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-hydroxy... See more...

Aliases for CYP39A1 Gene

Aliases for CYP39A1 Gene

  • Cytochrome P450 Family 39 Subfamily A Member 1 2 3 5
  • Cytochrome P450, Subfamily XXXIX (Oxysterol 7 Alpha-Hydroxylase), Polypeptide 1 2 3
  • Cytochrome P450, Family 39, Subfamily A, Polypeptide 1 2 3
  • 24-Hydroxycholesterol 7-Alpha-Hydroxylase 3 4
  • Oxysterol 7-Alpha-Hydroxylase 4
  • Cytochrome P450 39A1 4
  • EC 1.14.14.26 4
  • HCYP39A1 4
  • CYP39A1 5

External Ids for CYP39A1 Gene

Previous GeneCards Identifiers for CYP39A1 Gene

  • GC06M046519
  • GC06M046564
  • GC06M046625
  • GC06M046240

Summaries for CYP39A1 Gene

Entrez Gene Summary for CYP39A1 Gene

  • 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. [provided by RefSeq, Jul 2013]

GeneCards Summary for CYP39A1 Gene

CYP39A1 (Cytochrome P450 Family 39 Subfamily A Member 1) is a Protein Coding gene. Diseases associated with CYP39A1 include Leber Plus Disease. Among its related pathways are Cytochrome P450 - arranged by substrate type and Synthesis of bile acids and bile salts. Gene Ontology (GO) annotations related to this gene include iron ion binding and oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen. An important paralog of this gene is CYP7B1.

UniProtKB/Swiss-Prot Summary for CYP39A1 Gene

  • A cytochrome P450 monooxygenase involved in neural cholesterol clearance through bile acid synthesis (PubMed:25201972, PubMed:10748047). Catalyzes 7-alpha hydroxylation of (24S)-hydroxycholesterol, a neural oxysterol that is metabolized to bile acids in the liver (PubMed:25201972, PubMed:10748047). 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) (PubMed:25201972, PubMed:10748047).

Gene Wiki entry for CYP39A1 Gene

Additional gene information for CYP39A1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CYP39A1 Gene

Genomics for CYP39A1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CYP39A1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J046651 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 605.3 +0.5 549 3.8 SP1 PRDM10 REST ZNF512 RFX1 SIX5 MTA2 ZNF143 ZIC2 PKNOX1 SLC25A27 CYP39A1 TDRD6 PLA2G7 piR-35729-052 RCAN2
GH06J046729 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 21 -80.8 -80752 5.6 CTCF PRDM1 ZNF776 ZSCAN4 POLR2A PATZ1 ZNF501 EZH2 ZNF239 ZNF341 PLA2G7 SLC25A27 TDRD6 CYP39A1 CD2AP LOC101926934
GH06J046453 Enhancer 0.8 Ensembl dbSUPER 23 +200.3 200348 0.2 ZNF174 ZNF300 ZNF776 ZNF37A ZNF561 ZBTB44 ZNF491 ZIK1 ZNF662 NFIC SLC25A27 CYP39A1 RPL36P10 lnc-SLC25A27-3 LOC101926898 RCAN2 ENPP5
GH06J046326 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 9.9 +327.1 327062 0.4 ATF7 PRDM10 ZNF629 ZNF692 ZIC2 POLR2A PATZ1 ZNF501 ZNF600 ZNF341 RCAN2 CYP39A1 LOC101926915 RPL36P10 lnc-SLC25A27-3 ENPP5
GH06J047403 Enhancer 0.9 Ensembl ENCODE 12.7 -753.0 -752952 5.6 PRDM10 REST SP1 ZNF341 ZNF148 ZNF561 TCF7L2 ZXDB ZNF157 CEBPB CD2AP ADGRF2 CYP39A1 RF00017-5591 ENSG00000287485 TNFRSF21 RF00017-5590
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CYP39A1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CYP39A1

Top Transcription factor binding sites by QIAGEN in the CYP39A1 gene promoter:
  • Cart-1
  • CUTL1
  • FAC1
  • HOXA3
  • LyF-1
  • MIF-1
  • Pax-4a
  • PPAR-alpha
  • Sox5
  • STAT5A

Genomic Locations for CYP39A1 Gene

Genomic Locations for CYP39A1 Gene
chr6:46,549,580-46,652,849
(GRCh38/hg38)
Size:
103,270 bases
Orientation:
Minus strand
chr6:46,517,445-46,620,523
(GRCh37/hg19)
Size:
103,079 bases
Orientation:
Minus strand

Genomic View for CYP39A1 Gene

Genes around CYP39A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CYP39A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CYP39A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CYP39A1 Gene

Proteins for CYP39A1 Gene

  • Protein details for CYP39A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NYL5-CP39A_HUMAN
    Recommended name:
    24-hydroxycholesterol 7-alpha-hydroxylase
    Protein Accession:
    Q9NYL5
    Secondary Accessions:
    • Q5VTT0
    • Q96FW5

    Protein attributes for CYP39A1 Gene

    Size:
    469 amino acids
    Molecular mass:
    54116 Da
    Cofactor:
    Name=heme; Xref=ChEBI:CHEBI:30413;
    Quaternary structure:
    No Data Available

neXtProt entry for CYP39A1 Gene

Post-translational modifications for CYP39A1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CYP39A1 Gene

Domains & Families for CYP39A1 Gene

Gene Families for CYP39A1 Gene

Protein Domains for CYP39A1 Gene

InterPro:
Blocks:
  • E-class P450 group IV signature
ProtoNet:

Suggested Antigen Peptide Sequences for CYP39A1 Gene

GenScript: Design optimal peptide antigens:
  • Cytochrome P450 39A1 (CP39A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NYL5

UniProtKB/Swiss-Prot:

CP39A_HUMAN :
  • Belongs to the cytochrome P450 family.
Family:
  • Belongs to the cytochrome P450 family.
genes like me logo Genes that share domains with CYP39A1: view

Function for CYP39A1 Gene

Molecular function for CYP39A1 Gene

UniProtKB/Swiss-Prot Function:
A cytochrome P450 monooxygenase involved in neural cholesterol clearance through bile acid synthesis (PubMed:25201972, PubMed:10748047). Catalyzes 7-alpha hydroxylation of (24S)-hydroxycholesterol, a neural oxysterol that is metabolized to bile acids in the liver (PubMed:25201972, PubMed:10748047). 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) (PubMed:25201972, PubMed:10748047).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(24S)-hydroxycholesterol + O2 + reduced [NADPH--hemoprotein reductase] = (24S)-7alpha-dihydroxycholesterol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase]; Xref=Rhea:RHEA:46124, Rhea:RHEA-COMP:11964, Rhea:RHEA-COMP:11965, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:34310, ChEBI:CHEBI:37640, ChEBI:CHEBI:57618, ChEBI:CHEBI:58210; EC=1.14.14.26; Evidence={ECO:0000269|PubMed:25201972};.

Enzyme Numbers (IUBMB) for CYP39A1 Gene

Phenotypes From GWAS Catalog for CYP39A1 Gene

Gene Ontology (GO) - Molecular Function for CYP39A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004497 monooxygenase activity IEA --
GO:0005506 iron ion binding IEA --
GO:0008387 steroid 7-alpha-hydroxylase activity IBA 21873635
GO:0008395 steroid hydroxylase activity IBA 21873635
GO:0008396 oxysterol 7-alpha-hydroxylase activity TAS --
genes like me logo Genes that share ontologies with CYP39A1: view
genes like me logo Genes that share phenotypes with CYP39A1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CYP39A1

CRISPR Products

miRNA for CYP39A1 Gene

miRTarBase miRNAs that target CYP39A1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CYP39A1

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CYP39A1 Gene

Localization for CYP39A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CYP39A1 Gene

Endoplasmic reticulum membrane. Multi-pass membrane protein. Microsome membrane. Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CYP39A1 gene
Compartment Confidence
endoplasmic reticulum 5
mitochondrion 2
peroxisome 2
nucleus 2
plasma membrane 1
extracellular 1
cytoskeleton 1
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CYP39A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0031090 organelle membrane IEA --
genes like me logo Genes that share ontologies with CYP39A1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CYP39A1 Gene

Pathways & Interactions for CYP39A1 Gene

genes like me logo Genes that share pathways with CYP39A1: view

Pathways by source for CYP39A1 Gene

UniProtKB/Swiss-Prot Q9NYL5-CP39A_HUMAN

  • Pathway: Steroid metabolism; cholesterol degradation.
  • Pathway: Lipid metabolism; bile acid biosynthesis.

Gene Ontology (GO) - Biological Process for CYP39A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006699 bile acid biosynthetic process IBA,TAS --
GO:0006707 cholesterol catabolic process IEA --
GO:0007586 digestion TAS 10748047
GO:0008202 steroid metabolic process IEA --
genes like me logo Genes that share ontologies with CYP39A1: view

No data available for SIGNOR curated interactions for CYP39A1 Gene

Drugs & Compounds for CYP39A1 Gene

(5) Drugs for CYP39A1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Oxygen Approved, Vet_approved Pharma 0
Water Approved Pharma 0
NADP Experimental Pharma 0
NADPH Experimental Pharma 0
heme Pharma Agonist 0

(2) Additional Compounds for CYP39A1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
(24R)-Cholest-5-ene-3-beta,24-diol
  • (24R)-24-Hydroxycholesterol
  • 24(R)-Hydoxycholesterol
  • 5-Cholesten-3-beta,24(R)-diol
  • Cholest-5-ene-3,24-diol
  • Cholest-5-ene-3-beta,24-diol
(24R)-Cholest-5-ene-3-beta,7-alpha,24-triol
  • (24R)-Cholest-5-ene 3-b,7-a,24-triol
  • (24R)-Cholest-5-ene-3beta,7alpha,24-triol
  • 5a-Cholesta-7,24-dien-3-b-ol
  • 5a-Cholesta-7,24-dien-3-beta-ol
genes like me logo Genes that share compounds with CYP39A1: view

Transcripts for CYP39A1 Gene

mRNA/cDNA for CYP39A1 Gene

3 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CYP39A1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CYP39A1 Gene

No ASD Table

Relevant External Links for CYP39A1 Gene

GeneLoc Exon Structure for
CYP39A1

Expression for CYP39A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CYP39A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CYP39A1 Gene

This gene is overexpressed in Liver (x9.0).

Protein differential expression in normal tissues from HIPED for CYP39A1 Gene

This gene is overexpressed in Kidney (60.5) and Heart (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CYP39A1 Gene



Protein tissue co-expression partners for CYP39A1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CYP39A1

SOURCE GeneReport for Unigene cluster for CYP39A1 Gene:

Hs.387367

mRNA Expression by UniProt/SwissProt for CYP39A1 Gene:

Q9NYL5-CP39A_HUMAN
Tissue specificity: Liver specific.

Evidence on tissue expression from TISSUES for CYP39A1 Gene

  • Liver(4.6)
  • Skin(4.4)
  • Gall bladder(2.4)
  • Nervous system(2.1)
genes like me logo Genes that share expression patterns with CYP39A1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CYP39A1 Gene

Orthologs for CYP39A1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CYP39A1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CYP39A1 30 31
  • 99.64 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CYP39A1 30 31
  • 88.89 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CYP39A1 30 31
  • 85.61 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Cyp39a1 30 17 31
  • 80.69 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Cyp39a1 30
  • 78.75 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia CYP39A1 31
  • 69 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CYP39A1 31
  • 57 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CYP39A1 30 31
  • 63.69 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CYP39A1 31
  • 53 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100486848 30
  • 59.71 (n)
Zebrafish
(Danio rerio)
Actinopterygii cyp39a1 30 31
  • 58.56 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5434 30
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 21 (a)
OneToMany
-- 31
  • 19 (a)
OneToMany
Species where no ortholog for CYP39A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CYP39A1 Gene

ENSEMBL:
Gene Tree for CYP39A1 (if available)
TreeFam:
Gene Tree for CYP39A1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CYP39A1: view image

Paralogs for CYP39A1 Gene

Paralogs for CYP39A1 Gene

(1) SIMAP similar genes for CYP39A1 Gene using alignment to 1 proteins:

  • CP39A_HUMAN
genes like me logo Genes that share paralogs with CYP39A1: view

Variants for CYP39A1 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for CYP39A1 Gene

CP39A_HUMAN-Q9NYL5
Variations in CYP39A1 are associated with elevated serum (24S)-hydroxycholesterol levels among a cohort of American residents.

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CYP39A1 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs12192544 - p.Arg23Pro
rs17856332 - p.Tyr288His
rs2277119 - p.Arg103His
rs41273654 - p.Lys329Gln
rs7761731 - p.Asn324Lys

Additional dbSNP identifiers (rs#s) for CYP39A1 Gene

Structural Variations from Database of Genomic Variants (DGV) for CYP39A1 Gene

Variant ID Type Subtype PubMed ID
esv2662881 CNV deletion 23128226
esv3608885 CNV loss 21293372
nsv1109774 CNV deletion 24896259
nsv348640 CNV deletion 16902084

Variation tolerance for CYP39A1 Gene

Residual Variation Intolerance Score: 68.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.32; 85.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CYP39A1 Gene

Human Gene Mutation Database (HGMD)
CYP39A1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CYP39A1

Disorders for CYP39A1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CYP39A1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
leber plus disease
  • lca
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CYP39A1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with CYP39A1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CYP39A1 Gene

Publications for CYP39A1 Gene

  1. Expression cloning of an oxysterol 7alpha-hydroxylase selective for 24-hydroxycholesterol. (PMID: 10748047) Li-Hawkins J … Russell DW (The Journal of biological chemistry 2000) 2 3 4
  2. A Large-scale genetic association study of esophageal adenocarcinoma risk. (PMID: 20453000) Liu CY … Christiani DC (Carcinogenesis 2010) 3 41
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3
  5. CYP39A1 polymorphism is associated with toxicity during intensive induction chemotherapy in patients with advanced head and neck cancer. (PMID: 26475344) Melchardt T … Egle A (BMC cancer 2015) 3

Products for CYP39A1 Gene

  • Signalway Proteins for CYP39A1

Sources for CYP39A1 Gene