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    GDPD3 glycerophosphodiester phosphodiesterase domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 79153, updated on 3-Nov-2024

    Summary

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    Official Symbol
    GDPD3provided by HGNC
    Official Full Name
    glycerophosphodiester phosphodiesterase domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:28638
    See related
    Ensembl:ENSG00000102886 MIM:616318; AllianceGenome:HGNC:28638
    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
    GDE7
    Summary
    Enables phosphoric diester hydrolase activity. Involved in N-acylethanolamine metabolic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in esophagus (RPKM 15.4), colon (RPKM 11.2) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GDPD3 in Genome Data Viewer
    Location:
    16p11.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30104810..30113537, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (30387452..30396184, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30116131..30124858, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30101709-30102582 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10690 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30107354-30107960 Neighboring gene T-box transcription factor 6 Neighboring gene YPEL3 divergent transcript Neighboring gene yippee like 3 Neighboring gene Sharpr-MPRA regulatory region 9068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7356 Neighboring gene mitogen-activated protein kinase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30187986-30188486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10693 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7357 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30195204-30195744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30195745-30196286 Neighboring gene CORO1A antisense RNA 1 Neighboring gene coronin 1A

    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. GDE7 produces cyclic phosphatidic acid in the ER lumen functioning as a lysophospholipid mediator. Kitakaze K, et al. Commun Biol, 2023 May 16. PMID 37193762, Free PMC Article
    2. Human GDPD3 overexpression promotes liver steatosis by increasing lysophosphatidic acid production and fatty acid uptake. Key CC, et al. J Lipid Res, 2020 Jul. PMID 32430316, Free PMC Article
    3. Development of a selective fluorescence-based enzyme assay for glycerophosphodiesterase family members GDE4 and GDE7. Kitakaze K, et al. J Lipid Res, 2021. PMID 34673020, Free PMC Article
    4. Calcium-dependent generation of N-acylethanolamines and lysophosphatidic acids by glycerophosphodiesterase GDE7. Rahman IA, et al. Biochim Biophys Acta, 2016 Dec. PMID 27637550
    5. A pancreatic cancer-specific expression profile. Gress TM, et al. Oncogene, 1996 Oct 17. PMID 8895530

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. GDE7 produces cyclic phosphatidic acid in the ER lumen functioning as a lysophospholipid mediator.
      Title: GDE7 produces cyclic phosphatidic acid in the ER lumen functioning as a lysophospholipid mediator.
    2. Development of a selective fluorescence-based enzyme assay for glycerophosphodiesterase family members GDE4 and GDE7.
      Title: Development of a selective fluorescence-based enzyme assay for glycerophosphodiesterase family members GDE4 and GDE7.
    3. Human GDPD3 overexpression promotes liver steatosis by increasing lysophosphatidic acid production and fatty acid uptake.
      Title: Human GDPD3 overexpression promotes liver steatosis by increasing lysophosphatidic acid production and fatty acid uptake.
    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

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    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)

    Genotypes

    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

    • MGC4171, FLJ22603

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables lysophospholipase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphoric diester hydrolase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphoric diester hydrolase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in N-acylethanolamine metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in glycerophospholipid catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phosphatidylcholine catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in perinuclear region of cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    lysophospholipase D GDPD3
    Names
    glycerophosphodiester phosphodiesterase 7
    glycerophosphodiester phosphodiesterase domain-containing protein 3

    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_024307.3 → NP_077283.2  lysophospholipase D GDPD3

      See identical proteins and their annotated locations for NP_077283.2

      Status: VALIDATED

      Source sequence(s)
      BC002714
      Consensus CDS
      CCDS10671.2
      UniProtKB/Swiss-Prot
      Q7L5L3, Q9H652
      Related
      ENSP00000384363.3, ENST00000406256.8
      Conserved Domains (2) summary
      cd08612
      Location:13 → 310
      GDPD_GDE4; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4 and similar proteins
      pfam03009
      Location:44 → 301
      GDPD; Glycerophosphoryl diester phosphodiesterase family

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      30104810..30113537 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_007064912.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      30387452..30396184 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7L5L3.3 GenPept UniProtKB/Swiss-Prot:Q7L5L3

    Gene LinkOut

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

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