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Aliases for PPM1D Gene

Aliases for PPM1D Gene

  • Protein Phosphatase, Mg2+/Mn2+ Dependent 1D 2 3 5
  • Protein Phosphatase 1D Magnesium-Dependent, Delta Isoform 2 3
  • Wild-Type P53-Induced Phosphatase 1 2 3
  • PP2C-DELTA 3 4
  • WIP1 3 4
  • Protein Phosphatase Magnesium-Dependent 1 Delta 4
  • Protein Phosphatase, Mg2+/Mn2+ Dependent, 1D 2
  • Protein Phosphatase 2C, Delta Isoform 2
  • Protein Phosphatase 2C Delta Isoform 3
  • Protein Phosphatase 2C Isoform Delta 4
  • P53-Induced Protein Phosphatase 1 4
  • Protein Phosphatase Wip1 3
  • Protein Phosphatase 1D 3
  • EC 3.1.3.16 4
  • IDDGIP 3

External Ids for PPM1D Gene

Previous GeneCards Identifiers for PPM1D Gene

  • GC17P058414
  • GC17P061129
  • GC17P059019
  • GC17P059151
  • GC17P056032
  • GC17P058677
  • GC17P054048

Summaries for PPM1D Gene

Entrez Gene Summary for PPM1D Gene

  • The protein encoded by this gene is a member of the PP2C family of Ser/Thr protein phosphatases. PP2C family members are known to be negative regulators of cell stress response pathways. The expression of this gene is induced in a p53-dependent manner in response to various environmental stresses. While being induced by tumor suppressor protein TP53/p53, this phosphatase negatively regulates the activity of p38 MAP kinase, MAPK/p38, through which it reduces the phosphorylation of p53, and in turn suppresses p53-mediated transcription and apoptosis. This phosphatase thus mediates a feedback regulation of p38-p53 signaling that contributes to growth inhibition and the suppression of stress induced apoptosis. This gene is located in a chromosomal region known to be amplified in breast cancer. The amplification of this gene has been detected in both breast cancer cell line and primary breast tumors, which suggests a role of this gene in cancer development. [provided by RefSeq, Jul 2008]

GeneCards Summary for PPM1D Gene

PPM1D (Protein Phosphatase, Mg2+/Mn2+ Dependent 1D) is a Protein Coding gene. Diseases associated with PPM1D include Intellectual Developmental Disorder With Gastrointestinal Difficulties And High Pain Threshold and Breast Cancer. Among its related pathways are DNA Damage and Regulation of CFTR activity (norm and CF). GO annotations related to this gene include protein serine/threonine phosphatase activity. An important paralog of this gene is PPM1G.

UniProtKB/Swiss-Prot for PPM1D Gene

  • Required for the relief of p53-dependent checkpoint mediated cell cycle arrest. Binds to and dephosphorylates Ser-15 of TP53 and Ser-345 of CHEK1 which contributes to the functional inactivation of these proteins. Mediates MAPK14 dephosphorylation and inactivation (PubMed:21283629).

Gene Wiki entry for PPM1D Gene

Additional gene information for PPM1D Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PPM1D Gene

Genomics for PPM1D Gene

Regulatory Elements for PPM1D Gene

Enhancers for PPM1D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17H059824 2.7 VISTA FANTOM5 Ensembl ENCODE dbSUPER 48.4 -757.3 -757298 36 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 ZC3H11A NFYC TUBD1 PPM1D RPS6KB1 HEATR6 NDUFB8P2 SMG8 LOC101927755 DHX40 APPBP2 VMP1
GH17H061393 2 FANTOM5 Ensembl ENCODE dbSUPER 24.7 +805.3 805301 24 HDGF PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF143 PPM1D MED13 TBX2-AS1 TBX2 TBX4 APPBP2 C17orf82 LOC101927855
GH17H059616 1.8 FANTOM5 ENCODE dbSUPER 24.6 -980.5 -980509 6 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 MEF2D SSRP1 ZNF610 TUBD1 RPS6KB1 HEATR6 SKA2 PPM1D DHX40 RNFT1 NDUFB8P2 LOC100996660 APPBP2
GH17H059751 2 FANTOM5 Ensembl ENCODE dbSUPER 21.6 -838.7 -838699 20 HDGF PKNOX1 FOXA2 MLX ARID4B YBX1 FEZF1 DMAP1 SLC30A9 ZNF207 RPS6KB1 TUBD1 NDUFB8P2 PPM1D LOC101927755 ENSG00000274378 ENSG00000224738 MIR21 RNU6-450P HEATR6
GH17H061334 1.6 Ensembl ENCODE dbSUPER 23.6 +735.6 735582 2 FOXA2 MLX ARID4B FEZF1 DMAP1 ZNF2 YY1 SLC30A9 FOS SP3 PPM1D KRT18P61 ENSG00000263887 TBC1D3P2 MED13 NACA2 GC17P061333 ENSG00000273982
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PPM1D on UCSC Golden Path with GeneCards custom track

Promoters for PPM1D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000096503 817 4001 HDGF PKNOX1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1

Genomic Location for PPM1D Gene

Chromosome:
17
Start:
60,600,183 bp from pter
End:
60,666,280 bp from pter
Size:
66,098 bases
Orientation:
Plus strand

Genomic View for PPM1D Gene

Genes around PPM1D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PPM1D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PPM1D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PPM1D Gene

Proteins for PPM1D Gene

  • Protein details for PPM1D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15297-PPM1D_HUMAN
    Recommended name:
    Protein phosphatase 1D
    Protein Accession:
    O15297
    Secondary Accessions:
    • Q53XP4
    • Q6P991
    • Q8IVR6

    Protein attributes for PPM1D Gene

    Size:
    605 amino acids
    Molecular mass:
    66675 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    • Interacts with CHEK1 and CHEK2; dephosphorylates them. Interacts with MAPK14 (PubMed:21283629).

    Alternative splice isoforms for PPM1D Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PPM1D Gene

Post-translational modifications for PPM1D Gene

  • Ubiquitination at Lys238
  • Modification sites at PhosphoSitePlus

Other Protein References for PPM1D Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PPM1D (PPM1D)
  • Abcam antibodies for PPM1D
  • Santa Cruz Biotechnology (SCBT) Antibodies for PPM1D

No data available for DME Specific Peptides for PPM1D Gene

Domains & Families for PPM1D Gene

Gene Families for PPM1D Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for PPM1D Gene

Graphical View of Domain Structure for InterPro Entry

O15297

UniProtKB/Swiss-Prot:

PPM1D_HUMAN :
  • Belongs to the PP2C family.
Family:
  • Belongs to the PP2C family.
genes like me logo Genes that share domains with PPM1D: view

Function for PPM1D Gene

Molecular function for PPM1D Gene

UniProtKB/Swiss-Prot CatalyticActivity:
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate.
UniProtKB/Swiss-Prot Function:
Required for the relief of p53-dependent checkpoint mediated cell cycle arrest. Binds to and dephosphorylates Ser-15 of TP53 and Ser-345 of CHEK1 which contributes to the functional inactivation of these proteins. Mediates MAPK14 dephosphorylation and inactivation (PubMed:21283629).
UniProtKB/Swiss-Prot Induction:
By p53/TP53.

Enzyme Numbers (IUBMB) for PPM1D Gene

Phenotypes From GWAS Catalog for PPM1D Gene

Gene Ontology (GO) - Molecular Function for PPM1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0004721 phosphoprotein phosphatase activity IEA --
GO:0004722 protein serine/threonine phosphatase activity IDA 20801214
GO:0005515 protein binding IPI 17936559
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with PPM1D: view
genes like me logo Genes that share phenotypes with PPM1D: view

Human Phenotype Ontology for PPM1D Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PPM1D Gene

MGI Knock Outs for PPM1D:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PPM1D
  • Applied Biological Materials Clones for PPM1D
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Transcription Factor Targets and HOMER Transcription for PPM1D Gene

Localization for PPM1D Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PPM1D gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PPM1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,TAS 28343630
GO:0005829 cytosol IDA 28343630
genes like me logo Genes that share ontologies with PPM1D: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PPM1D Gene

Pathways & Interactions for PPM1D Gene

genes like me logo Genes that share pathways with PPM1D: view

Pathways by source for PPM1D Gene

1 Cell Signaling Technology pathway for PPM1D Gene
2 BioSystems pathways for PPM1D Gene
1 KEGG pathway for PPM1D Gene

SIGNOR curated interactions for PPM1D Gene

Activates:
Inactivates:

Gene Ontology (GO) - Biological Process for PPM1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000086 G2/M transition of mitotic cell cycle IEA --
GO:0006470 protein dephosphorylation TAS 9177166
GO:0007049 cell cycle IEA --
GO:0008285 negative regulation of cell proliferation TAS 9177166
GO:0009267 cellular response to starvation IEA --
genes like me logo Genes that share ontologies with PPM1D: view

Drugs & Compounds for PPM1D Gene

(9) Drugs for PPM1D Gene - From: ApexBio, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Manganese Approved Nutra 35
CCT007093 Pharma PPM1D inhibitor 0
GSK 2830371 Pharma 0

(1) Additional Compounds for PPM1D Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Phosphate
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
14265-44-2

(2) ApexBio Compounds for PPM1D Gene

Compound Action Cas Number
CCT007093 PPM1D inhibitor 176957-55-4
GSK 2830371 1404456-53-6
genes like me logo Genes that share compounds with PPM1D: view

Drug Products

Transcripts for PPM1D Gene

mRNA/cDNA for PPM1D Gene

Unigene Clusters for PPM1D Gene

Protein phosphatase, Mg2+/Mn2+ dependent, 1D:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PPM1D
  • Applied Biological Materials Clones for PPM1D
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for PPM1D Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b
SP1: - -
SP2: - - -
SP3: -
SP4:

Relevant External Links for PPM1D Gene

GeneLoc Exon Structure for
PPM1D
ECgene alternative splicing isoforms for
PPM1D

Expression for PPM1D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PPM1D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PPM1D Gene

This gene is overexpressed in Platelet (55.0) and Placenta (14.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PPM1D Gene



Protein tissue co-expression partners for PPM1D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PPM1D Gene:

PPM1D

SOURCE GeneReport for Unigene cluster for PPM1D Gene:

Hs.286073

Evidence on tissue expression from TISSUES for PPM1D Gene

  • Nervous system(4.6)
  • Skin(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PPM1D Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • reproductive
  • skeletal muscle
Organs:
Thorax:
  • breast
genes like me logo Genes that share expression patterns with PPM1D: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PPM1D Gene

Orthologs for PPM1D Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PPM1D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PPM1D 33 34
  • 99.5 (n)
dog
(Canis familiaris)
Mammalia PPM1D 34 33
  • 93.06 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PPM1D 33 34
  • 89.81 (n)
rat
(Rattus norvegicus)
Mammalia Ppm1d 33
  • 87.7 (n)
mouse
(Mus musculus)
Mammalia Ppm1d 33 16 34
  • 87.19 (n)
oppossum
(Monodelphis domestica)
Mammalia PPM1D 34
  • 77 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PPM1D 34
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves PPM1D 33 34
  • 72.71 (n)
lizard
(Anolis carolinensis)
Reptilia PPM1D 34
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ppm1d 33
  • 64.65 (n)
African clawed frog
(Xenopus laevis)
Amphibia ppm1d-prov 33
zebrafish
(Danio rerio)
Actinopterygii ppm1da 33 34
  • 61.68 (n)
ppm1db 34
  • 53 (a)
OneToMany
zgc55836 33
fruit fly
(Drosophila melanogaster)
Insecta Pp2C1 35 34
  • 47 (a)
worm
(Caenorhabditis elegans)
Secernentea Y54F10BM.1 35 34
  • 38 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PTC4 34
  • 16 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 20 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6123 33
Species where no ortholog for PPM1D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PPM1D Gene

ENSEMBL:
Gene Tree for PPM1D (if available)
TreeFam:
Gene Tree for PPM1D (if available)

Paralogs for PPM1D Gene

Paralogs for PPM1D Gene

genes like me logo Genes that share paralogs with PPM1D: view

Variants for PPM1D Gene

Sequence variations from dbSNP and Humsavar for PPM1D Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs112711419 Likely benign 60,631,789(+) ATCAA(C/T)TCCCA intron-variant
rs138641521 Likely benign 60,633,832(+) TATTT(A/G)TGTGA intron-variant
rs143487178 Likely benign 60,652,011(+) AATAG(A/C)GATTT intron-variant
rs144142345 Likely benign 60,648,133(+) TTGGT(A/G)CTTCT intron-variant
rs148672464 Likely benign 60,622,227(+) CTTTA(C/T)TACTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PPM1D Gene

Variant ID Type Subtype PubMed ID
esv3410224 CNV insertion 20981092
esv3640930 CNV loss 21293372
nsv1061134 CNV gain 25217958

Variation tolerance for PPM1D Gene

Residual Variation Intolerance Score: 57.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.26; 40.64% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PPM1D Gene

Human Gene Mutation Database (HGMD)
PPM1D
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PPM1D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PPM1D Gene

Disorders for PPM1D Gene

MalaCards: The human disease database

(3) MalaCards diseases for PPM1D Gene - From: OMIM, ClinVar, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • iddgip
breast cancer
  • breast cancer, invasive ductal
medulloblastoma
  • medulloblastoma, somatic
- elite association - COSMIC cancer census association via MalaCards
Search PPM1D in MalaCards View complete list of genes associated with diseases

Relevant External Links for PPM1D

Genetic Association Database (GAD)
PPM1D
Human Genome Epidemiology (HuGE) Navigator
PPM1D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PPM1D
genes like me logo Genes that share disorders with PPM1D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PPM1D Gene

Publications for PPM1D Gene

  1. Regulation of the antioncogenic Chk2 kinase by the oncogenic Wip1 phosphatase. (PMID: 16311512) Fujimoto H … Minami Y (Cell death and differentiation 2006) 3 4 22 60
  2. PPM1D dephosphorylates Chk1 and p53 and abrogates cell cycle checkpoints. (PMID: 15870257) Lu X … Donehower LA (Genes & development 2005) 3 4 22 60
  3. Wip1, a novel human protein phosphatase that is induced in response to ionizing radiation in a p53-dependent manner. (PMID: 9177166) Fiscella M … Appella E (Proceedings of the National Academy of Sciences of the United States of America 1997) 2 3 4 60
  4. LZAP inhibits p38 MAPK (p38) phosphorylation and activity by facilitating p38 association with the wild-type p53 induced phosphatase 1 (WIP1). (PMID: 21283629) An H … Yarbrough WG (PloS one 2011) 3 4 60
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60

Products for PPM1D Gene

  • Addgene plasmids for PPM1D

Sources for PPM1D Gene

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