CYP39A1
gene geneOn this page
Summary
CYP39A1 (cytochrome P450 family 39 subfamily A member 1, HGNC:17449) is a protein-coding gene on chromosome 6p12.3, encoding 24-hydroxycholesterol 7-alpha-hydroxylase (Q9NYL5). A cytochrome P450 monooxygenase involved in neural cholesterol clearance through bile acid synthesis.
This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This endoplasmic reticulum protein is involved in the conversion of cholesterol to bile acids. Its substrates include the oxysterols 25-hydroxycholesterol, 27-hydroxycholesterol and 24-hydroxycholesterol. Alternate splicing results in multiple transcript variants.
Source: NCBI Gene 51302 — RefSeq curated summary.
At a glance
- GWAS associations: 1
- Clinical variants (ClinVar): 77 total
- MANE Select transcript:
NM_016593
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:17449 |
| Approved symbol | CYP39A1 |
| Name | cytochrome P450 family 39 subfamily A member 1 |
| Location | 6p12.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Ensembl gene | ENSG00000146233 |
| Ensembl biotype | protein_coding |
| OMIM | 605994 |
| Entrez | 51302 |
Gene structure
Transcript identifiers
Ensembl transcripts: 9 — 6 protein_coding, 3 protein_coding_CDS_not_defined
ENST00000275016, ENST00000476076, ENST00000480804, ENST00000489657, ENST00000619708, ENST00000889607, ENST00000889608, ENST00000889609, ENST00000889610
RefSeq mRNA: 3 — MANE Select: NM_016593
NM_001278738, NM_001278739, NM_016593
CCDS: CCDS4916, CCDS75465
Canonical transcript exons
ENST00000275016 — 12 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000974599 | 46639494 | 46639668 |
| ENSE00000974600 | 46637829 | 46637978 |
| ENSE00000974602 | 46630963 | 46631070 |
| ENSE00000974605 | 46588034 | 46588129 |
| ENSE00000974606 | 46587077 | 46587165 |
| ENSE00000974607 | 46553767 | 46553854 |
| ENSE00001085542 | 46652406 | 46652818 |
| ENSE00001085545 | 46642163 | 46642298 |
| ENSE00003623898 | 46595987 | 46596120 |
| ENSE00003630506 | 46625418 | 46625508 |
| ENSE00003634943 | 46636389 | 46636482 |
| ENSE00003744930 | 46549580 | 46550437 |
Expression profiles
Bgee: expression breadth ubiquitous, 218 present calls, max score 92.84.
FANTOM5 (CAGE): breadth broad, TPM avg 1.2141 / max 65.6152, expressed in 461 samples.
FANTOM5 promoters (5 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 73848 | 0.5643 | 310 |
| 73845 | 0.4233 | 125 |
| 73849 | 0.0919 | 38 |
| 73846 | 0.0846 | 31 |
| 73847 | 0.0500 | 21 |
Top tissues by expression
282 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| parotid gland | UBERON:0001831 | 92.84 | gold quality |
| right lobe of liver | UBERON:0001114 | 90.69 | gold quality |
| liver | UBERON:0002107 | 90.01 | gold quality |
| mucosa of stomach | UBERON:0001199 | 85.57 | gold quality |
| skin of abdomen | UBERON:0001416 | 84.78 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 83.39 | gold quality |
| hair follicle | UBERON:0002073 | 83.32 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 83.15 | gold quality |
| choroid plexus epithelium | UBERON:0003911 | 83.14 | gold quality |
| zone of skin | UBERON:0000014 | 82.96 | gold quality |
| corpus epididymis | UBERON:0004359 | 82.90 | gold quality |
| skin of leg | UBERON:0001511 | 82.41 | gold quality |
| upper leg skin | UBERON:0004262 | 82.31 | gold quality |
| germinal epithelium of ovary | UBERON:0001304 | 81.12 | gold quality |
| left ovary | UBERON:0002119 | 81.08 | gold quality |
| gall bladder | UBERON:0002110 | 80.52 | gold quality |
| ovary | UBERON:0000992 | 79.68 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 79.37 | gold quality |
| skin of hip | UBERON:0001554 | 78.82 | gold quality |
| saliva-secreting gland | UBERON:0001044 | 78.81 | gold quality |
| right ovary | UBERON:0002118 | 78.75 | gold quality |
| olfactory segment of nasal mucosa | UBERON:0005386 | 78.32 | gold quality |
| prostate gland | UBERON:0002367 | 78.05 | gold quality |
| mammalian vulva | UBERON:0000997 | 76.56 | gold quality |
| adrenal tissue | UBERON:0018303 | 76.14 | gold quality |
| rectum | UBERON:0001052 | 76.09 | gold quality |
| pigmented layer of retina | UBERON:0001782 | 76.06 | gold quality |
| retina | UBERON:0000966 | 76.05 | gold quality |
| minor salivary gland | UBERON:0001830 | 75.52 | gold quality |
| body of pancreas | UBERON:0001150 | 75.30 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 0.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 5.15 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
53 targeting CYP39A1, 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-513A-5P | 100.00 | 69.77 | 2465 |
| HSA-MIR-126-5P | 100.00 | 72.71 | 3180 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-4282 | 99.99 | 75.36 | 6408 |
| HSA-MIR-548P | 99.98 | 72.25 | 3784 |
| HSA-MIR-27A-3P | 99.98 | 72.13 | 2955 |
| HSA-MIR-27B-3P | 99.98 | 72.13 | 2955 |
| HSA-MIR-9985 | 99.98 | 72.11 | 2939 |
| HSA-MIR-4482-3P | 99.98 | 72.50 | 3147 |
| HSA-MIR-551B-5P | 99.96 | 71.28 | 3493 |
| HSA-MIR-128-3P | 99.95 | 71.17 | 2484 |
| HSA-MIR-216A-3P | 99.95 | 71.19 | 2505 |
| HSA-MIR-767-5P | 99.95 | 70.85 | 993 |
| HSA-MIR-5680 | 99.91 | 69.83 | 3421 |
| HSA-MIR-3681-3P | 99.88 | 70.46 | 2254 |
| HSA-MIR-106B-5P | 99.88 | 74.72 | 2795 |
| HSA-MIR-20A-5P | 99.88 | 74.76 | 2769 |
| HSA-MIR-5003-3P | 99.85 | 69.29 | 2517 |
| HSA-MIR-944 | 99.82 | 70.85 | 3042 |
| HSA-MIR-3121-3P | 99.82 | 71.96 | 3630 |
| HSA-MIR-374C-5P | 99.80 | 72.06 | 2910 |
| HSA-MIR-655-3P | 99.80 | 72.19 | 2909 |
| HSA-MIR-33A-3P | 99.70 | 70.27 | 3362 |
| HSA-MIR-586 | 99.65 | 70.40 | 2051 |
| HSA-MIR-548AH-5P | 99.52 | 69.73 | 2626 |
| HSA-MIR-3609 | 99.52 | 69.89 | 2587 |
| HSA-MIR-7159-3P | 99.51 | 70.17 | 1920 |
| HSA-MIR-12132 | 99.47 | 68.90 | 1341 |
| HSA-MIR-582-5P | 99.47 | 70.79 | 2635 |
Literature-anchored findings (GeneRIF, showing 6)
- The rs754203 SNP in CYP46A1 was associated with a risk for POAG. This polymorphism was not associated with changes in plasma 24S-hydroxycholesterol. (PMID:19553612)
- GSTA1 and CYP39A1 were found to be associated with busulfan clearance. When combined, the two haplotypes explained 17% of the variability in busulfan clearance. (PMID:24192117)
- The CYP39A1 polymorphism rs7761731 may help to identify patients at high risk for treatment related toxicity. (PMID:26475344)
- Orphan Nuclear Receptor RORalpha Regulates Enzymatic Metabolism of Cerebral 24S-Hydroxycholesterol through CYP39A1 Intronic Response Element Activation. (PMID:32392803)
- Association of Rare CYP39A1 Variants With Exfoliation Syndrome Involving the Anterior Chamber of the Eye. (PMID:33620406)
- Association of the CYP39A1 G204E Genetic Variant with Increased Risk of Glaucoma and Blindness in Patients with Exfoliation Syndrome. (PMID:34763023)
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | cyp39a1 | ENSDARG00000017982 |
| mus_musculus | Cyp39a1 | ENSMUSG00000023963 |
| rattus_norvegicus | Cyp39a1 | ENSRNOG00000010519 |
Paralogs (2): CYP7A1 (ENSG00000167910), CYP7B1 (ENSG00000172817)
Protein
Protein identifiers
24-hydroxycholesterol 7-alpha-hydroxylase — Q9NYL5 (reviewed: Q9NYL5)
Alternative names: Cytochrome P450 39A1, Oxysterol 7-alpha-hydroxylase
All UniProt accessions (2): Q9NYL5, A0A087WTD2
UniProt curated annotations — full annotation on UniProt →
Function. A cytochrome P450 monooxygenase involved in neural cholesterol clearance through bile acid synthesis. Catalyzes 7-alpha hydroxylation of (24S)-hydroxycholesterol, a neural oxysterol that is metabolized to bile acids in the liver. Mechanistically, uses molecular oxygen inserting one oxygen atom into a substrate, and reducing the second into a water molecule, with two electrons provided by NADPH via cytochrome P450 reductase (CPR; NADPH-ferrihemoprotein reductase).
Subcellular location. Endoplasmic reticulum membrane. Microsome membrane.
Tissue specificity. Liver specific.
Pathway. Steroid metabolism; cholesterol degradation. Lipid metabolism; bile acid biosynthesis.
Polymorphism. Variations in CYP39A1 are associated with elevated serum (24S)-hydroxycholesterol levels among a cohort of American residents.
Similarity. Belongs to the cytochrome P450 family.
RefSeq proteins (3): NP_001265667, NP_001265668, NP_057677* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR001128 | Cyt_P450 | Family |
| IPR002403 | Cyt_P450_E_grp-IV | Family |
| IPR024204 | Cyt_P450_CYP7A1-type | Family |
| IPR036396 | Cyt_P450_sf | Homologous_superfamily |
| IPR050529 | CYP51A1-like | Family |
Pfam: PF00067
Catalyzed reactions (Rhea), 1 shown:
- (24S)-hydroxycholesterol + reduced [NADPH–hemoprotein reductase] + O2 = (24S)-7alpha-dihydroxycholesterol + oxidized [NADPH–hemoprotein reductase] + H2O + H(+) (RHEA:46124)
UniProt features (11 total): sequence variant 5, transmembrane region 3, signal peptide 1, chain 1, binding site 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9NYL5-F1 | 92.06 | 0.78 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Ligand- & substrate-binding residues (1): 414 (axial binding residue)
Function
Pathways and Gene Ontology
Reactome pathways
2 pathways
| ID | Pathway |
|---|---|
| R-HSA-193775 | Synthesis of bile acids and bile salts via 24-hydroxycholesterol |
| R-HSA-211976 | Endogenous sterols |
MSigDB gene sets: 164 (showing top):
GOBP_DIGESTION, REACTOME_BIOLOGICAL_OXIDATIONS, BENPORATH_ES_WITH_H3K27ME3, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, GOBP_STEROL_HOMEOSTASIS, RORA1_01, YANG_BREAST_CANCER_ESR1_LASER_DN, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, REACTOME_ENDOGENOUS_STEROLS, TGACCTY_ERR1_Q2, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_BIOSYNTHETIC_PROCESS, GOBP_BILE_ACID_BIOSYNTHETIC_PROCESS, GOBP_LIPID_HOMEOSTASIS, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS
GO Biological Process (9): bile acid biosynthetic process (GO:0006699), cholesterol catabolic process (GO:0006707), digestion (GO:0007586), sterol metabolic process (GO:0016125), cholesterol homeostasis (GO:0042632), lipid metabolic process (GO:0006629), steroid metabolic process (GO:0008202), cholesterol metabolic process (GO:0008203), small molecule biosynthetic process (GO:0044283)
GO Molecular Function (11): iron ion binding (GO:0005506), steroid hydroxylase activity (GO:0008395), oxysterol 7-alpha-hydroxylase activity (GO:0008396), heme binding (GO:0020037), 24S-hydroxycholesterol 7-alpha-hydroxylase activity (GO:0033782), monooxygenase activity (GO:0004497), protein binding (GO:0005515), steroid 7-alpha-hydroxylase activity (GO:0008387), oxidoreductase activity (GO:0016491), oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705), metal ion binding (GO:0046872)
GO Cellular Component (4): endoplasmic reticulum membrane (GO:0005789), intracellular membrane-bounded organelle (GO:0043231), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)
Reactome top-level categories
Rollup of top-2 pathways:
| Category | Pathways |
|---|---|
| Synthesis of bile acids and bile salts | 1 |
| Cytochrome P450 - arranged by substrate type | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| steroid 7-alpha-hydroxylase activity | 2 |
| oxidoreductase activity | 2 |
| bile acid metabolic process | 1 |
| monocarboxylic acid biosynthetic process | 1 |
| cholesterol metabolic process | 1 |
| sterol catabolic process | 1 |
| alcohol catabolic process | 1 |
| multicellular organismal process | 1 |
| steroid metabolic process | 1 |
| sterol homeostasis | 1 |
| primary metabolic process | 1 |
| lipid metabolic process | 1 |
| sterol metabolic process | 1 |
| secondary alcohol metabolic process | 1 |
| biosynthetic process | 1 |
| small molecule metabolic process | 1 |
| transition metal ion binding | 1 |
| monooxygenase activity | 1 |
| tetrapyrrole binding | 1 |
| oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen | 1 |
| binding | 1 |
| steroid hydroxylase activity | 1 |
| oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | 1 |
| catalytic activity | 1 |
| cation binding | 1 |
| organelle membrane | 1 |
| nuclear outer membrane-endoplasmic reticulum membrane network | 1 |
| endoplasmic reticulum subcompartment | 1 |
| intracellular anatomical structure | 1 |
| membrane-bounded organelle | 1 |
| intracellular organelle | 1 |
| cytoplasm | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
1690 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| CYP39A1 | NR1H4 | Q96RI1 | 783 |
| CYP39A1 | CYP46A1 | Q9Y6A2 | 676 |
| CYP39A1 | HSD3B7 | Q9H2F3 | 636 |
| CYP39A1 | CH25H | O95992 | 568 |
| CYP39A1 | BAAT | Q14032 | 548 |
| CYP39A1 | CYP20A1 | Q6UW02 | 532 |
| CYP39A1 | PPARA | Q07869 | 525 |
| CYP39A1 | SLC10A2 | Q12908 | 497 |
| CYP39A1 | HMGCR | P04035 | 482 |
| CYP39A1 | ABCB11 | O95342 | 462 |
| CYP39A1 | AKR1D1 | P51857 | 460 |
| CYP39A1 | SLC51A | Q86UW1 | 449 |
| CYP39A1 | GPBAR1 | Q8TDU6 | 442 |
| CYP39A1 | ESR1 | P03372 | 441 |
| CYP39A1 | SLC10A1 | Q14973 | 436 |
IntAct
8 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| CYP39A1 | HERC3 | psi-mi:“MI:0915”(physical association) | 0.590 |
| CYP39A1 | GLUL | psi-mi:“MI:0915”(physical association) | 0.370 |
| CYP39A1 | ORM2 | psi-mi:“MI:0915”(physical association) | 0.370 |
| CYP39A1 | SERINC1 | psi-mi:“MI:0915”(physical association) | 0.370 |
| CYP39A1 | SMYD3 | psi-mi:“MI:0915”(physical association) | 0.370 |
BioGRID (7): HERC3 (Affinity Capture-MS), HERC3 (Affinity Capture-MS), CYP39A1 (Positive Genetic), SERINC1 (Two-hybrid), ORM2 (Two-hybrid), GLUL (Two-hybrid), SMYD3 (Two-hybrid)
ESM2 similar proteins: B2RXA7, E1BHJ4, F1RE08, G3V7X8, O02766, O35074, O35084, O43174, O46491, O46515, O75881, O88962, O93323, P00189, P05108, P0DOX0, P10612, P14137, P15393, P17177, P17178, P18125, P22680, P46634, P51542, P79153, P79202, P97720, Q08D50, Q16647, Q28827, Q29626, Q2XV99, Q4G0S4, Q60991, Q62969, Q63688, Q64408, Q64505, Q6EIG3
Diamond homologs: A0A017SFB8, A0A017SR40, A0A068A9T2, A0A068AA98, A0A068ACU3, A0A084API1, A0A0F7U0K0, A0A0P0ZEA9, A0A1B4XBH0, A0A1B4XBH8, A0A1E3B0R7, A0A1L7VEQ6, A0A1L9WQK2, A0A1R3RGJ7, A0A1V1FNM9, A0A2P1DPA5, A0A397HSG2, A0A3S9NM20, A0A411KUQ5, A0A455ZIK8, A0A481WPJ6, A0A4P8DJC8, A0A831A9C9, A0A8K1AW54, A1C8C2, A2R6G9, A8C7R4, B6HFX9, B8NHD9, B8NM64, C8V7P3, C8VJR0, C9K1X6, D1MX85, E9KMQ3, G0KYB2, G1XU01, G3Y420, I7C6E8, K2RLM2
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
77 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 53 |
| Likely benign | 10 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2408 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 6:46583418:A:AC | donor_gain | 1.0000 |
| 6:46583419:C:CC | donor_gain | 1.0000 |
| 6:46587073:TGAC:T | donor_loss | 1.0000 |
| 6:46587075:ACC:A | donor_loss | 1.0000 |
| 6:46587076:CCT:C | donor_loss | 1.0000 |
| 6:46587096:T:TA | donor_gain | 1.0000 |
| 6:46591978:T:C | donor_gain | 1.0000 |
| 6:46636385:TTACC:T | donor_loss | 1.0000 |
| 6:46636386:TAC:T | donor_loss | 1.0000 |
| 6:46636387:A:AC | donor_gain | 1.0000 |
| 6:46636387:AC:A | donor_gain | 1.0000 |
| 6:46636387:ACCAT:A | donor_loss | 1.0000 |
| 6:46636388:C:A | donor_loss | 1.0000 |
| 6:46636388:C:CA | donor_gain | 1.0000 |
| 6:46636388:CC:C | donor_gain | 1.0000 |
| 6:46636388:CCA:C | donor_gain | 1.0000 |
| 6:46636388:CCAT:C | donor_gain | 1.0000 |
| 6:46636388:CCATG:C | donor_gain | 1.0000 |
| 6:46636478:AGTTT:A | acceptor_gain | 1.0000 |
| 6:46636479:GTTT:G | acceptor_gain | 1.0000 |
| 6:46636480:TTT:T | acceptor_gain | 1.0000 |
| 6:46636481:TT:T | acceptor_gain | 1.0000 |
| 6:46636481:TTC:T | acceptor_loss | 1.0000 |
| 6:46636483:C:CC | acceptor_gain | 1.0000 |
| 6:46636483:CTA:C | acceptor_loss | 1.0000 |
| 6:46636484:T:G | acceptor_loss | 1.0000 |
| 6:46636486:C:CT | acceptor_gain | 1.0000 |
| 6:46636487:A:AC | acceptor_gain | 1.0000 |
| 6:46636487:A:C | acceptor_gain | 1.0000 |
| 6:46637823:TGTTA:T | donor_loss | 1.0000 |
AlphaMissense
3099 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 6:46596051:T:A | E334V | 0.991 |
| 6:46587159:A:G | W390R | 0.983 |
| 6:46587159:A:T | W390R | 0.983 |
| 6:46587106:A:C | F407L | 0.982 |
| 6:46587106:A:T | F407L | 0.982 |
| 6:46587108:A:G | F407L | 0.982 |
| 6:46596043:G:T | R337S | 0.982 |
| 6:46587157:C:A | W390C | 0.977 |
| 6:46587157:C:G | W390C | 0.977 |
| 6:46642284:A:C | F64L | 0.974 |
| 6:46642284:A:T | F64L | 0.974 |
| 6:46642286:A:G | F64L | 0.974 |
| 6:46588058:A:C | F379L | 0.973 |
| 6:46588058:A:T | F379L | 0.973 |
| 6:46588060:A:G | F379L | 0.973 |
| 6:46642251:A:C | F75L | 0.973 |
| 6:46642251:A:T | F75L | 0.973 |
| 6:46642253:A:G | F75L | 0.973 |
| 6:46596050:T:A | E334D | 0.970 |
| 6:46596050:T:G | E334D | 0.970 |
| 6:46596042:C:G | R337P | 0.967 |
| 6:46596051:T:G | E334A | 0.967 |
| 6:46642279:A:T | V66D | 0.964 |
| 6:46596043:G:C | R337G | 0.963 |
| 6:46596061:A:G | C331R | 0.962 |
| 6:46588101:A:G | L365S | 0.961 |
| 6:46636464:T:A | K219N | 0.961 |
| 6:46636464:T:G | K219N | 0.961 |
| 6:46642252:A:G | F75S | 0.961 |
| 6:46587158:C:G | W390S | 0.960 |
dbSNP variants (sampled 300 via entrez): RS1000036463 (6:46632950 T>C), RS1000055341 (6:46609913 T>C), RS1000058560 (6:46618170 T>A), RS1000121095 (6:46608802 C>T), RS1000168292 (6:46567927 G>A), RS1000173815 (6:46608574 C>T), RS1000175868 (6:46621349 T>G), RS1000252495 (6:46559035 G>T), RS1000274025 (6:46615528 G>A), RS1000310421 (6:46639000 C>A), RS1000310449 (6:46633552 A>T), RS1000344599 (6:46602241 G>A,C), RS1000399610 (6:46644804 T>C), RS1000480268 (6:46565361 G>A), RS1000517231 (6:46557325 C>G,T)
Disease associations
OMIM: gene MIM:605994 | 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 |
|---|---|---|
| GCST007450_5 | Normal facial asymmetry (deformation magnitude) | 7.000000e-06 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0009751 | facial asymmetry measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
PharmGKB variants
2 variants.
| Variant | Genes | Level | Score | #Clin annots | Drugs |
|---|---|---|---|---|---|
| rs3757241 | CYP39A1, SLC25A27 | 0.00 | 0 | ||
| rs10807344 | CYP39A1, SLC25A27 | 0.00 | 0 |
GtoPdb / IUPHAR curated pharmacology
(IUPHAR/BPS Guide to Pharmacology — expert-curated)
Target class: enzyme — CYP39, CYP46 and CYP51 families
CTD chemical–gene interactions
32 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects cotreatment, increases expression, affects expression | 7 |
| Benzo(a)pyrene | decreases expression, increases expression, increases methylation | 3 |
| Aflatoxin B1 | affects expression, decreases expression | 3 |
| trichostatin A | decreases expression, increases expression | 2 |
| sodium arsenite | decreases expression, increases expression | 2 |
| Acetaminophen | decreases expression | 2 |
| Nickel | decreases expression | 2 |
| Tobacco Smoke Pollution | decreases expression, increases expression | 2 |
| Cyclosporine | decreases expression, increases expression | 2 |
| methylmercuric chloride | decreases expression | 1 |
| pirinixic acid | affects binding, increases activity, increases expression | 1 |
| sulforaphane | increases expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | increases expression | 1 |
| perfluorooctanoic acid | decreases expression | 1 |
| ochratoxin A | increases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, increases expression | 1 |
| obeticholic acid | decreases expression | 1 |
| belinostat | increases expression | 1 |
| abrine | decreases expression | 1 |
| dorsomorphin | increases expression, affects cotreatment | 1 |
| Arsenic Trioxide | decreases expression | 1 |
| Fulvestrant | increases methylation | 1 |
| Vorinostat | increases expression | 1 |
| Carbamazepine | increases expression | 1 |
| Niclosamide | increases expression | 1 |
| Tetrachlorodibenzodioxin | increases expression | 1 |
| Thimerosal | increases expression | 1 |
| Tretinoin | increases expression | 1 |
| Antirheumatic Agents | increases expression | 1 |
| Okadaic Acid | 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.