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

    Gene ID: 51302, updated on 10-Dec-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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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 variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

      UniProtKB/TrEMBL
      B7Z786

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

      UniProtKB/TrEMBL
      B7Z786

    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

      UniProtKB/TrEMBL
      B7Z786

    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

      UniProtKB/TrEMBL
      B7Z786

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

      UniProtKB/TrEMBL
      B7Z786

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

      UniProtKB/TrEMBL
      B7Z786

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

      UniProtKB/TrEMBL
      B7Z786

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

      UniProtKB/TrEMBL
      B7Z786

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

      UniProtKB/TrEMBL
      B7Z786
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NYL5.2 GenPept UniProtKB/Swiss-Prot:Q9NYL5

    Gene LinkOut

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