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CYP39A1 cytochrome P450 family 39 subfamily A member 1 [ Homo sapiens (human) ]

Gene ID: 51302, updated on 27-Nov-2024

Summary

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Official Symbol
CYP39A1provided by HGNC
Official Full Name
cytochrome P450 family 39 subfamily A member 1provided by HGNC
Primary source
HGNC:HGNC:17449
See related
Ensembl:ENSG00000146233 MIM:605994; AllianceGenome:HGNC:17449
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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]
Expression
Broad expression in liver (RPKM 10.7), prostate (RPKM 4.4) and 14 other tissues See more
Orthologs
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Genomic context

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See CYP39A1 in Genome Data Viewer
Location:
6p12.3
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (46549580..46652818, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (46387235..46490468, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (46517317..46620555, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene regulator of calcineurin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:46426210-46426710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:46426711-46427211 Neighboring gene ribosomal protein L36 pseudogene 10 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:46455408-46456020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17270 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17271 Neighboring gene RCAN2 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:46543303-46543803 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:46542802-46543302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17273 Neighboring gene solute carrier family 25 member 27 Neighboring gene TDRD6 and SLC25A27 antisense RNA 1 Neighboring gene tudor domain containing 6 Neighboring gene phospholipase A2 group VII

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Association of the CYP39A1 G204E Genetic Variant with Increased Risk of Glaucoma and Blindness in Patients with Exfoliation Syndrome. Bell K, et al. Ophthalmology, 2022 Apr. PMID 34763023
  2. Association of Rare CYP39A1 Variants With Exfoliation Syndrome Involving the Anterior Chamber of the Eye. Genetics of Exfoliation Syndrome Partnership, et al. JAMA, 2021 Feb 23. PMID 33620406, Free PMC Article
  3. CYP39A1 polymorphism is associated with toxicity during intensive induction chemotherapy in patients with advanced head and neck cancer. Melchardt T, et al. BMC Cancer, 2015 Oct 16. PMID 26475344, Free PMC Article
  4. Orphan Nuclear Receptor RORα Regulates Enzymatic Metabolism of Cerebral 24S-Hydroxycholesterol through CYP39A1 Intronic Response Element Activation. Matsuoka H, et al. Int J Mol Sci, 2020 May 7. PMID 32392803, Free PMC Article
  5. Effect of genetic variants GSTA1 and CYP39A1 and age on busulfan clearance in pediatric patients undergoing hematopoietic stem cell transplantation. ten Brink MH, et al. Pharmacogenomics, 2013 Nov. PMID 24192117

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Association of the CYP39A1 G204E Genetic Variant with Increased Risk of Glaucoma and Blindness in Patients with Exfoliation Syndrome.
    Title: Association of the CYP39A1 G204E Genetic Variant with Increased Risk of Glaucoma and Blindness in Patients with Exfoliation Syndrome.
  2. Association of Rare CYP39A1 Variants With Exfoliation Syndrome Involving the Anterior Chamber of the Eye.
    Title: Association of Rare CYP39A1 Variants With Exfoliation Syndrome Involving the Anterior Chamber of the Eye.
  3. Orphan Nuclear Receptor RORalpha Regulates Enzymatic Metabolism of Cerebral 24S-Hydroxycholesterol through CYP39A1 Intronic Response Element Activation.
    Title: Orphan Nuclear Receptor RORα Regulates Enzymatic Metabolism of Cerebral 24S-Hydroxycholesterol through CYP39A1 Intronic Response Element Activation.
  4. The CYP39A1 polymorphism rs7761731 may help to identify patients at high risk for treatment related toxicity.
    Title: CYP39A1 polymorphism is associated with toxicity during intensive induction chemotherapy in patients with advanced head and neck cancer.
  5. GSTA1 and CYP39A1 were found to be associated with busulfan clearance. When combined, the two haplotypes explained 17% of the variability in busulfan clearance.
    Title: Effect of genetic variants GSTA1 and CYP39A1 and age on busulfan clearance in pediatric patients undergoing hematopoietic stem cell transplantation.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: A Large-scale genetic association study of esophageal adenocarcinoma risk.
  7. The rs754203 SNP in CYP46A1 was associated with a risk for POAG. This polymorphism was not associated with changes in plasma 24S-hydroxycholesterol.
    Title: Primary open-angle glaucoma: association with cholesterol 24S-hydroxylase (CYP46A1) gene polymorphism and plasma 24-hydroxycholesterol levels.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See Variation Viewer (GRCh37.p13)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 24-hydroxycholesterol 7alpha-hydroxylase activity IEA
Inferred from Electronic Annotation
more info
  
enables heme binding IEA
Inferred from Electronic Annotation
more info
  
enables iron ion binding IEA
Inferred from Electronic Annotation
more info
  
enables oxysterol 7-alpha-hydroxylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables oxysterol 7-alpha-hydroxylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables oxysterol 7-alpha-hydroxylase activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables steroid 7-alpha-hydroxylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in bile acid biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in bile acid biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in bile acid biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in bile acid biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in cholesterol catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in cholesterol homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in digestion TAS
Traceable Author Statement
more info
 PubMed 
involved_in sterol metabolic process TAS
Traceable Author Statement
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in intracellular membrane-bounded organelle TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
24-hydroxycholesterol 7-alpha-hydroxylase
Names
cytochrome P450, family 39, subfamily A, polypeptide 1
cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1
NP_001265667.1
NP_001265668.1
NP_057677.2
XP_005249228.1
XP_016866410.1
XP_016866411.1
XP_016866412.1
XP_016866413.1
XP_047274814.1
XP_047274815.1
XP_047274816.1
XP_054211546.1
XP_054211547.1
XP_054211548.1
XP_054211549.1
XP_054211550.1
XP_054211551.1
XP_054211552.1
XP_054211553.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007962.1 RefSeqGene

    Range
    4969..108207
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001278738.2 → NP_001265667.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AK292263, AK301604, AL035670, DC336695
    UniProtKB/TrEMBL
    B7Z786
    Conserved Domains (1) summary
    cl12078
    Location:35 → 440
    p450; Cytochrome P450

  2. NM_001278739.2 → NP_001265668.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in its 5' UTR and uses a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK292263, AK307986, AL035670, DC336695
    Consensus CDS
    CCDS75465.1
    UniProtKB/TrEMBL
    A0A087WTD2
    Related
    ENSP00000477769.1, ENST00000619708.4
    Conserved Domains (1) summary
    cl12078
    Location:111 → 288
    p450; Cytochrome P450

  3. NM_016593.5 → NP_057677.2  24-hydroxycholesterol 7-alpha-hydroxylase isoform 1

    See identical proteins and their annotated locations for NP_057677.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK292263, AL035670, DC336695
    Consensus CDS
    CCDS4916.1
    UniProtKB/Swiss-Prot
    Q5VTT0, Q96FW5, Q9NYL5
    UniProtKB/TrEMBL
    B7Z786
    Related
    ENSP00000275016.2, ENST00000275016.3
    Conserved Domains (1) summary
    cl12078
    Location:35 → 460
    p450; Cytochrome P450

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    46549580..46652818 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010924.2 → XP_016866413.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X4

    UniProtKB/TrEMBL
    B7Z786

  2. XM_047418860.1 → XP_047274816.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X8

  3. XM_017010922.2 → XP_016866411.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X2

    UniProtKB/TrEMBL
    B7Z786

  4. XM_017010923.2 → XP_016866412.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X3

    UniProtKB/TrEMBL
    B7Z786

  5. XM_017010921.2 → XP_016866410.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X1

    UniProtKB/TrEMBL
    B7Z786

  6. XM_047418858.1 → XP_047274814.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X6

  7. XM_047418859.1 → XP_047274815.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X7

  8. XM_005249171.5 → XP_005249228.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X5

    UniProtKB/TrEMBL
    B7Z786
    Conserved Domains (1) summary
    cl12078
    Location:35 → 417
    p450; Cytochrome P450

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    46387235..46490468 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355574.1 → XP_054211549.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X4

  2. XM_054355578.1 → XP_054211553.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X8

  3. XM_054355571.1 → XP_054211546.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X1

  4. XM_054355573.1 → XP_054211548.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X3

  5. XM_054355572.1 → XP_054211547.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X2

  6. XM_054355577.1 → XP_054211552.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X7

  7. XM_054355576.1 → XP_054211551.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X6

  8. XM_054355575.1 → XP_054211550.1  24-hydroxycholesterol 7-alpha-hydroxylase isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NYL5.2 GenPept UniProtKB/Swiss-Prot:Q9NYL5

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