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

Gene ID: 5528, updated on 20-Apr-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
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Genomic context

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Location:
6p21.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (42984570..43012342)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42813692..42841440)
105.20220307 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: 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. A novel nonsense mutation in PPP2R5D is associated with neurodevelopmental disorders and shows incomplete penetrance in a Chinese pedigree. Liu R, et al. Clin Neurol Neurosurg, 2022 Dec. PMID 36403339
  2. PPP2R5D promotes hepatitis C virus infection by binding to viral NS5B and enhancing viral RNA replication. Anwar MI, et al. Virol J, 2022 Jul 14. PMID 35836293, Free PMC Article
  3. Rare missense variants in the PPP2R5D gene associated with Parkinson's disease in the Han Chinese population. Ning P, et al. Neurosci Lett, 2022 Apr 17. PMID 35257824
  4. PPP2R5D-Related Neurodevelopmental Disorder or Developmental and Epileptic Encephalopathy?: A Novel Phenotypic Description and Review of Published Cases. Madaan P, et al. Neuropediatrics, 2022 Feb. PMID 34448180
  5. A Novel Missense Variant in the Gene PPP2R5D Causes a Rare Neurodevelopmental Disorder with Increased Phenotype. Yan L, et al. Biomed Res Int, 2021. PMID 33628804, Free PMC Article

See all (113) 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
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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)

Genotypes

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 phosphoprotein phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
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 TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of peptidyl-threonine phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in nervous system development TAS
Traceable Author Statement
more info
 PubMed 
involved_in positive regulation of protein dephosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in protein dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein dephosphorylation IDA
Inferred from Direct Assay
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_2023_10

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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