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    PPP2R5D protein phosphatase 2 regulatory subunit B'delta [ Homo sapiens (human) ]

    Gene ID: 5528, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PPP2R5Dprovided by HGNC
    Official Full Name
    protein phosphatase 2 regulatory subunit B'deltaprovided by HGNC
    Primary source
    HGNC:HGNC:9312
    See related
    Ensembl:ENSG00000112640 MIM:601646; AllianceGenome:HGNC:9312
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    B56D; HJS1; MRD35; B56delta
    Summary
    The product of this gene belongs to the phosphatase 2A regulatory subunit B family. Protein phosphatase 2A is one of the four major Ser/Thr phosphatases, and it is implicated in the negative control of cell growth and division. It consists of a common heteromeric core enzyme, which is composed of a catalytic subunit and a constant regulatory subunit, that associates with a variety of regulatory subunits. The B regulatory subunit might modulate substrate selectivity and catalytic activity. This gene encodes a delta isoform of the regulatory subunit B56 subfamily. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 23.6), brain (RPKM 18.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PPP2R5D in Genome Data Viewer
    Location:
    6p21.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (42984570..43012342)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42813692..42841440)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (42952308..42980080)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene CNPY3-GNMT readthrough Neighboring gene ReSE screen-validated silencer GRCh37_chr6:42935679-42935875 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:42938260-42939130 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:42939131-42939999 Neighboring gene glycine N-methyltransferase Neighboring gene peroxisomal biogenesis factor 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:42946179-42947120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24582 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:42947525-42947721 Neighboring gene uncharacterized LOC124900215 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:42948960-42949178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24583 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17212 Neighboring gene Sharpr-MPRA regulatory region 14905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:42979352-42979852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:42988913-42989644 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:42989645-42990376 Neighboring gene male-enhanced antigen 1 Neighboring gene kelch domain containing 3 Neighboring gene ribosomal RNA processing 36

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Molecular cloning of a 74-kDa regulatory subunit (B" or delta) of human protein phosphatase 2A. Tanabe O, et al. FEBS Lett, 1996 Jan 22. PMID 8566219
    2. Reduction of protein phosphatase 2A (PP2A) complexity reveals cellular functions and dephosphorylation motifs of the PP2A/B'δ holoenzyme. Jong CJ, et al. J Biol Chem, 2020 Apr 24. PMID 32156701, Free PMC Article
    3. Critical role of PP2A-B56 family protein degradation in HIV-1 Vif mediated G2 cell cycle arrest. Nagata K, et al. Biochem Biophys Res Commun, 2020 Jun 18. PMID 32446377
    4. Parallel Tests of Whole Exome Sequencing and Copy Number Variant Sequencing Increase the Diagnosis Yields of Rare Pediatric Disorders. Hu X, et al. Front Genet, 2020. PMID 32595695, Free PMC Article
    5. Early-Onset Parkinsonism Is a Manifestation of the PPP2R5D p.E200K Mutation. Kim CY, et al. Ann Neurol, 2020 Nov. PMID 32743835, Free PMC Article

    See all (118) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical, neuroimaging and molecular characteristics of PPP2R5D-related neurodevelopmental disorders: an expanded series with functional characterisation and genotype-phenotype analysis.
      Title: Clinical, neuroimaging and molecular characteristics of PPP2R5D-related neurodevelopmental disorders: an expanded series with functional characterisation and genotype-phenotype analysis.
    2. A novel nonsense mutation in PPP2R5D is associated with neurodevelopmental disorders and shows incomplete penetrance in a Chinese pedigree.
      Title: A novel nonsense mutation in PPP2R5D is associated with neurodevelopmental disorders and shows incomplete penetrance in a Chinese pedigree.
    3. PPP2R5D promotes hepatitis C virus infection by binding to viral NS5B and enhancing viral RNA replication.
      Title: PPP2R5D promotes hepatitis C virus infection by binding to viral NS5B and enhancing viral RNA replication.
    4. Rare missense variants in the PPP2R5D gene associated with Parkinson's disease in the Han Chinese population.
      Title: Rare missense variants in the PPP2R5D gene associated with Parkinson's disease in the Han Chinese population.
    5. PPP2R5D-Related Neurodevelopmental Disorder or Developmental and Epileptic Encephalopathy?: A Novel Phenotypic Description and Review of Published Cases.
      Title: PPP2R5D-Related Neurodevelopmental Disorder or Developmental and Epileptic Encephalopathy?: A Novel Phenotypic Description and Review of Published Cases.
    6. Co-Occurrence of Fragile X Syndrome with a Second Genetic Condition: Three Independent Cases of Double Diagnosis.
      Title: Co-Occurrence of Fragile X Syndrome with a Second Genetic Condition: Three Independent Cases of Double Diagnosis.
    7. A disorder-related variant (E420K) of a PP2A-regulatory subunit (PPP2R5D) causes constitutively active AKT-mTOR signaling and uncoordinated cell growth.
      Title: A disorder-related variant (E420K) of a PP2A-regulatory subunit (PPP2R5D) causes constitutively active AKT-mTOR signaling and uncoordinated cell growth.
    8. Reduction of protein phosphatase 2A (PP2A) complexity reveals cellular functions and dephosphorylation motifs of the PP2A/B'delta holoenzyme.
      Title: Reduction of protein phosphatase 2A (PP2A) complexity reveals cellular functions and dephosphorylation motifs of the PP2A/B'δ holoenzyme.
    9. Critical role of PP2A-B56 family protein degradation in HIV-1 Vif mediated G2 cell cycle arrest.
      Title: Critical role of PP2A-B56 family protein degradation in HIV-1 Vif mediated G2 cell cycle arrest.
    10. Early-Onset Parkinsonism Is a Manifestation of the PPP2R5D p.E200K Mutation.
      Title: Early-Onset Parkinsonism Is a Manifestation of the PPP2R5D p.E200K Mutation.
    Submit: New GeneRIF Correction See all GeneRIFs (22)

    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

    Associated conditions

    Description Tests
    Hogue-Janssens syndrome 1
    MedGen: C5779996 OMIM: 616355 GeneReviews: PPP2R5D-Related Neurodevelopmental Disorder
    		Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-05-26)

    ClinGen Genome Curation Page
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2021-05-26)

    ClinGen Genome Curation PagePubMed

    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
    Tat tat HIV-1 Tat upregulates the total levels of PP2A protein and downregulates the inactive form of phosphorylated PP2A, which leads to inhibit hTERT activity directly or indirectly in CD4+ T cells PubMed
    tat Protein phosphatase-2A (PP2A) and protein phosphatase-1 (PP1) regulate HIV-1 Tat-activated transcription through dephosphorylation of CDK9 PubMed
    tat An increase in the amount of PP2A core enzyme with a concomitant decrease in the amount of PP2A holoenzyme inhibits HIV-1 Tat-stimulated transcription from the HIV-1 LTR promoter, indicating a role for PP2A in the modulation of HIV-1 gene expression PubMed
    Vpr vpr Amino-acid peptide sequence (residues 77-92) of HIV-1 Vpr binds to PP2A1. The sequence from HIV-1 89.6 strain is a cell penetrating and death domain PubMed
    vpr HIV-1 Vpr was found to upregulate PP2A in fission yeast PubMed
    vpr HIV-1 Vpr forms a complex with HIV-1 nucleocapsid that directly activates PP2A PubMed
    nucleocapsid gag HIV-1 Vpr forms a complex with HIV-1 nucleocapsid that directly activates PP2A PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • MGC2134, MGC8949

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein phosphatase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein phosphatase regulator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in meiotic sister chromatid cohesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of protein phosphatase type 2A complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform

    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.

    Genomic

    1. NG_050636.1 RefSeqGene

      Range
      5072..32844
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001270476.2 → NP_001257405.1  serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform isoform 4

      See identical proteins and their annotated locations for NP_001257405.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice junction at the 5' end of an exon compared to variant 1, resulting in a transcript that is translated from a downstream AUG. The resulting isoform (4) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AK122701, AL136304, BC001095, DA388594
      UniProtKB/TrEMBL
      Q59EF0
      Conserved Domains (1) summary
      pfam01603
      Location:1 → 362
      B56; Protein phosphatase 2A regulatory B subunit (B56 family)

    2. NM_006245.4 → NP_006236.1  serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform isoform 1

      See identical proteins and their annotated locations for NP_006236.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript, and encodes the longest isoform (1).
      Source sequence(s)
      BC010692, DA388594
      Consensus CDS
      CCDS4878.1
      UniProtKB/Swiss-Prot
      A8K3I9, B5BUA6, O00494, O00696, Q14738, Q15171, Q5TC39
      UniProtKB/TrEMBL
      A8K6Y2
      Related
      ENSP00000417963.1, ENST00000485511.6
      Conserved Domains (2) summary
      pfam01603
      Location:110 → 513
      B56; Protein phosphatase 2A regulatory B subunit (B56 family)
      cl27532
      Location:56 → 122
      B56; Protein phosphatase 2A regulatory B subunit (B56 family)

    3. NM_180976.3 → NP_851307.1  serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform isoform 2

      See identical proteins and their annotated locations for NP_851307.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (2), that is missing an internal segment compared to isoform 1.
      Source sequence(s)
      BC001175, DA388594
      Consensus CDS
      CCDS55002.1
      UniProtKB/TrEMBL
      A8K6Y2
      Related
      ENSP00000377669.3, ENST00000394110.7
      Conserved Domains (1) summary
      pfam01603
      Location:82 → 481
      B56; Protein phosphatase 2A regulatory B subunit (B56 family)

    4. NM_180977.3 → NP_851308.1  serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform isoform 3

      See identical proteins and their annotated locations for NP_851308.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (3), that is missing an internal segment compared to isoform 1.
      Source sequence(s)
      AB000635, BC001095, DA388594
      Consensus CDS
      CCDS43464.1
      UniProtKB/TrEMBL
      Q59EF0
      Related
      ENSP00000420674.1, ENST00000461010.5
      Conserved Domains (1) summary
      pfam01603
      Location:6 → 407
      B56; Protein phosphatase 2A regulatory B subunit (B56 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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      42984570..43012342
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      42813692..42841440
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14738.1 GenPept UniProtKB/Swiss-Prot:Q14738

    Gene LinkOut

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

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