P3H3
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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
| Field | Value |
|---|---|
| HGNC ID | HGNC:19318 |
| Approved symbol | P3H3 |
| Name | prolyl 3-hydroxylase 3 |
| Location | 12p13.31 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | GRCB, HSU47926 |
| Ensembl gene | ENSG00000110811 |
| Ensembl biotype | protein_coding |
| OMIM | 610342 |
| Entrez | 10536 |
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
| Exon | Start | End |
|---|---|---|
| ENSE00003716307 | 6837732 | 6837849 |
| ENSE00003717606 | 6831216 | 6831352 |
| ENSE00003718001 | 6830353 | 6830554 |
| ENSE00003719383 | 6833742 | 6833809 |
| ENSE00003719454 | 6839297 | 6839847 |
| ENSE00003731100 | 6833925 | 6834049 |
| ENSE00003733737 | 6836985 | 6837086 |
| ENSE00003735096 | 6830639 | 6830770 |
| ENSE00003735524 | 6829859 | 6830011 |
| ENSE00003736780 | 6839000 | 6839140 |
| ENSE00003745173 | 6837423 | 6837573 |
| ENSE00003746469 | 6833592 | 6833644 |
| ENSE00003750871 | 6828407 | 6828938 |
| ENSE00003751035 | 6831825 | 6831914 |
| ENSE00003751828 | 6837958 | 6838033 |
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 ID | TPM avg | Samples expressed |
|---|---|---|
| 123766 | 15.9799 | 1349 |
| 123763 | 3.9989 | 1051 |
| 123762 | 1.4916 | 777 |
| 123764 | 0.8672 | 567 |
| 123765 | 0.4185 | 268 |
| 123767 | 0.2943 | 142 |
| 206557 | 0.0562 | 16 |
| 123768 | 0.0060 | 1 |
Top tissues by expression
287 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| stromal cell of endometrium | CL:0002255 | 97.87 | gold quality |
| adenohypophysis | UBERON:0002196 | 96.56 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 95.54 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 95.46 | gold quality |
| cerebellar cortex | UBERON:0002129 | 95.28 | gold quality |
| body of uterus | UBERON:0009853 | 95.07 | gold quality |
| pituitary gland | UBERON:0000007 | 95.06 | gold quality |
| apex of heart | UBERON:0002098 | 94.45 | gold quality |
| right ovary | UBERON:0002118 | 94.39 | gold quality |
| ascending aorta | UBERON:0001496 | 94.20 | gold quality |
| thoracic aorta | UBERON:0001515 | 94.15 | gold quality |
| descending thoracic aorta | UBERON:0002345 | 94.12 | gold quality |
| left ovary | UBERON:0002119 | 93.75 | gold quality |
| endocervix | UBERON:0000458 | 92.95 | gold quality |
| cerebellum | UBERON:0002037 | 92.64 | gold quality |
| left uterine tube | UBERON:0001303 | 92.58 | gold quality |
| right coronary artery | UBERON:0001625 | 92.28 | gold quality |
| tendon of biceps brachii | UBERON:0008188 | 91.83 | gold quality |
| left coronary artery | UBERON:0001626 | 90.84 | gold quality |
| aorta | UBERON:0000947 | 90.81 | gold quality |
| ectocervix | UBERON:0012249 | 90.78 | gold quality |
| mucosa of stomach | UBERON:0001199 | 90.75 | gold quality |
| right atrium auricular region | UBERON:0006631 | 89.96 | gold quality |
| coronary artery | UBERON:0001621 | 89.91 | gold quality |
| ovary | UBERON:0000992 | 88.73 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 88.67 | gold quality |
| popliteal artery | UBERON:0002250 | 88.50 | gold quality |
| tibial artery | UBERON:0007610 | 88.50 | gold quality |
| cardiac atrium | UBERON:0002081 | 88.02 | gold quality |
| muscle layer of sigmoid colon | UBERON:0035805 | 87.17 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 2.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-7316 | yes | 22.80 |
| E-ANND-3 | yes | 7.61 |
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):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-32-5P | 99.98 | 75.21 | 1964 |
| HSA-MIR-92A-3P | 99.98 | 75.21 | 1960 |
| HSA-MIR-92B-3P | 99.98 | 75.25 | 1955 |
| HSA-MIR-25-3P | 99.98 | 74.60 | 1817 |
| HSA-MIR-363-3P | 99.98 | 74.72 | 1821 |
| HSA-MIR-367-3P | 99.98 | 74.83 | 1819 |
| HSA-MIR-137-3P | 99.87 | 74.74 | 2401 |
| HSA-MIR-221-5P | 99.86 | 65.45 | 1052 |
| HSA-MIR-8073 | 99.86 | 65.21 | 1118 |
| HSA-MIR-92A-2-5P | 99.75 | 67.01 | 2164 |
| HSA-MIR-4306 | 99.72 | 70.50 | 3630 |
| HSA-MIR-4441 | 99.49 | 66.56 | 3216 |
| HSA-MIR-6731-5P | 99.28 | 67.42 | 2375 |
| HSA-MIR-8085 | 99.28 | 67.56 | 2362 |
| HSA-MIR-877-3P | 99.09 | 68.10 | 1637 |
| HSA-MIR-4297 | 98.77 | 66.95 | 2013 |
| HSA-MIR-6852-3P | 98.54 | 67.60 | 1468 |
| HSA-MIR-6793-3P | 97.66 | 65.78 | 1084 |
| HSA-MIR-5196-3P | 97.57 | 65.98 | 979 |
| HSA-MIR-3192-5P | 96.98 | 65.76 | 1926 |
| HSA-MIR-6759-3P | 96.94 | 68.31 | 823 |
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | p3h3 | ENSDARG00000057879 |
| mus_musculus | P3h3 | ENSMUSG00000023191 |
| rattus_norvegicus | P3h3 | ENSRNOG00000071218 |
Paralogs (2): P3H2 (ENSG00000090530), P3H1 (ENSG00000117385)
Protein
Protein identifiers
Prolyl 3-hydroxylase 3 — Q8IVL6 (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 ID | Names | Canonical? |
|---|---|---|
| Q8IVL6-1 | 1 | yes |
| Q8IVL6-2 | 2 |
RefSeq proteins (1): NP_055077* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR005123 | Oxoglu/Fe-dep_dioxygenase_dom | Domain |
| IPR006620 | Pro_4_hyd_alph | Domain |
| IPR011990 | TPR-like_helical_dom_sf | Homologous_superfamily |
| IPR039575 | P3H | Family |
| IPR044862 | Pro_4_hyd_alph_FE2OG_OXY | Domain |
| IPR056585 | Leprecan_dom | Domain |
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.
| Substrate | Km (mM) | Measurements |
|---|---|---|
| L-PROLINE | 0.2–0.56 | 4 |
| 2-OXOGLUTARATE | 0.047–0.11 | 3 |
| L-PIPECOLIC ACID | 3.8–100 | 2 |
| 2-OXOGLUTARATE | 0.003–0.08 | 2 |
| 3,4-DEHYDRO-L-PROLINE | 8.4 | 1 |
| L-2-AZETIDINECARBOXYLIC ACID | 2.1 | 1 |
| (GLY-L-PRO-L-4-HYDROXYPROLINE)5 | 0.07 | 1 |
| L-LEU-L-ASN-GLY-L-LEU-L-4HYP-GLY-L-PRO-L-ILE-GLY | 0.26 | 1 |
| L-PRO-L-THR-GLY-L-PRO-L-ARG-GLY-L-PHE-L-PRO-GLY- | 0.07 | 1 |
| L-SER-L-LYS-GLY-L-GLU-L-GLN-GLY-L-PHE-L-MET-GLY- | 0.26 | 1 |
| O2 | 0.03 | 1 |
| PROCOLLAGEN | — | 1 |
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)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q8IVL6-F1 | 81.07 | 0.49 |
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
| ID | Pathway |
|---|---|
| R-HSA-1650814 | Collagen 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:
| Category | Pathways |
|---|---|
| Collagen formation | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| oxidoreductase activity | 2 |
| cell population proliferation | 1 |
| regulation of cell population proliferation | 1 |
| negative regulation of cellular process | 1 |
| protein hydroxylation | 1 |
| peptidyl-lysine modification | 1 |
| metabolic process | 1 |
| biosynthetic process | 1 |
| collagen metabolic process | 1 |
| transition metal ion binding | 1 |
| procollagen-proline dioxygenase activity | 1 |
| peptidyl-proline 3-dioxygenase activity | 1 |
| vitamin binding | 1 |
| carboxylic acid binding | 1 |
| monosaccharide binding | 1 |
| heterocyclic compound binding | 1 |
| binding | 1 |
| catalytic activity | 1 |
| cation binding | 1 |
| cytoplasm | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
| protein-containing complex | 1 |
Protein interactions and networks
STRING
1092 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| P3H3 | DCN | P07585 | 964 |
| P3H3 | RMDN3 | Q96TC7 | 837 |
| P3H3 | CENPB | P07199 | 715 |
| P3H3 | DHRS2 | Q13268 | 703 |
| P3H3 | KLRK1 | P26718 | 700 |
| P3H3 | SFTPB | P07988 | 693 |
| P3H3 | SFTPC | P11686 | 666 |
| P3H3 | MAF | O75444 | 657 |
| P3H3 | HNRNPR | O43390 | 652 |
| P3H3 | TYRP1 | P17643 | 636 |
| P3H3 | FN1 | P02751 | 621 |
| P3H3 | BCL2 | P10415 | 621 |
| P3H3 | PLG | P00747 | 595 |
| P3H3 | TP53 | P04637 | 591 |
| P3H3 | PLOD1 | Q02809 | 562 |
IntAct
114 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| C1QTNF9 | C1QTNF9B | psi-mi:“MI:0914”(association) | 0.780 |
| SOCS7 | NCK2 | psi-mi:“MI:0914”(association) | 0.670 |
| FASLG | PRMT2 | psi-mi:“MI:0914”(association) | 0.640 |
| ZNF414 | AHCYL1 | psi-mi:“MI:0914”(association) | 0.640 |
| HRG | PLSCR1 | psi-mi:“MI:0914”(association) | 0.590 |
| OS9 | AGRN | psi-mi:“MI:0914”(association) | 0.530 |
| P3H3 | HSPA8 | psi-mi:“MI:0914”(association) | 0.530 |
| EMILIN3 | ZZEF1 | psi-mi:“MI:0914”(association) | 0.530 |
| INSL5 | COCH | psi-mi:“MI:0914”(association) | 0.530 |
| PLAUR | XRCC3 | psi-mi:“MI:0914”(association) | 0.530 |
| C1QTNF9B | PLOD3 | psi-mi:“MI:0914”(association) | 0.530 |
| KNG1 | CTSV | psi-mi:“MI:0914”(association) | 0.530 |
| ADAMTS4 | MANBA | psi-mi:“MI:0914”(association) | 0.530 |
| C1orf54 | EXTL3 | psi-mi:“MI:0914”(association) | 0.530 |
| IGFBP4 | MYCBP2 | psi-mi:“MI:0914”(association) | 0.530 |
| CRP | QSOX1 | psi-mi:“MI:0914”(association) | 0.530 |
| PLOD3 | PLOD2 | psi-mi:“MI:0914”(association) | 0.530 |
| PPP1R13L | HSPA8 | psi-mi:“MI:0914”(association) | 0.530 |
| TAF1C | DNAJA2 | psi-mi:“MI:0914”(association) | 0.530 |
| COL1A1 | GOLIM4 | psi-mi:“MI:0914”(association) | 0.500 |
| CPSF6 | DDX39A | psi-mi:“MI:0914”(association) | 0.480 |
| TK2 | psi-mi:“MI:0915”(physical association) | 0.400 | |
| SCGB2A2 | GXYLT2 | psi-mi:“MI:0914”(association) | 0.350 |
| PLAUR | DDX11L8 | psi-mi:“MI:0914”(association) | 0.350 |
| OLFM4 | DDX11L8 | psi-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:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| Collagen biosynthesis and modifying enzymes | 7 | 12.7× | 3e-04 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| collagen fibril organization | 8 | 15.8× | 4e-05 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
68 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 44 |
| Likely benign | 7 |
| Benign | 1 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2498 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 12:6829848:C:CA | acceptor_gain | 1.0000 |
| 12:6829855:TCA:T | acceptor_loss | 1.0000 |
| 12:6829857:A:AG | acceptor_gain | 1.0000 |
| 12:6829857:AGTT:A | acceptor_gain | 1.0000 |
| 12:6829858:G:GT | acceptor_gain | 1.0000 |
| 12:6829858:GT:G | acceptor_gain | 1.0000 |
| 12:6829858:GTT:G | acceptor_gain | 1.0000 |
| 12:6829858:GTTG:G | acceptor_gain | 1.0000 |
| 12:6829858:GTTGA:G | acceptor_gain | 1.0000 |
| 12:6829943:GC:G | donor_gain | 1.0000 |
| 12:6830010:GG:G | donor_gain | 1.0000 |
| 12:6830011:GG:G | donor_gain | 1.0000 |
| 12:6830012:G:GC | donor_loss | 1.0000 |
| 12:6830012:G:GG | donor_gain | 1.0000 |
| 12:6830013:T:G | donor_loss | 1.0000 |
| 12:6830350:CAG:C | acceptor_loss | 1.0000 |
| 12:6830351:A:AG | acceptor_gain | 1.0000 |
| 12:6830351:A:T | acceptor_loss | 1.0000 |
| 12:6830352:G:GA | acceptor_loss | 1.0000 |
| 12:6830352:G:GG | acceptor_gain | 1.0000 |
| 12:6830352:GGCA:G | acceptor_gain | 1.0000 |
| 12:6830552:CAGGT:C | donor_loss | 1.0000 |
| 12:6830553:AGG:A | donor_loss | 1.0000 |
| 12:6830554:GGTA:G | donor_loss | 1.0000 |
| 12:6830555:G:GC | donor_loss | 1.0000 |
| 12:6830740:C:G | donor_gain | 1.0000 |
| 12:6830769:GG:G | donor_gain | 1.0000 |
| 12:6830770:GG:G | donor_gain | 1.0000 |
| 12:6831214:A:AG | acceptor_gain | 1.0000 |
| 12:6831214:AGT:A | acceptor_gain | 1.0000 |
AlphaMissense
4693 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 12:6837758:A:C | S580R | 0.997 |
| 12:6837760:T:A | S580R | 0.997 |
| 12:6837760:T:G | S580R | 0.997 |
| 12:6838005:T:C | F626S | 0.996 |
| 12:6838005:T:G | F626C | 0.996 |
| 12:6839110:G:C | W672C | 0.995 |
| 12:6839110:G:T | W672C | 0.995 |
| 12:6829898:T:C | F180L | 0.993 |
| 12:6829900:C:A | F180L | 0.993 |
| 12:6829900:C:G | F180L | 0.993 |
| 12:6839036:T:C | F648L | 0.993 |
| 12:6839038:C:A | F648L | 0.993 |
| 12:6839038:C:G | F648L | 0.993 |
| 12:6837782:T:A | C588S | 0.992 |
| 12:6837783:G:C | C588S | 0.992 |
| 12:6828570:G:T | G44W | 0.991 |
| 12:6837550:T:C | L563P | 0.991 |
| 12:6839025:G:C | R644P | 0.991 |
| 12:6839060:C:G | H656D | 0.991 |
| 12:6837540:T:C | F560L | 0.990 |
| 12:6837542:C:A | F560L | 0.990 |
| 12:6837542:C:G | F560L | 0.990 |
| 12:6839028:T:C | L645P | 0.990 |
| 12:6837777:A:T | D586V | 0.989 |
| 12:6839108:T:A | W672R | 0.989 |
| 12:6839108:T:C | W672R | 0.989 |
| 12:6828571:G:A | G44E | 0.988 |
| 12:6837783:G:A | C588Y | 0.988 |
| 12:6837784:C:G | C588W | 0.988 |
| 12:6837840:G:C | R607P | 0.988 |
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):
| Study | Trait | p-value |
|---|---|---|
| GCST001450_2 | Response to Vitamin E supplementation | 4.000000e-06 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
PharmGKB clinical annotations
1 annotations.
| Variant | Type | Level | Drugs | Phenotypes |
|---|---|---|---|---|
| rs5441 | Efficacy | 3 | sertraline | Major Depressive Disorder |
PharmGKB variants
1 variants.
| Variant | Genes | Level | Score | #Clin annots | Drugs |
|---|---|---|---|---|---|
| rs5441 | GNB3, P3H3 | 3 | 2.75 | 1 | sertraline |
CTD chemical–gene interactions
33 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | decreases expression, increases methylation | 3 |
| sodium arsenite | decreases expression, increases abundance | 2 |
| Benzo(a)pyrene | affects methylation, increases methylation | 2 |
| aristolochic acid I | decreases expression | 1 |
| bisphenol A | decreases expression | 1 |
| cobaltous chloride | decreases expression | 1 |
| perfluorooctanoic acid | decreases expression | 1 |
| manganese chloride | increases abundance, decreases expression | 1 |
| benzo(e)pyrene | decreases methylation | 1 |
| perfluorooctane sulfonic acid | increases expression | 1 |
| 2-palmitoylglycerol | increases expression | 1 |
| bisphenol B | increases expression | 1 |
| abrine | decreases expression | 1 |
| jinfukang | increases expression, affects cotreatment | 1 |
| Temozolomide | affects response to substance | 1 |
| Sunitinib | decreases expression | 1 |
| Air Pollutants | affects expression, increases abundance | 1 |
| Arsenic | increases abundance, decreases expression | 1 |
| Carmustine | affects response to substance | 1 |
| Cisplatin | affects cotreatment, increases expression | 1 |
| Copper | affects binding, increases expression | 1 |
| Disulfiram | affects binding, increases expression | 1 |
| Doxorubicin | increases expression | 1 |
| Estradiol | affects cotreatment, increases expression | 1 |
| Ivermectin | decreases expression | 1 |
| Manganese | decreases expression, increases abundance | 1 |
| Methapyrilene | decreases methylation | 1 |
| Ozone | affects expression, increases abundance | 1 |
| Smoke | decreases expression | 1 |
| Tobacco Smoke Pollution | decreases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.