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

Gene ID: 257068, updated on 2-Nov-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, Nov 2024]
Expression
Broad expression in kidney (RPKM 2.6), liver (RPKM 2.6) and 21 other tissues See more
Orthologs
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Genomic context

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See PLCXD2 in Genome Data Viewer
Location:
3q13.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (111674676..111727007)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (114395502..114447848)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (111393523..111445854)

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 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)

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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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_2024_08

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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