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    GPCPD1 glycerophosphocholine phosphodiesterase 1 [ Homo sapiens (human) ]

    Gene ID: 56261, updated on 2-Nov-2024

    Summary

    Official Symbol
    GPCPD1provided by HGNC
    Official Full Name
    glycerophosphocholine phosphodiesterase 1provided by HGNC
    Primary source
    HGNC:HGNC:26957
    See related
    Ensembl:ENSG00000125772 MIM:614124; AllianceGenome:HGNC:26957
    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
    EDI3; GDE5; GDPD6; PREI4
    Summary
    Predicted to enable glycerophosphocholine phosphodiesterase activity. Predicted to be involved in glycerophospholipid catabolic process. Predicted to act upstream of or within skeletal muscle tissue development. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 31.5), spleen (RPKM 13.3) and 24 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See GPCPD1 in Genome Data Viewer
    Location:
    20p12.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (5544439..5611006, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (5585120..5651341, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (5525085..5591652, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1729 Neighboring gene NANOG hESC enhancer GRCh37_chr20:5509506-5510047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17520 Neighboring gene ribosomal protein S18 pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:5533770-5534499 Neighboring gene eukaryotic translation initiation factor 4E pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 4324 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12656 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:5590486-5591358 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12657 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5606161-5606662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17522 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17525 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17526 Neighboring gene uncharacterized LOC124904864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5637190-5637690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5637691-5638191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5668750-5669250 Neighboring gene Sharpr-MPRA regulatory region 5332 Neighboring gene uncharacterized LOC105372514

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ11085, KIAA1434, MGC26147

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables glycerophosphocholine phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables starch binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in glycerophospholipid catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in skeletal muscle tissue development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    glycerophosphocholine phosphodiesterase GPCPD1
    Names
    endometrial differential 3
    glycerophosphocholine phosphodiesterase GDE1 homolog
    glycerophosphodiester phosphodiesterase 5
    preimplantation protein 4
    putative glycerophosphocholine phosphodiesterase GPCPD1
    putative glycerophosphodiester phosphodiesterase 5
    NP_062539.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_019593.5NP_062539.1  glycerophosphocholine phosphodiesterase GPCPD1

      See identical proteins and their annotated locations for NP_062539.1

      Status: VALIDATED

      Source sequence(s)
      AB037855, AL049446, BC027588, BG674365, BI561344, BP421674, T79323
      Consensus CDS
      CCDS13090.1
      UniProtKB/Swiss-Prot
      D3DW06, Q9BQL8, Q9NPB8, Q9NUX0
      Related
      ENSP00000368305.4, ENST00000379019.7
      Conserved Domains (2) summary
      cd05814
      Location:4127
      CBM20_Prei4; Prei4, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Preimplantation protein 4 (Prei4) is a protein of unknown function that is expressed during mouse preimplantation embryogenesis. In addition to the N-terminal CBM20 domain, Prei4 ...
      cd08607
      Location:319611
      GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      5544439..5611006 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      5585120..5651341 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)