P3H3

gene
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Also known as GRCBHSU47926

Summary

P3H3 (prolyl 3-hydroxylase 3, HGNC:19318) is a protein-coding gene on chromosome 12p13.31, encoding Prolyl 3-hydroxylase 3 (Q8IVL6). 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.

The protein encoded by this gene belongs to the leprecan family of proteoglycans, which function as collagen prolyl hydroxylases that are required for proper collagen biosynthesis, folding and assembly. This protein, like other family members, is thought to reside in the endoplasmic reticulum. Epigenetic inactivation of this gene is associated with breast and other cancers, suggesting that it may function as a tumor suppressor.

Source: NCBI Gene 10536 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 68 total
  • MANE Select transcript: NM_014262

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19318
Approved symbolP3H3
Nameprolyl 3-hydroxylase 3
Location12p13.31
Locus typegene with protein product
StatusApproved
AliasesGRCB, HSU47926
Ensembl geneENSG00000110811
Ensembl biotypeprotein_coding
OMIM610342
Entrez10536

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 8 retained_intron, 6 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000290510, ENST00000536140, ENST00000538102, ENST00000540406, ENST00000541956, ENST00000542976, ENST00000544200, ENST00000544813, ENST00000544949, ENST00000545596, ENST00000612048, ENST00000913254, ENST00000942943, ENST00000942944, ENST00000942945, ENST00000942946

RefSeq mRNA: 1 — MANE Select: NM_014262 NM_014262

CCDS: CCDS61027

Canonical transcript exons

ENST00000290510 — 15 exons

ExonStartEnd
ENSE0000371630768377326837849
ENSE0000371760668312166831352
ENSE0000371800168303536830554
ENSE0000371938368337426833809
ENSE0000371945468392976839847
ENSE0000373110068339256834049
ENSE0000373373768369856837086
ENSE0000373509668306396830770
ENSE0000373552468298596830011
ENSE0000373678068390006839140
ENSE0000374517368374236837573
ENSE0000374646968335926833644
ENSE0000375087168284076828938
ENSE0000375103568318256831914
ENSE0000375182868379586838033

Expression profiles

Bgee: expression breadth ubiquitous, 179 present calls, max score 97.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.1124 / max 219.8853, expressed in 1385 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
12376615.97991349
1237633.99891051
1237621.4916777
1237640.8672567
1237650.4185268
1237670.2943142
2065570.056216
1237680.00601

Top tissues by expression

287 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225597.87gold quality
adenohypophysisUBERON:000219696.56gold quality
right hemisphere of cerebellumUBERON:001489095.54gold quality
cerebellar hemisphereUBERON:000224595.46gold quality
cerebellar cortexUBERON:000212995.28gold quality
body of uterusUBERON:000985395.07gold quality
pituitary glandUBERON:000000795.06gold quality
apex of heartUBERON:000209894.45gold quality
right ovaryUBERON:000211894.39gold quality
ascending aortaUBERON:000149694.20gold quality
thoracic aortaUBERON:000151594.15gold quality
descending thoracic aortaUBERON:000234594.12gold quality
left ovaryUBERON:000211993.75gold quality
endocervixUBERON:000045892.95gold quality
cerebellumUBERON:000203792.64gold quality
left uterine tubeUBERON:000130392.58gold quality
right coronary arteryUBERON:000162592.28gold quality
tendon of biceps brachiiUBERON:000818891.83gold quality
left coronary arteryUBERON:000162690.84gold quality
aortaUBERON:000094790.81gold quality
ectocervixUBERON:001224990.78gold quality
mucosa of stomachUBERON:000119990.75gold quality
right atrium auricular regionUBERON:000663189.96gold quality
coronary arteryUBERON:000162189.91gold quality
ovaryUBERON:000099288.73gold quality
esophagogastric junction muscularis propriaUBERON:003584188.67gold quality
popliteal arteryUBERON:000225088.50gold quality
tibial arteryUBERON:000761088.50gold quality
cardiac atriumUBERON:000208188.02gold quality
muscle layer of sigmoid colonUBERON:003580587.17gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-7316yes22.80
E-ANND-3yes7.61

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting P3H3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-137-3P99.8774.742401
HSA-MIR-221-5P99.8665.451052
HSA-MIR-807399.8665.211118
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-430699.7270.503630
HSA-MIR-444199.4966.563216
HSA-MIR-6731-5P99.2867.422375
HSA-MIR-808599.2867.562362
HSA-MIR-877-3P99.0968.101637
HSA-MIR-429798.7766.952013
HSA-MIR-6852-3P98.5467.601468
HSA-MIR-6793-3P97.6665.781084
HSA-MIR-5196-3P97.5765.98979
HSA-MIR-3192-5P96.9865.761926
HSA-MIR-6759-3P96.9468.31823

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriop3h3ENSDARG00000057879
mus_musculusP3h3ENSMUSG00000023191
rattus_norvegicusP3h3ENSRNOG00000071218

Paralogs (2): P3H2 (ENSG00000090530), P3H1 (ENSG00000117385)

Protein

Protein identifiers

Prolyl 3-hydroxylase 3Q8IVL6 (reviewed: Q8IVL6)

Alternative names: Leprecan-like protein 2, Protein B

All UniProt accessions (1): Q8IVL6

UniProt curated annotations — full annotation on UniProt →

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. Required for normal hydroxylation of lysine residues in type I collagen chains in skin, bone, tendon, aorta and cornea. Required for normal skin stability via its role in hydroxylation of lysine residues in collagen alpha chains and in collagen fibril assembly. Apparently not required for normal prolyl 3-hydroxylation on collagen chains, possibly because it functions redundantly with other prolyl 3-hydroxylases.

Subunit / interactions. Identified in a complex with PLOD1 and P3H4.

Subcellular location. Endoplasmic reticulum.

Tissue specificity. Detected in fetal cartilage (at protein level). Weak expression in heart, lung, ovary and skeletal muscle.

Similarity. Belongs to the leprecan family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8IVL6-11yes
Q8IVL6-22

RefSeq proteins (1): NP_055077* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR005123Oxoglu/Fe-dep_dioxygenase_domDomain
IPR006620Pro_4_hyd_alphDomain
IPR011990TPR-like_helical_dom_sfHomologous_superfamily
IPR039575P3HFamily
IPR044862Pro_4_hyd_alph_FE2OG_OXYDomain
IPR056585Leprecan_domDomain

Pfam: PF13640, PF23557

Enzyme classification (BRENDA):

  • EC 1.14.11.28 — proline 3-hydroxylase (BRENDA: 5 organisms, 4 substrates, 14 inhibitors, 11 Km, 1 kcat entries)
  • EC 1.14.11.7 — procollagen-proline 3-dioxygenase (BRENDA: 5 organisms, 27 substrates, 31 inhibitors, 8 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

12 substrates with measured Km, best-characterized 12. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
L-PROLINE0.2–0.564
2-OXOGLUTARATE0.047–0.113
L-PIPECOLIC ACID3.8–1002
2-OXOGLUTARATE0.003–0.082
3,4-DEHYDRO-L-PROLINE8.41
L-2-AZETIDINECARBOXYLIC ACID2.11
(GLY-L-PRO-L-4-HYDROXYPROLINE)50.071
L-LEU-L-ASN-GLY-L-LEU-L-4HYP-GLY-L-PRO-L-ILE-GLY0.261
L-PRO-L-THR-GLY-L-PRO-L-ARG-GLY-L-PHE-L-PRO-GLY-0.071
L-SER-L-LYS-GLY-L-GLU-L-GLN-GLY-L-PHE-L-MET-GLY-0.261
O20.031
PROCOLLAGEN1

Catalyzed reactions (Rhea), 1 shown:

  • L-prolyl-[collagen] + 2-oxoglutarate + O2 = trans-3-hydroxy-L-prolyl-[collagen] + succinate + CO2 (RHEA:22872)

UniProt features (27 total): sequence variant 5, repeat 4, compositionally biased region 3, binding site 3, glycosylation site 2, region of interest 2, signal peptide 1, chain 1, short sequence motif 1, active site 1, splice variant 1, sequence conflict 1, domain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8IVL6-F181.070.49

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 666

Ligand- & substrate-binding residues (3): 584; 586; 656

Glycosylation sites (2): 331, 462

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-1650814Collagen biosynthesis and modifying enzymes

MSigDB gene sets: 134 (showing top): MODULE_416, MYOGENIN_Q6, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, PAL_PRMT5_TARGETS_UP, GCANCTGNY_MYOD_Q6, CAGCTG_AP4_Q5, GOBP_PEPTIDYL_LYSINE_MODIFICATION, HIF1_Q3, GOBP_PROTEIN_HYDROXYLATION, DURCHDEWALD_SKIN_CARCINOGENESIS_UP, GOMF_L_ASCORBIC_ACID_BINDING, GOMF_DIOXYGENASE_ACTIVITY, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_16, GOMF_ORGANIC_ACID_BINDING, GOMF_VITAMIN_BINDING

GO Biological Process (4): negative regulation of cell population proliferation (GO:0008285), peptidyl-lysine hydroxylation (GO:0017185), collagen metabolic process (GO:0032963), collagen biosynthetic process (GO:0032964)

GO Molecular Function (8): iron ion binding (GO:0005506), procollagen-proline 3-dioxygenase activity (GO:0019797), L-ascorbic acid binding (GO:0031418), protein binding (GO:0005515), oxidoreductase activity (GO:0016491), oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705), metal ion binding (GO:0046872), dioxygenase activity (GO:0051213)

GO Cellular Component (2): endoplasmic reticulum (GO:0005783), catalytic complex (GO:1902494)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Collagen formation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
oxidoreductase activity2
cell population proliferation1
regulation of cell population proliferation1
negative regulation of cellular process1
protein hydroxylation1
peptidyl-lysine modification1
metabolic process1
biosynthetic process1
collagen metabolic process1
transition metal ion binding1
procollagen-proline dioxygenase activity1
peptidyl-proline 3-dioxygenase activity1
vitamin binding1
carboxylic acid binding1
monosaccharide binding1
heterocyclic compound binding1
binding1
catalytic activity1
cation binding1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
protein-containing complex1

Protein interactions and networks

STRING

1092 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
P3H3DCNP07585964
P3H3RMDN3Q96TC7837
P3H3CENPBP07199715
P3H3DHRS2Q13268703
P3H3KLRK1P26718700
P3H3SFTPBP07988693
P3H3SFTPCP11686666
P3H3MAFO75444657
P3H3HNRNPRO43390652
P3H3TYRP1P17643636
P3H3FN1P02751621
P3H3BCL2P10415621
P3H3PLGP00747595
P3H3TP53P04637591
P3H3PLOD1Q02809562

IntAct

114 interactions, top by confidence:

ABTypeScore
C1QTNF9C1QTNF9Bpsi-mi:“MI:0914”(association)0.780
SOCS7NCK2psi-mi:“MI:0914”(association)0.670
FASLGPRMT2psi-mi:“MI:0914”(association)0.640
ZNF414AHCYL1psi-mi:“MI:0914”(association)0.640
HRGPLSCR1psi-mi:“MI:0914”(association)0.590
OS9AGRNpsi-mi:“MI:0914”(association)0.530
P3H3HSPA8psi-mi:“MI:0914”(association)0.530
EMILIN3ZZEF1psi-mi:“MI:0914”(association)0.530
INSL5COCHpsi-mi:“MI:0914”(association)0.530
PLAURXRCC3psi-mi:“MI:0914”(association)0.530
C1QTNF9BPLOD3psi-mi:“MI:0914”(association)0.530
KNG1CTSVpsi-mi:“MI:0914”(association)0.530
ADAMTS4MANBApsi-mi:“MI:0914”(association)0.530
C1orf54EXTL3psi-mi:“MI:0914”(association)0.530
IGFBP4MYCBP2psi-mi:“MI:0914”(association)0.530
CRPQSOX1psi-mi:“MI:0914”(association)0.530
PLOD3PLOD2psi-mi:“MI:0914”(association)0.530
PPP1R13LHSPA8psi-mi:“MI:0914”(association)0.530
TAF1CDNAJA2psi-mi:“MI:0914”(association)0.530
COL1A1GOLIM4psi-mi:“MI:0914”(association)0.500
CPSF6DDX39Apsi-mi:“MI:0914”(association)0.480
TK2psi-mi:“MI:0915”(physical association)0.400
SCGB2A2GXYLT2psi-mi:“MI:0914”(association)0.350
PLAURDDX11L8psi-mi:“MI:0914”(association)0.350
OLFM4DDX11L8psi-mi:“MI:0914”(association)0.350

BioGRID (121): LEPREL2 (Affinity Capture-MS), LEPREL2 (Affinity Capture-MS), LEPREL2 (Affinity Capture-MS), LEPREL2 (Affinity Capture-MS), LEPREL2 (Affinity Capture-MS), LEPREL2 (Affinity Capture-MS), LEPREL2 (Affinity Capture-MS), LEPREL2 (Affinity Capture-MS), LEPREL2 (Affinity Capture-MS), LEPREL2 (Affinity Capture-MS), LEPREL2 (Affinity Capture-MS), LEPREL2 (Affinity Capture-MS), PLOD1 (Affinity Capture-MS), LEPREL2 (Affinity Capture-MS), KEAP1 (Affinity Capture-MS)

ESM2 similar proteins: A1L515, A4D2P6, A6QQD2, A8VU90, E1BDF2, O75808, O88995, P0CG25, P22083, Q0IIA6, Q2TA57, Q3B7L1, Q3MIP1, Q3U5Q7, Q3UR50, Q3UR97, Q3UV16, Q400G9, Q5BKX5, Q5EBM0, Q5GH72, Q5SZI1, Q5TM19, Q5U4P2, Q62994, Q659K9, Q6PRD1, Q7Z736, Q861W0, Q86UR1, Q8BNN1, Q8C0R7, Q8CG70, Q8IUW3, Q8IVL6, Q8N398, Q8NAG6, Q8NCW0, Q8R2H1, Q8VCE9

Diamond homologs: O75718, Q32P28, Q3V1T4, Q4KLM6, Q64375, Q6JHU7, Q6JHU8, Q6PK18, Q8CG70, Q8CG71, Q8IVL5, Q8IVL6, Q8K2B0, Q90830, Q92791, Q9CYD3, Q9R1J8, Q5M843, Q5XGE0, Q9D136

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 133 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Collagen biosynthesis and modifying enzymes712.7×3e-04

GO biological processes:

GO termPartnersFoldFDR
collagen fibril organization815.8×4e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

68 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance44
Likely benign7
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2498 predictions. Top by Δscore:

VariantEffectΔscore
12:6829848:C:CAacceptor_gain1.0000
12:6829855:TCA:Tacceptor_loss1.0000
12:6829857:A:AGacceptor_gain1.0000
12:6829857:AGTT:Aacceptor_gain1.0000
12:6829858:G:GTacceptor_gain1.0000
12:6829858:GT:Gacceptor_gain1.0000
12:6829858:GTT:Gacceptor_gain1.0000
12:6829858:GTTG:Gacceptor_gain1.0000
12:6829858:GTTGA:Gacceptor_gain1.0000
12:6829943:GC:Gdonor_gain1.0000
12:6830010:GG:Gdonor_gain1.0000
12:6830011:GG:Gdonor_gain1.0000
12:6830012:G:GCdonor_loss1.0000
12:6830012:G:GGdonor_gain1.0000
12:6830013:T:Gdonor_loss1.0000
12:6830350:CAG:Cacceptor_loss1.0000
12:6830351:A:AGacceptor_gain1.0000
12:6830351:A:Tacceptor_loss1.0000
12:6830352:G:GAacceptor_loss1.0000
12:6830352:G:GGacceptor_gain1.0000
12:6830352:GGCA:Gacceptor_gain1.0000
12:6830552:CAGGT:Cdonor_loss1.0000
12:6830553:AGG:Adonor_loss1.0000
12:6830554:GGTA:Gdonor_loss1.0000
12:6830555:G:GCdonor_loss1.0000
12:6830740:C:Gdonor_gain1.0000
12:6830769:GG:Gdonor_gain1.0000
12:6830770:GG:Gdonor_gain1.0000
12:6831214:A:AGacceptor_gain1.0000
12:6831214:AGT:Aacceptor_gain1.0000

AlphaMissense

4693 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:6837758:A:CS580R0.997
12:6837760:T:AS580R0.997
12:6837760:T:GS580R0.997
12:6838005:T:CF626S0.996
12:6838005:T:GF626C0.996
12:6839110:G:CW672C0.995
12:6839110:G:TW672C0.995
12:6829898:T:CF180L0.993
12:6829900:C:AF180L0.993
12:6829900:C:GF180L0.993
12:6839036:T:CF648L0.993
12:6839038:C:AF648L0.993
12:6839038:C:GF648L0.993
12:6837782:T:AC588S0.992
12:6837783:G:CC588S0.992
12:6828570:G:TG44W0.991
12:6837550:T:CL563P0.991
12:6839025:G:CR644P0.991
12:6839060:C:GH656D0.991
12:6837540:T:CF560L0.990
12:6837542:C:AF560L0.990
12:6837542:C:GF560L0.990
12:6839028:T:CL645P0.990
12:6837777:A:TD586V0.989
12:6839108:T:AW672R0.989
12:6839108:T:CW672R0.989
12:6828571:G:AG44E0.988
12:6837783:G:AC588Y0.988
12:6837784:C:GC588W0.988
12:6837840:G:CR607P0.988

dbSNP variants (sampled 300 via entrez): RS1000061715 (12:6829050 T>A), RS1000633921 (12:6830301 C>T), RS1001117334 (12:6836634 C>G,T), RS1002497738 (12:6836769 C>G,T), RS1002774305 (12:6827749 A>G), RS1002947990 (12:6834103 C>A,G,T), RS1003215409 (12:6827561 G>A), RS1003286664 (12:6839006 G>A,C,T), RS1003288243 (12:6832561 C>T), RS1003320609 (12:6832289 C>T), RS1003904844 (12:6837619 C>A,T), RS1004325225 (12:6839491 C>T), RS1004340210 (12:6839219 T>C), RS1004491595 (12:6834188 G>A), RS1004644248 (12:6827019 C>G,T)

Disease associations

OMIM: gene MIM:610342 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST001450_2Response to Vitamin E supplementation4.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

1 annotations.

VariantTypeLevelDrugsPhenotypes
rs5441Efficacy3sertralineMajor Depressive Disorder

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs5441GNB3, P3H332.751sertraline

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, increases methylation3
sodium arsenitedecreases expression, increases abundance2
Benzo(a)pyreneaffects methylation, increases methylation2
aristolochic acid Idecreases expression1
bisphenol Adecreases expression1
cobaltous chloridedecreases expression1
perfluorooctanoic aciddecreases expression1
manganese chlorideincreases abundance, decreases expression1
benzo(e)pyrenedecreases methylation1
perfluorooctane sulfonic acidincreases expression1
2-palmitoylglycerolincreases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
jinfukangincreases expression, affects cotreatment1
Temozolomideaffects response to substance1
Sunitinibdecreases expression1
Air Pollutantsaffects expression, increases abundance1
Arsenicincreases abundance, decreases expression1
Carmustineaffects response to substance1
Cisplatinaffects cotreatment, increases expression1
Copperaffects binding, increases expression1
Disulfiramaffects binding, increases expression1
Doxorubicinincreases expression1
Estradiolaffects cotreatment, increases expression1
Ivermectindecreases expression1
Manganesedecreases expression, increases abundance1
Methapyrilenedecreases methylation1
Ozoneaffects expression, increases abundance1
Smokedecreases expression1
Tobacco Smoke Pollutiondecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.