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

Gene ID: 1564, updated on 5-Mar-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (42139576..42144483, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (42619075..42623972, complement)
105.20220307 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 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
  • 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. Accurately genotyping CYP2D6: not for the faint of heart. Nofziger C, et al. Pharmacogenomics, 2018 Aug 1. PMID 30020016
  3. 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
  4. 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
  5. 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

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. Observational study of genotype prevalence. (HuGE Navigator)
    Title: Frequency of the frame-shifting CYP2D7 138delT polymorphism in a large, ethnically diverse sample population.
  3. 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 arachidonic acid 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_2023_10

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

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