030 RCV003496008 RCV003496010 RCV003495990 RCV003495715 RCV003496617 RCV003496047 RCV003496633 RCV003600501 RCV003600596 RCV003601543 RCV003601802 RCV003601804 RCV003601734 RCV003601646 RCV003601666 RCV003602171 RCV003602159 RCV003602088 RCV003602322 RCV003600105 RCV003601182 RCV003601119 RCV003601921 RCV003820780 RCV003819388 RCV003836467 RCV003857370 RCV003874384 RCV003874804 RCV000625576 RCV000625827 RCV000686866 RCV000692569 RCV000686871 RCV002487599 RCV001869131 RCV000786860 RCV000809286 RCV000822886 RCV000811339 RCV002538347 RCV001860594 RCV001067198 RCV001036321 RCV001261598 RCV001287330
Osteogenesis imperfecta type III	Pathogenic; Likely pathogenic	rs72659351, rs1570452407, rs1570453963	RCV005864433 RCV000860007 RCV000860008
Osteogenesis Imperfecta, Recessive	Likely pathogenic; Pathogenic	rs72659356	RCV000778981
P3H1-related disorder	Likely pathogenic; Pathogenic	rs72659353, rs1652551021, rs72659351	RCV003405619 RCV003394025 RCV003914795

Show/Hide Unknown Diseases (25)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Conflicting classifications of pathogenicity; Benign	rs113593896, rs67014447	RCV005895605 RCV005900896
Adrenocortical carcinoma, hereditary	Benign; Uncertain significance	rs67014447, rs377368053	RCV005900899 RCV005896846
Cervical cancer	Conflicting classifications of pathogenicity	rs113593896, rs114044880	RCV005895609 RCV005898048
Cholangiocarcinoma	Benign	rs67014447, rs3738498	RCV005896245 RCV005900895
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Benign	rs67014447	RCV005896246
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity	rs113593896, rs140254470	RCV005895610 RCV005907173
Colon adenocarcinoma	Conflicting classifications of pathogenicity; Uncertain significance	rs113593896, rs114044880, rs368972030	RCV005895604 RCV005898046 RCV005913658
Colorectal cancer	Conflicting classifications of pathogenicity; Benign	rs113593896, rs67014447	RCV005895611 RCV005900903
Familial pancreatic carcinoma	Benign	rs67014447	RCV005900902
Gastric cancer	Conflicting classifications of pathogenicity	rs113593896	RCV005895613
Hepatocellular carcinoma	Conflicting classifications of pathogenicity; Benign; Uncertain significance	rs113593896, rs3738498, rs747865105	RCV005895607 RCV005900890 RCV005913664
Long QT syndrome 12	Uncertain significance	rs750377534	RCV005861201
Lung cancer	Conflicting classifications of pathogenicity; Uncertain significance	rs113593896, rs114044880, rs750943926	RCV005895616 RCV005898049 RCV005913659
Lymphoma	Benign	rs67014447	RCV005900905
Malignant lymphoma, large B-cell, diffuse	Benign	rs3738498	RCV005900892
Malignant tumor of esophagus	Conflicting classifications of pathogenicity; Benign; Uncertain significance	rs113593896, rs67014447, rs114044880, rs147230023	RCV005895608 RCV005900897 RCV005898047 RCV005900259
Malignant tumor of urinary bladder	Conflicting classifications of pathogenicity	rs113593896	RCV005895606
Melanoma	Conflicting classifications of pathogenicity	rs113593896	RCV005895615
Nonpapillary renal cell carcinoma	Benign	rs67014447	RCV005900898
Ovarian cancer	Benign	rs67014447	RCV005900900
Ovarian serous cystadenocarcinoma	Conflicting classifications of pathogenicity	rs113593896, rs3738497	RCV005895614 RCV005896847
Sarcoma	Conflicting classifications of pathogenicity; Benign; Uncertain significance	rs113593896, rs67014447, rs191121940	RCV005895612 RCV005900904 RCV005902091
Thymoma	Benign	rs67014447, rs3738498	RCV005896244 RCV005900894
Uterine carcinosarcoma	Benign	rs67014447, rs3738498	RCV005900906 RCV005900893
Uveal melanoma	Benign	rs67014447, rs3738498	RCV005900901 RCV005900891

Show/Hide Text Mining Associations (34)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)