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    CYP2R1 cytochrome P450 family 2 subfamily R member 1 [ Homo sapiens (human) ]

    Gene ID: 120227, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CYP2R1provided by HGNC
    Official Full Name
    cytochrome P450 family 2 subfamily R member 1provided by HGNC
    Primary source
    HGNC:HGNC:20580
    See related
    Ensembl:ENSG00000186104 MIM:608713; AllianceGenome:HGNC:20580
    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 enzyme is a microsomal vitamin D hydroxylase that converts vitamin D into the active ligand for the vitamin D receptor. A mutation in this gene has been associated with selective 25-hydroxyvitamin D deficiency. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in skin (RPKM 2.2), testis (RPKM 2.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CYP2R1 in Genome Data Viewer
    Location:
    11p15.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (14877440..14892443, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (14973806..14988811, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (14898986..14913989, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene phosphodiesterase 3B Neighboring gene uncharacterized LOC107984315 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:14737137-14737723 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:14737724-14738309 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:14748217-14748780 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:14764591-14765090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14799188-14799688 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:14838787-14838962 Neighboring gene uncharacterized LOC124902639 Neighboring gene MPRA-validated peak1207 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14929307-14929806 Neighboring gene calcitonin pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14993078-14993724 Neighboring gene calcitonin related polypeptide alpha

    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. Triangular relationship between CYP2R1 gene polymorphism, serum 25(OH)D(3) levels and T2DM in a Chinese rural population. Wang Y, et al. Gene, 2018 Dec 15. PMID 30081191
    2. Evaluation of the Associations of GC and CYP2R1 Genes and Gene-Obesity Interactions with Type 2 Diabetes Risk in a Chinese Rural Population. Zhao Y, et al. Ann Nutr Metab, 2020. PMID 32971523
    3. Differential Frequency of CYP2R1 Variants Across Populations Reveals Pathway Selection for Vitamin D Homeostasis. Casella A, et al. J Clin Endocrinol Metab, 2020 May 1. PMID 32115644, Free PMC Article
    4. Genetic Polymorphisms in the Vitamin D Pathway and Non-small Cell Lung Cancer Survival. Kong J, et al. Pathol Oncol Res, 2020 Jul. PMID 31625015, Free PMC Article
    5. Polymorphisms in CYP2R1 Gene Associated with Serum Vitamin D Levels and Status in a Chinese Rural Population. Wang Y, et al. Biomed Environ Sci, 2019 Jul. PMID 31331440

    See all (118) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Relationship between Vitamin D3 Deficiency, Metabolic Syndrome and VDR, GC, and CYP2R1 Gene Polymorphisms.
      Title: Relationship between Vitamin D3 Deficiency, Metabolic Syndrome and VDR, GC, and CYP2R1 Gene Polymorphisms.
    2. Gene expression profiling of vitamin D metabolism enzymes in leukemia and lymphoma patients: molecular aspect interplay of VDR, CYP2R1, and CYP24A1.
      Title: Gene expression profiling of vitamin D metabolism enzymes in leukemia and lymphoma patients: molecular aspect interplay of VDR, CYP2R1, and CYP24A1.
    3. Single nucleotide polymorphisms in vitamin D binding protein and 25-hydroxylase genes affect vitamin D levels in adolescents of Arab ethnicity in Kuwait.
      Title: Single nucleotide polymorphisms in vitamin D binding protein and 25-hydroxylase genes affect vitamin D levels in adolescents of Arab ethnicity in Kuwait.
    4. Association of Single Nucleotide Polymorphism in VDR, GC Globulin and CYP2R1 with the Risk of Esophageal Cancer.
      Title: Association of Single Nucleotide Polymorphism in VDR, GC Globulin and CYP2R1 with the Risk of Esophageal Cancer.
    5. Correlation of CYP2R1 gene promoter methylation with circulating vitamin D levels among healthy adults.
      Title: Correlation of CYP2R1 gene promoter methylation with circulating vitamin D levels among healthy adults.
    6. Biomarkers of ulcerative colitis disease activity CXCL1, CYP2R1, LPCAT1, and NEU4 and their relationship to immune infiltrates.
      Title: Biomarkers of ulcerative colitis disease activity CXCL1, CYP2R1, LPCAT1, and NEU4 and their relationship to immune infiltrates.
    7. Association of CYP2R1 and VDR Polymorphisms with Metabolic Syndrome Components in Non-Diabetic Brazilian Adolescents.
      Title: Association of CYP2R1 and VDR Polymorphisms with Metabolic Syndrome Components in Non-Diabetic Brazilian Adolescents.
    8. 25-Hydroxyvitamin D Serum Levels Linked to Single Nucleotide Polymorphisms (SNPs) (rs2228570, rs2282679, rs10741657) in Skeletal Muscle Aging in Institutionalized Elderly Men Not Supplemented with Vitamin D.
      Title: 25-Hydroxyvitamin D Serum Levels Linked to Single Nucleotide Polymorphisms (SNPs) (rs2228570, rs2282679, rs10741657) in Skeletal Muscle Aging in Institutionalized Elderly Men Not Supplemented with Vitamin D.
    9. Clinical presentation and molecular genetic analysis of a Sudanese family with a novel mutation in the CYP2R1 gene.
      Title: Clinical presentation and molecular genetic analysis of a Sudanese family with a novel mutation in the CYP2R1 gene.
    10. Genetic variants of vitamin D metabolism-related DHCR7/NADSYN1 locus and CYP2R1 gene are associated with clinical features of Parkinson's disease.
      Title: Genetic variants of vitamin D metabolism-related DHCR7/NADSYN1 locus and CYP2R1 gene are associated with clinical features of Parkinson's disease.
    Submit: New GeneRIF Correction See all GeneRIFs (105)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Vitamin D hydroxylation-deficient rickets, type 1B
    MedGen: C1838657 OMIM: 600081 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Common genetic determinants of vitamin D insufficiency: a genome-wide association study.
    EBI GWAS Catalog
    Genome-wide association study of circulating vitamin D levels.
    EBI GWAS Catalog
    Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study.
    EBI GWAS Catalog

    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

    Clone Names

    • MGC4663

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables D3 vitamins binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables heme binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables heme binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables iron ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 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 oxygen IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables vitamin D3 25-hydroxylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables vitamin D3 25-hydroxylase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in calcitriol biosynthetic process from calciol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in organic acid metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to cesium ion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to ionizing radiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vitamin D metabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in vitamin metabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in xenobiotic metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    vitamin D 25-hydroxylase
    Names
    cytochrome P450 2R1
    cytochrome P450, family 2, R1
    cytochrome P450, family 2, subfamily R, polypeptide 1
    NP_001364143.1
    NP_001364144.1
    NP_001364145.1
    NP_001364146.1
    NP_001364156.1
    NP_001387487.1
    NP_001387488.1
    NP_001387489.1
    NP_001387490.1
    NP_001387491.1
    NP_001387492.1
    NP_001387493.1
    NP_001387494.1
    NP_001387495.1
    NP_001387496.1
    NP_001387497.1
    NP_078790.2
    XP_016872679.1
    XP_047282316.1
    XP_047282317.1
    XP_047282318.1
    XP_047282319.1
    XP_054223627.1
    XP_054223628.1
    XP_054223629.1
    XP_054223630.1
    XP_054223631.1

    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_007936.1 RefSeqGene

      Range
      4975..19766
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001377214.1 → NP_001364143.1  vitamin D 25-hydroxylase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC090835
      Conserved Domains (1) summary
      cl41757
      Location:1 → 382
      cytochrome_P450; cytochrome P450 (CYP) superfamily

    2. NM_001377215.1 → NP_001364144.1  vitamin D 25-hydroxylase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC090835
      Conserved Domains (1) summary
      cl41757
      Location:1 → 382
      cytochrome_P450; cytochrome P450 (CYP) superfamily

    3. NM_001377216.1 → NP_001364145.1  vitamin D 25-hydroxylase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC090835
      Conserved Domains (1) summary
      cl41757
      Location:1 → 382
      cytochrome_P450; cytochrome P450 (CYP) superfamily

    4. NM_001377217.1 → NP_001364146.1  vitamin D 25-hydroxylase isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC090835
      Conserved Domains (1) summary
      cl41757
      Location:21 → 443
      cytochrome_P450; cytochrome P450 (CYP) superfamily

    5. NM_001377227.1 → NP_001364156.1  vitamin D 25-hydroxylase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC090835
      Conserved Domains (1) summary
      cl41757
      Location:1 → 382
      cytochrome_P450; cytochrome P450 (CYP) superfamily

    6. NM_001400558.1 → NP_001387487.1  vitamin D 25-hydroxylase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC090835

    7. NM_001400559.1 → NP_001387488.1  vitamin D 25-hydroxylase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC090835

    8. NM_001400560.1 → NP_001387489.1  vitamin D 25-hydroxylase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC090835

    9. NM_001400561.1 → NP_001387490.1  vitamin D 25-hydroxylase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC090835

    10. NM_001400562.1 → NP_001387491.1  vitamin D 25-hydroxylase isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC090835
      Consensus CDS
      CCDS91446.1
      UniProtKB/TrEMBL
      E9PJT9

    11. NM_001400563.1 → NP_001387492.1  vitamin D 25-hydroxylase isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC090835
      Consensus CDS
      CCDS91446.1
      UniProtKB/TrEMBL
      E9PJT9

    12. NM_001400564.1 → NP_001387493.1  vitamin D 25-hydroxylase isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC090835
      Consensus CDS
      CCDS91446.1
      UniProtKB/TrEMBL
      E9PJT9

    13. NM_001400565.1 → NP_001387494.1  vitamin D 25-hydroxylase isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC090835
      Consensus CDS
      CCDS91446.1
      UniProtKB/TrEMBL
      E9PJT9
      Related
      ENSP00000435484.1, ENST00000532378.5

    14. NM_001400566.1 → NP_001387495.1  vitamin D 25-hydroxylase isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC090835

    15. NM_001400567.1 → NP_001387496.1  vitamin D 25-hydroxylase isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC090835

    16. NM_001400568.1 → NP_001387497.1  vitamin D 25-hydroxylase isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC090835

    17. NM_024514.5 → NP_078790.2  vitamin D 25-hydroxylase isoform 1

      See identical proteins and their annotated locations for NP_078790.2

      Status: REVIEWED

      Source sequence(s)
      AC090835, AY323817
      Consensus CDS
      CCDS7818.1
      UniProtKB/Swiss-Prot
      Q2M3H3, Q5RT65, Q6VVX0
      Related
      ENSP00000334592.5, ENST00000334636.10
      Conserved Domains (1) summary
      pfam00067
      Location:57 → 497
      p450; Cytochrome P450

    RNA

    1. NR_174512.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC090835

    2. NR_174513.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC090835

    3. NR_174514.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC090835

    4. NR_174515.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC090835

    5. NR_174516.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC090835

    6. NR_174517.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC090835

    7. NR_174518.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC090835

    8. NR_174519.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC090835

    9. NR_174520.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC090835

    10. NR_174521.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC090835

    11. NR_174522.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC090835

    12. NR_174523.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC090835

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      14877440..14892443 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047426361.1 → XP_047282317.1  vitamin D 25-hydroxylase isoform X1

    2. XM_017017190.3 → XP_016872679.1  vitamin D 25-hydroxylase isoform X1

      Conserved Domains (1) summary
      pfam00067
      Location:18 → 442
      p450; Cytochrome P450

    3. XM_047426360.1 → XP_047282316.1  vitamin D 25-hydroxylase isoform X1

    4. XM_047426362.1 → XP_047282318.1  vitamin D 25-hydroxylase isoform X2

    5. XM_047426363.1 → XP_047282319.1  vitamin D 25-hydroxylase isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      14973806..14988811 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367654.1 → XP_054223629.1  vitamin D 25-hydroxylase isoform X1

    2. XM_054367653.1 → XP_054223628.1  vitamin D 25-hydroxylase isoform X1

    3. XM_054367652.1 → XP_054223627.1  vitamin D 25-hydroxylase isoform X1

    4. XM_054367655.1 → XP_054223630.1  vitamin D 25-hydroxylase isoform X2

    5. XM_054367656.1 → XP_054223631.1  vitamin D 25-hydroxylase isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6VVX0.1 GenPept UniProtKB/Swiss-Prot:Q6VVX0

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