CYP39A1

gene
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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

FieldValue
HGNC IDHGNC:17449
Approved symbolCYP39A1
Namecytochrome P450 family 39 subfamily A member 1
Location6p12.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000146233
Ensembl biotypeprotein_coding
OMIM605994
Entrez51302

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

ExonStartEnd
ENSE000009745994663949446639668
ENSE000009746004663782946637978
ENSE000009746024663096346631070
ENSE000009746054658803446588129
ENSE000009746064658707746587165
ENSE000009746074655376746553854
ENSE000010855424665240646652818
ENSE000010855454664216346642298
ENSE000036238984659598746596120
ENSE000036305064662541846625508
ENSE000036349434663638946636482
ENSE000037449304654958046550437

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 IDTPM avgSamples expressed
738480.5643310
738450.4233125
738490.091938
738460.084631
738470.050021

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
parotid glandUBERON:000183192.84gold quality
right lobe of liverUBERON:000111490.69gold quality
liverUBERON:000210790.01gold quality
mucosa of stomachUBERON:000119985.57gold quality
skin of abdomenUBERON:000141684.78gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.39gold quality
hair follicleUBERON:000207383.32gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099183.15gold quality
choroid plexus epitheliumUBERON:000391183.14gold quality
zone of skinUBERON:000001482.96gold quality
corpus epididymisUBERON:000435982.90gold quality
skin of legUBERON:000151182.41gold quality
upper leg skinUBERON:000426282.31gold quality
germinal epithelium of ovaryUBERON:000130481.12gold quality
left ovaryUBERON:000211981.08gold quality
gall bladderUBERON:000211080.52gold quality
ovaryUBERON:000099279.68gold quality
esophagogastric junction muscularis propriaUBERON:003584179.37gold quality
skin of hipUBERON:000155478.82gold quality
saliva-secreting glandUBERON:000104478.81gold quality
right ovaryUBERON:000211878.75gold quality
olfactory segment of nasal mucosaUBERON:000538678.32gold quality
prostate glandUBERON:000236778.05gold quality
mammalian vulvaUBERON:000099776.56gold quality
adrenal tissueUBERON:001830376.14gold quality
rectumUBERON:000105276.09gold quality
pigmented layer of retinaUBERON:000178276.06gold quality
retinaUBERON:000096676.05gold quality
minor salivary glandUBERON:000183075.52gold quality
body of pancreasUBERON:000115075.30gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no5.15

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):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-126-5P100.0072.713180
HSA-MIR-186-5P99.9970.833707
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-428299.9975.366408
HSA-MIR-548P99.9872.253784
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-767-5P99.9570.85993
HSA-MIR-568099.9169.833421
HSA-MIR-3681-3P99.8870.462254
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-94499.8270.853042
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-374C-5P99.8072.062910
HSA-MIR-655-3P99.8072.192909
HSA-MIR-33A-3P99.7070.273362
HSA-MIR-58699.6570.402051
HSA-MIR-548AH-5P99.5269.732626
HSA-MIR-360999.5269.892587
HSA-MIR-7159-3P99.5170.171920
HSA-MIR-1213299.4768.901341
HSA-MIR-582-5P99.4770.792635

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

OrganismSymbolGene ID
danio_reriocyp39a1ENSDARG00000017982
mus_musculusCyp39a1ENSMUSG00000023963
rattus_norvegicusCyp39a1ENSRNOG00000010519

Paralogs (2): CYP7A1 (ENSG00000167910), CYP7B1 (ENSG00000172817)

Protein

Protein identifiers

24-hydroxycholesterol 7-alpha-hydroxylaseQ9NYL5 (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)

IDNameType
IPR001128Cyt_P450Family
IPR002403Cyt_P450_E_grp-IVFamily
IPR024204Cyt_P450_CYP7A1-typeFamily
IPR036396Cyt_P450_sfHomologous_superfamily
IPR050529CYP51A1-likeFamily

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)

ModelpLDDTFraction very-high
AF-Q9NYL5-F192.060.78

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

IDPathway
R-HSA-193775Synthesis of bile acids and bile salts via 24-hydroxycholesterol
R-HSA-211976Endogenous 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:

CategoryPathways
Synthesis of bile acids and bile salts1
Cytochrome P450 - arranged by substrate type1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
steroid 7-alpha-hydroxylase activity2
oxidoreductase activity2
bile acid metabolic process1
monocarboxylic acid biosynthetic process1
cholesterol metabolic process1
sterol catabolic process1
alcohol catabolic process1
multicellular organismal process1
steroid metabolic process1
sterol homeostasis1
primary metabolic process1
lipid metabolic process1
sterol metabolic process1
secondary alcohol metabolic process1
biosynthetic process1
small molecule metabolic process1
transition metal ion binding1
monooxygenase activity1
tetrapyrrole binding1
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 oxygen1
binding1
steroid hydroxylase activity1
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen1
catalytic activity1
cation binding1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
intracellular anatomical structure1
membrane-bounded organelle1
intracellular organelle1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

1690 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CYP39A1NR1H4Q96RI1783
CYP39A1CYP46A1Q9Y6A2676
CYP39A1HSD3B7Q9H2F3636
CYP39A1CH25HO95992568
CYP39A1BAATQ14032548
CYP39A1CYP20A1Q6UW02532
CYP39A1PPARAQ07869525
CYP39A1SLC10A2Q12908497
CYP39A1HMGCRP04035482
CYP39A1ABCB11O95342462
CYP39A1AKR1D1P51857460
CYP39A1SLC51AQ86UW1449
CYP39A1GPBAR1Q8TDU6442
CYP39A1ESR1P03372441
CYP39A1SLC10A1Q14973436

IntAct

8 interactions, top by confidence:

ABTypeScore
CYP39A1HERC3psi-mi:“MI:0915”(physical association)0.590
CYP39A1GLULpsi-mi:“MI:0915”(physical association)0.370
CYP39A1ORM2psi-mi:“MI:0915”(physical association)0.370
CYP39A1SERINC1psi-mi:“MI:0915”(physical association)0.370
CYP39A1SMYD3psi-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):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance53
Likely benign10
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2408 predictions. Top by Δscore:

VariantEffectΔscore
6:46583418:A:ACdonor_gain1.0000
6:46583419:C:CCdonor_gain1.0000
6:46587073:TGAC:Tdonor_loss1.0000
6:46587075:ACC:Adonor_loss1.0000
6:46587076:CCT:Cdonor_loss1.0000
6:46587096:T:TAdonor_gain1.0000
6:46591978:T:Cdonor_gain1.0000
6:46636385:TTACC:Tdonor_loss1.0000
6:46636386:TAC:Tdonor_loss1.0000
6:46636387:A:ACdonor_gain1.0000
6:46636387:AC:Adonor_gain1.0000
6:46636387:ACCAT:Adonor_loss1.0000
6:46636388:C:Adonor_loss1.0000
6:46636388:C:CAdonor_gain1.0000
6:46636388:CC:Cdonor_gain1.0000
6:46636388:CCA:Cdonor_gain1.0000
6:46636388:CCAT:Cdonor_gain1.0000
6:46636388:CCATG:Cdonor_gain1.0000
6:46636478:AGTTT:Aacceptor_gain1.0000
6:46636479:GTTT:Gacceptor_gain1.0000
6:46636480:TTT:Tacceptor_gain1.0000
6:46636481:TT:Tacceptor_gain1.0000
6:46636481:TTC:Tacceptor_loss1.0000
6:46636483:C:CCacceptor_gain1.0000
6:46636483:CTA:Cacceptor_loss1.0000
6:46636484:T:Gacceptor_loss1.0000
6:46636486:C:CTacceptor_gain1.0000
6:46636487:A:ACacceptor_gain1.0000
6:46636487:A:Cacceptor_gain1.0000
6:46637823:TGTTA:Tdonor_loss1.0000

AlphaMissense

3099 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:46596051:T:AE334V0.991
6:46587159:A:GW390R0.983
6:46587159:A:TW390R0.983
6:46587106:A:CF407L0.982
6:46587106:A:TF407L0.982
6:46587108:A:GF407L0.982
6:46596043:G:TR337S0.982
6:46587157:C:AW390C0.977
6:46587157:C:GW390C0.977
6:46642284:A:CF64L0.974
6:46642284:A:TF64L0.974
6:46642286:A:GF64L0.974
6:46588058:A:CF379L0.973
6:46588058:A:TF379L0.973
6:46588060:A:GF379L0.973
6:46642251:A:CF75L0.973
6:46642251:A:TF75L0.973
6:46642253:A:GF75L0.973
6:46596050:T:AE334D0.970
6:46596050:T:GE334D0.970
6:46596042:C:GR337P0.967
6:46596051:T:GE334A0.967
6:46642279:A:TV66D0.964
6:46596043:G:CR337G0.963
6:46596061:A:GC331R0.962
6:46588101:A:GL365S0.961
6:46636464:T:AK219N0.961
6:46636464:T:GK219N0.961
6:46642252:A:GF75S0.961
6:46587158:C:GW390S0.960

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):

StudyTraitp-value
GCST007450_5Normal facial asymmetry (deformation magnitude)7.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0009751facial asymmetry measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

2 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs3757241CYP39A1, SLC25A270.000
rs10807344CYP39A1, SLC25A270.000

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.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression7
Benzo(a)pyrenedecreases expression, increases expression, increases methylation3
Aflatoxin B1affects expression, decreases expression3
trichostatin Adecreases expression, increases expression2
sodium arsenitedecreases expression, increases expression2
Acetaminophendecreases expression2
Nickeldecreases expression2
Tobacco Smoke Pollutiondecreases expression, increases expression2
Cyclosporinedecreases expression, increases expression2
methylmercuric chloridedecreases expression1
pirinixic acidaffects binding, increases activity, increases expression1
sulforaphaneincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
perfluorooctanoic aciddecreases expression1
ochratoxin Aincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
obeticholic aciddecreases expression1
belinostatincreases expression1
abrinedecreases expression1
dorsomorphinincreases expression, affects cotreatment1
Arsenic Trioxidedecreases expression1
Fulvestrantincreases methylation1
Vorinostatincreases expression1
Carbamazepineincreases expression1
Niclosamideincreases expression1
Tetrachlorodibenzodioxinincreases expression1
Thimerosalincreases expression1
Tretinoinincreases expression1
Antirheumatic Agentsincreases expression1
Okadaic Aciddecreases 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.