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    PLCXD3 phosphatidylinositol specific phospholipase C X domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 345557, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PLCXD3provided by HGNC
    Official Full Name
    phosphatidylinositol specific phospholipase C X domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:31822
    See related
    Ensembl:ENSG00000182836 MIM:617016; AllianceGenome:HGNC:31822
    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
    Summary
    Predicted to enable phosphoric diester hydrolase activity. Predicted to be involved in lipid catabolic process and signal transduction. Predicted to be located in cytoplasm. Predicted to be active in glutamatergic synapse. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in heart (RPKM 12.4), ovary (RPKM 9.3) and 8 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    5p13.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (41306952..41510601, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (41563425..41766981, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (41307054..41510703, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374739 Neighboring gene NANOG hESC enhancer GRCh37_chr5:41230420-41230921 Neighboring gene NANOG hESC enhancer GRCh37_chr5:41252597-41253129 Neighboring gene complement C6 Neighboring gene uncharacterized LOC124900969 Neighboring gene uncharacterized LOC102723740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15985 Neighboring gene uncharacterized LOC105374740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:41510229-41511057 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:41587798-41587931 Neighboring gene t-complex 1 pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:41717601-41717785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22505 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:41775532-41776072 Neighboring gene Sharpr-MPRA regulatory region 14195 Neighboring gene 3-oxoacid CoA-transferase 1 Neighboring gene Sharpr-MPRA regulatory region 14906 Neighboring gene NANOG hESC enhancer GRCh37_chr5:41822074-41822575 Neighboring gene uncharacterized LOC102723752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22506 Neighboring gene OXCT1 antisense RNA 1

    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. Genetic Variants of the PLCXD3 Gene Are Associated with Risk of Metabolic Syndrome in the Emirati Population. Aljaibeji H, et al. Genes (Basel), 2020 Jun 18. PMID 32570874, Free PMC Article
    2. Variants of PLCXD3 are not associated with variant or sporadic Creutzfeldt-Jakob disease in a large international study. Balendra R, et al. BMC Med Genet, 2016 Apr 7. PMID 27055460, Free PMC Article
    3. Integrated analysis miRNA and mRNA profiling in patients with severe oligozoospermia reveals miR-34c-3p downregulates PLCXD3 expression. Li Z, et al. Oncotarget, 2016 Aug 16. PMID 27486773, Free PMC Article
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article
    5. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genetic Variants of the PLCXD3 Gene Are Associated with Risk of Metabolic Syndrome in the Emirati Population.
      Title: Genetic Variants of the PLCXD3 Gene Are Associated with Risk of Metabolic Syndrome in the Emirati Population.
    2. One potential miRNA-target gene pair, miR-34c-3p and PLCXD3 (Phosphatidylinositol-Specific Phospholipase C, X Domain Containing 3), was identified in patients with severe oligozoospermia.
      Title: Integrated analysis miRNA and mRNA profiling in patients with severe oligozoospermia reveals miR-34c-3p downregulates PLCXD3 expression.
    3. We found no supportive evidence that PLCXD3 variants are associated with sporadic Creutzfeldt-Jakob disease.
      Title: Variants of PLCXD3 are not associated with variant or sporadic Creutzfeldt-Jakob disease in a large international study.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphoric diester hydrolase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in lipid catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    PI-PLC X 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_001005473.3 → NP_001005473.1  PI-PLC X domain-containing protein 3

      See identical proteins and their annotated locations for NP_001005473.1

      Status: VALIDATED

      Source sequence(s)
      AC008830, AK127142, BX648329
      Consensus CDS
      CCDS34150.1
      UniProtKB/Swiss-Prot
      A6NL04, Q63HM9
      UniProtKB/TrEMBL
      B3KXD1
      Related
      ENSP00000367032.3, ENST00000377801.8
      Conserved Domains (1) summary
      cd08616
      Location:19 → 311
      PI-PLCXD1c; Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing 1

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      41306952..41510601 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017009438.3 → XP_016864927.1  PI-PLC X domain-containing protein 3 isoform X1

      Conserved Domains (1) summary
      cd08616
      Location:1 → 239
      PI-PLCXD1c; Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing 1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      41563425..41766981 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352510.1 → XP_054208485.1  PI-PLC X domain-containing protein 3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q63HM9.2 GenPept UniProtKB/Swiss-Prot:Q63HM9

    Gene LinkOut

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

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