HomeAboutRankingsData Sources
© 2026 GeneE
🧬
GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
ⓘGeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
CYP39A1
cytochrome P450 family 39 subfamily A member 1
Chromosome 6 · 6p12.3
NCBI Gene: 51302Ensembl: ENSG00000146233.8HGNC: HGNC:17449UniProt: A0A087WTD2
17PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
bile acid biosynthetic processprotein bindingcholesterol homeostasissteroid hydroxylase activityDental malocclusionauditory system diseasecancerhepatocellular carcinoma
✦AI Summary

CYP39A1 is a cytochrome P450 monooxygenase primarily involved in neural cholesterol clearance through bile acid synthesis 12. It catalyzes 7-alpha hydroxylation of (24S)-hydroxycholesterol, a neural oxysterol metabolized to bile acids in the liver, using molecular oxygen and NADPH via cytochrome P450 reductase 12. Beyond canonical oxysterol metabolism, CYP39A1 exhibits tumor-suppressive functions. In hepatocellular carcinoma (HCC), CYP39A1 expression is dramatically reduced in >90% of patients, and its restoration blocks tumor formation in both sexes through a non-enzymatic mechanism involving c-Myc inhibition 3. Similarly, in colorectal cancer, CYP39A1 knockdown reduces tumor cell migration, invasion, angiogenesis, and lymphangiogenesis 4. Downregulation correlates with poor prognosis across cancers 56. Genetically, loss-of-function CYP39A1 variants associate with significant ocular pathology. The G204E variant confers 7.1-fold increased blindness risk and 5.1-fold increased exfoliation glaucoma risk in exfoliation syndrome patients 7. Rare damaging CYP39A1 variants show 3.55-fold association with exfoliation syndrome development 8, with 34 of 42 identified variants demonstrating >78% enzymatic activity reduction. CYP39A1 also influences busulfan clearance in pediatric stem cell transplantation, explaining 17% of pharmacokinetic variability when combined with GSTA1 9.

Sources cited
1
In hepatocellular carcinoma (HCC), CYP39A1 expression is dramatically reduced in >90% of patients, and its restoration blocks tumor formation in both sexes through a non-enzymatic mechanism involving c-Myc inhibition .
PMID: 34996827
2
Similarly, in colorectal cancer, CYP39A1 knockdown reduces tumor cell migration, invasion, angiogenesis, and lymphangiogenesis .
PMID: 37820439
3
The G204E variant confers 7.1-fold increased blindness risk and 5.1-fold increased exfoliation glaucoma risk in exfoliation syndrome patients .
PMID: 34763023
4
Rare damaging CYP39A1 variants show 3.55-fold association with exfoliation syndrome development , with 34 of 42 identified variants demonstrating >78% enzymatic activity reduction.
PMID: 33620406
5
CYP39A1 also influences busulfan clearance in pediatric stem cell transplantation, explaining 17% of pharmacokinetic variability when combined with GSTA1 .
PMID: 24192117
Disease Associationsⓘ20
Dental malocclusionOpen Targets
0.28Weak
auditory system diseaseOpen Targets
0.23Weak
cancerOpen Targets
0.17Weak
hepatocellular carcinomaOpen Targets
0.08Suggestive
neoplasmOpen Targets
0.07Suggestive
plasma fibronectin deficiencyOpen Targets
0.07Suggestive
Hereditary persistence of alpha-fetoproteinOpen Targets
0.04Suggestive
congenital enteropathy due to enteropeptidase deficiencyOpen Targets
0.03Suggestive
gastric mucosal hypertrophyOpen Targets
0.03Suggestive
exfoliation syndromeOpen Targets
0.03Suggestive
Congenital deficiency in alpha-fetoproteinOpen Targets
0.03Suggestive
placenta praeviaOpen Targets
0.03Suggestive
Infantile dystonia-parkinsonismOpen Targets
0.03Suggestive
parkinsonism-dystonia, infantileOpen Targets
0.03Suggestive
Acute hepatic failureOpen Targets
0.02Suggestive
cholangiocarcinomaOpen Targets
0.02Suggestive
ptosisOpen Targets
0.02Suggestive
tooth diseaseOpen Targets
0.02Suggestive
Parkinson diseaseOpen Targets
0.02Suggestive
glaucomaOpen Targets
0.02Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
FDFT1Protein interaction99%CH25HProtein interaction98%NR1H4Protein interaction81%HSD3B7Protein interaction78%LSSProtein interaction75%MSMO1Protein interaction75%
Tissue Expression6 tissues
Liver
100%
Ovary
23%
Heart
22%
Lung
3%
Brain
2%
Bone Marrow
0%
Gene Interaction Network
Click a node to explore
CYP39A1FDFT1CH25HNR1H4HSD3B7LSSMSMO1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q9NYL5
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.09LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.78 [0.57–1.09]
RankingsWhere CYP39A1 stands among ~20K protein-coding genes
  • #14,969of 20,598
    Most Researched17
  • #11,159of 17,882
    Most Constrained (LOEUF)1.09
Genes detectedCYP39A1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Blocking hepatocarcinogenesis by a cytochrome P450 family member with female-preferential expression.
PMID: 34996827
Gut · 2022
1.00
2
Expression of an oxysterol-metabolizing enzyme in colorectal cancer and its relation to tumor cell behavior and prognosis.
PMID: 37820439
Pathol Res Pract · 2023
0.90
3
Ligand-binding properties and catalytic activity of the purified human 24-hydroxycholesterol 7α-hydroxylase, CYP39A1.
PMID: 31247323
J Steroid Biochem Mol Biol · 2019
0.80
4
Association of CYP39A1, RUNX2 and oxidized alpha-1 antitrypsin expression in relation to cholangiocarcinoma progression.
PMID: 25556446
Asian Pac J Cancer Prev · 2014
0.70
5
Association of the CYP39A1 G204E Genetic Variant with Increased Risk of Glaucoma and Blindness in Patients with Exfoliation Syndrome.
PMID: 34763023
Ophthalmology · 2022
0.60