P3H1 (prolyl 3-hydroxylase 1)

Gene

• Entrez ID: 64175
• Gene name: Prolyl 3-hydroxylase 1
• Gene symbol: P3H1
• Synonyms: GROS1, LEPRE1, OI8
• 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

SNPs

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

miRNA

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

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003674	Function	Molecular_function	ND
GO:0005506	Function	Iron ion binding	IEA
GO:0005515	Function	Protein binding	ISS	15044469
GO:0005518	Function	Collagen binding	ISS	15044469
GO:0005783	Component	Endoplasmic reticulum	IBA	21873635
GO:0005783	Component	Endoplasmic reticulum	IDA	19846465, 20089953
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0006457	Process	Protein folding	IMP	17277775
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:0018126	Process	Protein hydroxylation	IMP	17277775
GO:0019511	Process	Peptidyl-proline hydroxylation	IEA
GO:0019797	Function	Procollagen-proline 3-dioxygenase activity	IBA	21873635
GO:0019797	Function	Procollagen-proline 3-dioxygenase activity	ISS	15044469
GO:0031418	Function	L-ascorbic acid binding	IEA
GO:0032963	Process	Collagen metabolic process	IBA	21873635
GO:0032963	Process	Collagen metabolic process	ISS	15044469
GO:0032991	Component	Protein-containing complex	ISS	15044469
GO:0050708	Process	Regulation of protein secretion	IMP	17277775
GO:0050821	Process	Protein stabilization	IMP	19846465, 22615817
GO:0060348	Process	Bone development	IMP	17277775, 22615817
GO:0061077	Process	Chaperone-mediated protein folding	ISS	15044469
GO:0062023	Component	Collagen-containing extracellular matrix	HDA	28327460
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:1901874	Process	Negative regulation of post-translational protein modification	IMP	17277775, 22615817

Other IDs

• MIM: 610339
• HGNC: 19316
• e!Ensembl: 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

Pathways

Reactome:

Collagen biosynthesis and modifying enzymes

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291, rs886041382, rs1057518991, rs1057518699, rs753254213, rs748294403, rs762552974, rs1135401795, rs1553121073, rs1553122926, rs1364690005, rs1554086554, rs1554210415, rs1554168326, rs1554776342, rs1553873247, rs1567860112, rs779009256, rs1557447255, rs1564568350, rs780011005, rs1597464953, rs1200336864, rs1569513017, rs1587459606, rs1570332505, rs748888652, rs1575155995, rs2087029320, rs1589669105, rs1601769604, rs1184981709, rs749201074
Osteogenesis imperfecta	Osteogenesis Imperfecta, Osteogenesis imperfecta, dominant perinatal lethal, Osteogenesis imperfecta type III (disorder), Osteogenesis imperfecta, type VIII, Osteogenesis imperfecta type 2, Osteogenesis imperfecta type 3	rs72659351, rs72659354, rs72659348, rs72659355, rs137853952, rs118203996, rs137853890, rs72659360, rs72659362, rs72659359, rs72659361, rs72659357, rs121918002, rs121918007, rs121918009, rs121918011, rs121918019, rs137853869, rs121434559, rs72659319, rs72659345, rs121912903, rs121912905, rs121912907, rs869254878, rs72658200, rs74315103, rs121912911, rs72658176, rs72656402, rs121912912, rs267606742, rs72659338, rs72645331, rs66721653, rs67368147, rs72653136, rs72653169, rs66523073, rs72656352, rs72645365, rs72667022, rs72645357, rs72656330, rs66527965, rs72645323, rs72656331, rs72667037, rs72654802, rs67682641, rs72653178, rs72653131, rs72656353, rs67828806, rs72656343, rs1906960583, rs72656314, rs67364703, rs72645347, rs72651618, rs66490707, rs72653170, rs72645320, rs137853892, rs1567856056, rs387906960, rs1555616552, rs137853865, rs137853866, rs193302872, rs193302871, rs193302873, rs137853893, rs193922137, rs72648320, rs193922138, rs193922139, rs193922140, rs193922141, rs193922143, rs193922144, rs193922145, rs193922147, rs193922148, rs193922149, rs193922151, rs193922152, rs193922154, rs72653173, rs193922155, rs193922157, rs72667023, rs193922158, rs72645328, rs193922162, rs72658154, rs193922166, rs193922167, rs193922173, rs72656387, rs193922175, rs587776916, rs398122891, rs318240762, rs372896892, rs398122834, rs749709000, rs397509383, rs397514674, rs398122518, rs398122519, rs398122520, rs387907325, rs387907333, rs387907334, rs387907354, rs387907355, rs387907356, rs387907357, rs727505392, rs786201032, rs786205217, rs786205218, rs786205219, rs786205220, rs797044559, rs794726873, rs72645353, rs869320752, rs137853943, rs797045033, rs863225043, rs869025223, rs869312908, rs878853274, rs72659347, rs72656370, rs886039693, rs67507747, rs762428889, rs72645318, rs886039880, rs369651701, rs886041866, rs886042260, rs886042286, rs886042603, rs886042897, rs72654794, rs72651642, rs140468248, rs137853944, rs1057517662, rs1057517663, rs74315111, rs72648337, rs1057518930, rs1057521085, rs1064794058, rs72658185, rs1555572249, rs67771061, rs1114167416, rs1114167417, rs72656386, rs1114167418, rs906553840, rs67729041, rs67865220, rs1114167412, rs67707918, rs68132885, rs72658119, rs72658143, rs72658150, rs72659310, rs67609234, rs1114167414, rs1114167415, rs72659325, rs67768540, rs1114167406, rs1114167405, rs1114167403, rs34940368, rs1114167402, rs72656340, rs1114167401, rs1114167400, rs72656338, rs1114167399, rs67815019, rs1114167398, rs67394386, rs1114167382, rs1114167396, rs1114167395, rs1114167381, rs1114167394, rs67445413, rs1114167380, rs1114167379, rs1114167392, rs67693970, rs1114167391, rs1114167378, rs72651661, rs1114167390, rs72651645, rs1114167389, rs1114167388, rs66555264, rs72651614, rs1114167387, rs1114167377, rs1114167375, rs1114167374, rs1114167385, rs72648326, rs72648322, rs72645369, rs1555574154, rs72645366, rs786205507, rs1114167411, rs72645356, rs72645337, rs72645334, rs72645321, rs1114167410, rs72667036, rs8179178, rs1114167408, rs1114167407, rs72667016, rs72667012, rs1114167384, rs1114167409, rs1085307634, rs1131692167, rs765659555, rs1131692326, rs1131692320, rs1135401953, rs137853883, rs1555573313, rs72667014, rs1555573621, rs1555572125, rs1260429820, rs67879854, rs1555574143, rs1328384458, rs72648343, rs1555574516, rs1555574641, rs972668240, rs72656392, rs66612022, rs66619856, rs1554395970, rs1555571755, rs1555571849, rs1555572075, rs1555572239, rs1555572458, rs1555573004, rs67543897, rs72648352, rs1555574113, rs1555574493, rs1555574497, rs1555574638, rs1555574802, rs1555571529, rs1555571647, rs1555571766, rs1555572401, rs1555572456, rs72651635, rs1555573484, rs1298621011, rs1555575086, rs1555572013, rs1555572120, rs1555572121, rs1555573039, rs1555574071, rs66664580, rs72667031, rs1555571874, rs72653151, rs72653147, rs1213427451, rs72651620, rs865999256, rs1555574144, rs1555574151, rs72645341, rs1555574496, rs1555574553, rs1555571916, rs1555178899, rs1555575370, rs1555572315, rs72645361, rs113994016, rs781272386, rs1554397369, rs1555572406, rs72651634, rs139593707, rs1555572316, rs72651640, rs1554396283, rs763159520, rs72658127, rs1553143741, rs1553143142, rs1554200383, rs1187611948, rs1554200371, rs1555572254, rs867628651, rs72653155, rs138570309, rs1410254723, rs1555573897, rs1228746935, rs72645368, rs1555574871, rs1555572640, rs1555573288, rs1555573629, rs1555575015, rs1555575889, rs1555572759, rs1555574158, rs1555574177, rs72667029, rs1555571942, rs1555574319, rs753683126, rs72651658, rs1554395470, rs1555572161, rs371243939, rs1555986267, rs1555986287, rs1555222973, rs779809838, rs1565789682, rs1557569037, rs1013320485, rs762525651, rs72656375, rs1567752926, rs1567752998, rs1567753046, rs1567753329, rs72653140, rs1567756567, rs72651644, rs1567760604, rs1567761950, rs1567763007, rs111594467, rs1567757112, rs1567759402, rs1567760123, rs67163049, rs1567756357, rs1567760736, rs1567761649, rs1567763447, rs1567763451, rs1567764387, rs1567764832, rs1567766329, rs72656326, rs1567753699, rs1567754277, rs72653168, rs72645370, rs1567762257, rs1567766338, rs72658193, rs72648357, rs1562906570, rs72659305, rs1567751388, rs1567753448, rs72651647, rs1567761800, rs1567762262, rs72648346, rs1565244847, rs1567757138, rs72656394, rs1562907287, rs1567754589, rs1598288342, rs1567855132, rs72659356, rs773269078, rs1570479611, rs762780039, rs1330779100, rs1598289920, rs72653133, rs1562906013, rs753338851, rs1570454914, rs1229143002, rs1570472113, rs137853939, rs768626850, rs1584324507, rs141011435, rs1598285120, rs72656324, rs1598288070, rs1598288593, rs1598289365, rs1598291438, rs72648330, rs1598296825, rs72648319, rs72648313, rs72645332, rs1598299070, rs1598300304, rs1473458290, rs1598285125, rs72653171, rs72653150, rs1181095991, rs1598295482, rs1598301459, rs72651667, rs1598298449, rs1597352358, rs1597355244, rs1597357740, rs1597357758, rs1597902342, rs1374482728, rs1597905563, rs1570452407, rs1570453963, rs1581634382, rs1597906442, rs1597908085, rs1597907877, rs1584316181, rs1584318953, rs72656389, rs1584319418, rs1584322737, rs1584330959, rs2586486, rs1598286543, rs72654797, rs1598288634, rs1598288656, rs1598290382, rs1598293920, rs1598295794, rs150572711, rs1598299275, rs1598300054, rs111953130, rs868166455, rs745891632, rs1021282486, rs780491808, rs1584320553, rs1598298699, rs72648321, rs1598288648, rs1598288967, rs72645352, rs1598298292, rs72645315, rs762979302, rs1598286050, rs1598301619, rs1584330396, rs72653156, rs1598295066, rs137853948, rs1598288002, rs1598289247, rs1652311421, rs1701306294, rs1906421838, rs72656351, rs72656348, rs1906537608, rs72656337, rs72656320, rs1906843530, rs1906847588, rs1906874191, rs1906878217, rs72651641, rs1907212702, rs1907330109, rs1907377731, rs1907418203, rs1907457376, rs72648333, rs1907617224, rs72667030, rs1907889665, rs1907921633, rs1908087291, rs1652352034, rs72648370, rs1555575835, rs1908083033, rs1907669327, rs112274185, rs72656327, rs1906695650, rs72645338, rs1907787005, rs1054264002, rs1791878922, rs1791894410, rs1791907178, rs369314029, rs1908050941, rs72653141, rs1907103040, rs1907351704, rs1907477506, rs1907512918, rs112042777, rs1907566530, rs1907770102, rs1791951769, rs1792108270, rs1387151592, rs72656385	18566967, 21438135, 19088120, 22281939, 17277775, 27509835, 29150909
Scoliosis	Scoliosis, unspecified	rs1057518828, rs147296805, rs758163506, rs1555613564, rs1596852902, rs1596853067, rs1596853085

Unknown
Disease name	Disease term	dbSNP ID	References
Defect of skull ossification	Defect of skull ossification
Lobstein disease	Lobstein Disease		18566967
Osteopenia	Osteopenia
Proptosis	Exophthalmos