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    CYP2D7 cytochrome P450 family 2 subfamily D member 7 (gene/pseudogene) [ Homo sapiens (human) ]

    Gene ID: 1564, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CYP2D7provided by HGNC
    Official Full Name
    cytochrome P450 family 2 subfamily D member 7 (gene/pseudogene)provided by HGNC
    Primary source
    HGNC:HGNC:2624
    See related
    AllianceGenome:HGNC:2624
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CYP2D; CYP2D6; CYP2D@; CYP2D7P; P450C2D; P450DB1; CYP2D7AP; CYP2D7P1; RNA40057
    Summary
    This gene is a member of the cytochrome P450 gene superfamily. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This gene is a segregating pseudogene, where some individuals may have an allele that encodes a functional enzyme, while other individuals have an allele encoding a protein that is predicted to be non-functional. In this case, the functional allele is thought to be rare. This locus is part of a cluster of cytochrome P450 genes on chromosome 22. [provided by RefSeq, Jan 2017]
    Annotation information
    Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
    Expression
    Broad expression in liver (RPKM 9.7), small intestine (RPKM 3.1) and 14 other tissues See more
    Orthologs
    all
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    Genomic context

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    See CYP2D7 in Genome Data Viewer
    Location:
    22q13.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (42139576..42144483, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (42619075..42623972, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (42535587..42540484, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene NDUFA6 divergent transcript Neighboring gene OLA1 pseudogene 1 Neighboring gene CYP2D6 promoter Neighboring gene cytochrome P450 family 2 subfamily D member 6 (gene/pseudogene) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42532244-42532832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42532833-42533420 Neighboring gene uncharacterized LOC105377203 Neighboring gene ccytochrome P450 family 2 subfamily D member 8, pseudogene

    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 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. Functional characterization of CYP2D7 gene variants. Jukic MM, et al. Pharmacogenomics, 2018 Aug 1. PMID 30040020
    2. Comment on "A frameshift mutation and alternate splicing in human brain generate a functional form of the pseudogene cytochrome P4502d7 that demethylates codeine to morphine", J Biol Chem 279: 27383-27389. Hoskins JM, et al. Drug Metab Dispos, 2005 Oct. PMID 16166400
    3. CYP2D7 splice variants in human liver and brain: does CYP2D7 encode functional protein? Gaedigk A, et al. Biochem Biophys Res Commun, 2005 Nov 4. PMID 16169517
    4. Frequency of the frame-shifting CYP2D7 138delT polymorphism in a large, ethnically diverse sample population. Bhathena A, et al. Drug Metab Dispos, 2007 Aug. PMID 17494644
    5. Accurately genotyping CYP2D6: not for the faint of heart. Nofziger C, et al. Pharmacogenomics, 2018 Aug 1. PMID 30020016

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Association Between CYP2D7 and TCF20 Polymorphisms and Coronary Heart Disease.
      Title: Association Between CYP2D7 and TCF20 Polymorphisms and Coronary Heart Disease.
    2. The loss of the stop codon in CYP2D7 does not result in the generation of enzymatically active protein in human liver.
      Title: Functional characterization of CYP2D7 gene variants.
    3. Observational study of genotype prevalence. (HuGE Navigator)
      Title: Frequency of the frame-shifting CYP2D7 138delT polymorphism in a large, ethnically diverse sample population.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Polymorphism of metabolic genes and susceptibility to occupational chronic manganism.
    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)

    Genotypes

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables aromatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables aromatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables heme binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables iron ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    		  
    Process Evidence Code Pubs
    involved_in arachidonate metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    NOT involved_in xenobiotic catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in xenobiotic catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in xenobiotic metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    NOT involved_in xenobiotic metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in xenobiotic metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    putative cytochrome P450 2D7
    Names
    Putative cytochrome P450 2D7
    cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 1
    cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 1
    cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing) cluster
    cytochrome P4502D6
    nonfunctional cytochrome P450 family 2 subfamily D polypeptide 6

    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.

    mRNA and Protein(s)

    1. NM_001348386.3 → NP_001335315.1  putative cytochrome P450 2D7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site resulting in a longer transcript compared to variant 1. This variant represents the allele which encodes the full-length protein but whether this protein has enzymatic activity is disputed.
      Source sequence(s)
      AC254562, AY220845, BC108679, X16866
      UniProtKB/Swiss-Prot
      A0A087X1C5, Q6XP50
      Conserved Domains (1) summary
      pfam00067
      Location:58 → 512
      p450; Cytochrome P450

    RNA

    1. NR_002570.6 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shortest transcript. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC254562, BC108679, X16866

    2. NR_145674.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2, noncoding) uses an alternate splice site resulting in a longer transcript compared to variant 1. This noncoding variant represents the reference genome allele, which does not encode a full-length protein and is predicted to be non-functional.
      Source sequence(s)
      AC254562, X16866

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      42139576..42144483 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_009646207.1 Reference GRCh38.p14 PATCHES

      Range
      42386..47285 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_009646208.1 Reference GRCh38.p14 PATCHES

      Range
      38858..43756 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_014040930.1 Reference GRCh38.p14 PATCHES

      Range
      32143..37048 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_014040931.1 Reference GRCh38.p14 PATCHES

      Range
      60584..65491 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_015148968.1 Reference GRCh38.p14 PATCHES

      Range
      30982..35880 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003315971.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      49769..54676 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_187682.1 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      61926..66823 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      42619075..42623972 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NG_002362.1: Suppressed sequence

      Description
      NG_002362.1: This RefSeq was permanently suppressed because it is now thought that this pseudogene is transcribed.

    2. NM_001002910.1: Suppressed sequence

      Description
      NM_001002910.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A0A087X1C5.1 GenPept UniProtKB/Swiss-Prot:A0A087X1C5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases
    Research Materials