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    PLCXD2 phosphatidylinositol specific phospholipase C X domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 257068, updated on 3-Apr-2024

    Summary

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    Official Symbol
    PLCXD2provided by HGNC
    Official Full Name
    phosphatidylinositol specific phospholipase C X domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:26462
    See related
    Ensembl:ENSG00000240891 MIM:617015; AllianceGenome:HGNC:26462
    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 nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in kidney (RPKM 2.6), liver (RPKM 2.6) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    3q13.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (111674676..111727007)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (114395502..114447848)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (111393523..111565294)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene CD96 molecule Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:111328685-111329884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:111335350-111335850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:111335851-111336351 Neighboring gene zinc finger BED-type containing 2 Neighboring gene NT5C3A pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20225 Neighboring gene PLCXD2 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 10775 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:111453476-111454675 Neighboring gene pleckstrin homology like domain family B member 2 Neighboring gene uncharacterized LOC107984087 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:111511689-111512190 Neighboring gene uncharacterized LOC105374040 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:111577934-111578520 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:111578521-111579105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20226

    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. Common genetic variation and performance on standardized cognitive tests. Cirulli ET, et al. Eur J Hum Genet, 2010 Jul. PMID 20125193, Free PMC Article
    2. Suppression of DDX39B sensitizes ovarian cancer cells to DNA-damaging chemotherapeutic agents via destabilizing BRCA1 mRNA. Xu Z, et al. Oncogene, 2020 Nov. PMID 32989256
    3. AMPK Interactome Reveals New Function in Non-homologous End Joining DNA Repair. Chen Z, et al. Mol Cell Proteomics, 2020 Mar. PMID 31900314, Free PMC Article
    4. CBFβ stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression. Kim DY, et al. Mol Cell, 2013 Feb 21. PMID 23333304, Free PMC Article
    5. An approach based on a genome-wide association study reveals candidate loci for narcolepsy. Shimada M, et al. Hum Genet, 2010 Oct. PMID 20677014

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: An approach based on a genome-wide association study reveals candidate loci for narcolepsy.
    2. 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

    EBI GWAS Catalog

    Description
    Common genetic variation and performance on standardized cognitive tests.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vif vif HIV-1 Vif upregulates the expression of phosphatidylinositol-specific phospholipase C, X domain containing 2 (PLCXD2) in Vif-expression T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: PHLDB2

    Homology

    Clone Names

    • FLJ31579

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphoric diester hydrolase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    PI-PLC X domain-containing protein 2

    NCBI Reference Sequences (RefSeq)

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    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_001413064.1 → NP_001399993.1  PI-PLC X domain-containing protein 2

      Status: VALIDATED

      Source sequence(s)
      AC055748
      UniProtKB/TrEMBL
      A0A1B0GW80
      Related
      ENSP00000490816.1, ENST00000636933.2

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      111674676..111727007
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      114395502..114447848
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001134478.1: Suppressed sequence

      Description
      NM_001134478.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.

    2. NM_001185106.1: Suppressed sequence

      Description
      NM_001185106.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.

    3. NM_153268.3: Suppressed sequence

      Description
      NM_153268.3: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q0VAA5.1 GenPept UniProtKB/Swiss-Prot:Q0VAA5

    Gene LinkOut

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

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