Gene Gene information from NCBI Gene database.
Entrez ID 8493
Gene name Protein phosphatase, Mg2+/Mn2+ dependent 1D
Gene symbol PPM1D
Synonyms (NCBI Gene)
IDDGIPJDVSPP2C-DELTAWIP1
Chromosome 17
Chromosome location 17q23.2
Summary 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
SNPs SNP information provided by dbSNP.
21
SNP ID Visualize variation Clinical significance Consequence
rs189669693 T>A,C Pathogenic Synonymous variant, non coding transcript variant, stop gained, coding sequence variant
rs747947002 AA>-,A,AAA Pathogenic, likely-pathogenic Coding sequence variant, frameshift variant, non coding transcript variant
rs763475304 A>-,AA Pathogenic Coding sequence variant, frameshift variant, non coding transcript variant
rs765769406 C>T Pathogenic, uncertain-significance Coding sequence variant, stop gained, non coding transcript variant
rs766524048 T>C,G Likely-pathogenic Coding sequence variant, stop gained, missense variant, non coding transcript variant
miRNA miRNA information provided by mirtarbase database.
831
miRTarBase ID miRNA Experiments Reference
MIRT005360 hsa-miR-16-5p Northern blotqRT-PCRWestern blot 20668064
MIRT004044 hsa-miR-29a-3p Luciferase reporter assayMicroarrayqRT-PCRWestern blot 21175813
MIRT005682 hsa-miR-153-3p Immunoblot 20668064
MIRT005682 hsa-miR-153-3p Luciferase reporter assay 20668064
MIRT005683 hsa-miR-145-5p ImmunoblotLuciferase reporter assay 20668064
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Transcription factor Regulation Reference
CREB1 Unknown 19015127
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
35
GO ID Ontology Definition Evidence Reference
GO:0000086 Process G2/M transition of mitotic cell cycle IEA
GO:0004674 Function Protein serine/threonine kinase activity TAS
GO:0004721 Function Phosphoprotein phosphatase activity IEA
GO:0004722 Function Protein serine/threonine phosphatase activity IBA
GO:0004722 Function Protein serine/threonine phosphatase activity IDA 20801214
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
605100 9277 ENSG00000170836
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O15297
Protein name Protein phosphatase 1D (EC 3.1.3.16) (Protein phosphatase 2C isoform delta) (PP2C-delta) (Protein phosphatase magnesium-dependent 1 delta) (p53-induced protein phosphatase 1)
Protein function Involved in the negative regulation of p53 expression (PubMed:23242139). 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 t
PDB 8T2J
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00481 PP2C 65 368 Protein phosphatase 2C Family
Tissue specificity TISSUE SPECIFICITY: Expressed in fetal and adult brain. Also detected in fetal liver and skeletal muscle, but not in their adult counterparts. {ECO:0000269|PubMed:28343630}.
Sequence
MAGLYSLGVSVFSDQGGRKYMEDVTQIVVEPEPTAEEKPSPRRSLSQPLPPRPSPAALPG
GEVSGKGPAVAAREARDPLPDAGASPAPSRCCRRRSSVAFFAVCDGHGGREAAQFAREHL
WGFIKKQKGFTSSEPAKVCAAIRKGFLACHLAMWKKLAEWPKTMTGLPSTSGTTASVVII
RGMKMYVAHVGDSGVVLGIQDDPKDDFVRAVEVTQDHKPELPKERERIEGLGGSVMNKSG
VNRVVWKRPRLTHNGPVRRSTVIDQIPFLAVARALGDLWSYDFFSGEFVVSPEPDTSVHT
LDPQKHKYIILGSDGLWNMIPPQDAISMCQDQEEKKYLMGEHGQSCAKMLVNRALGRWRQ
RMLRADNT
SAIVICISPEVDNQGNFTNEDELYLNLTDSPSYNSQETCVMTPSPCSTPPVK
SLEEDPWPRVNSKDHIPALVRSNAFSENFLEVSAEIARENVQGVVIPSKDPEPLEENCAK
ALTLRIHDSLNNSLPIGLVPTNSTNTVMDQKNLKMSTPGQMKAQEIERTPPTNFKRTLEE
SNSGPLMKKHRRNGLSRSSGAQPASLPTTSQRKNSVKLTMRRRLRGQKKIGNPLLHQHRK
TVCVC
Sequence length 605
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  p53 signaling pathway   Transcriptional regulation by RUNX2
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
21
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Autosomal dominant non-syndromic intellectual disability Pathogenic rs2143731129 RCV004584164
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Familial cancer of breast Pathogenic; Likely pathogenic rs2544465676, rs1057524700, rs1064797099, rs763475304, rs1271133647 RCV003883336
RCV002248662
RCV005222964
RCV002249629
RCV001196274
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Intellectual developmental disorder with gastrointestinal difficulties and high pain threshold Pathogenic; Likely pathogenic rs2031551825, rs2143719857, rs780195897, rs2143719799, rs2031551111, rs2031551927, rs2544465797, rs2031554958, rs146477590, rs2544465726, rs765655972, rs2544465676, rs747947002, rs2544470298, rs189669693
View all (11 more)
RCV001333146
RCV001782680
RCV002221867
RCV002251279
RCV002281595
View all (22 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neurodevelopmental delay Pathogenic rs2143730785 RCV002274364
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
BRAIN STEM NEOPLASMS CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BREAST CANCER HPO
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BREAST NEOPLASMS CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute Promyelocytic Leukemia Promyelocytic Leukemia BEFREE 28486685
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 23111975
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma, Clear Cell Adenocarcinoma BEFREE 12796361
★☆☆☆☆
Found in Text Mining only
Adenoid Cystic Carcinoma Adenocarcinoma BEFREE 25797250
★☆☆☆☆
Found in Text Mining only
Adult Medulloblastoma Medulloblastoma BEFREE 17932621, 19907922, 22379189, 24632620, 27086929
★☆☆☆☆
Found in Text Mining only
Agenesis of corpus callosum Agenesis Of Corpus Callosum BEFREE 25797250
★☆☆☆☆
Found in Text Mining only
Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis BEFREE 31676238
★☆☆☆☆
Found in Text Mining only
Aneurysm Aneurysm Pubtator 39382597 Associate
★☆☆☆☆
Found in Text Mining only
Anxiety Anxiety Disorder HPO_DG
★☆☆☆☆
Found in Text Mining only
Aplasia Cutis Congenita Aplasia Cutis Congenita BEFREE 25797250
★☆☆☆☆
Found in Text Mining only