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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for PPM1D |
 Gene summary |
| Gene information | Gene symbol | PPM1D | Gene ID | 8493 |
| Gene name | protein phosphatase, Mg2+/Mn2+ dependent 1D | |
| Synonyms | IDDGIP|PP2C-DELTA|WIP1 | |
| Cytomap | 17q23.2 | |
| Type of gene | protein-coding | |
| Description | protein phosphatase 1Dprotein phosphatase 1D magnesium-dependent, delta isoformprotein phosphatase 2C delta isoformprotein phosphatase Wip1wild-type p53-induced phosphatase 1 | |
| Modification date | 20180519 | |
| UniProtAcc | O15297 | |
| Context | PubMed: PPM1D [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| PPM1D | GO:0035970 | peptidyl-threonine dephosphorylation | 20801214 |
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Exon skipping events across known transcript of Ensembl for PPM1D from UCSC genome browser |
| Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Gene isoform structures and expression levels for PPM1D |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for PPM1D |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_154999 | 17 | 58677629:58678247:58700881:58701110:58711213:58711318 | 58700881:58701110 | ENSG00000170836.7 | ENST00000392995.3 |
| exon_skip_155003 | 17 | 58700881:58701110:58711213:58711338:58725252:58725443 | 58711213:58711338 | ENSG00000170836.7 | ENST00000392995.3,ENST00000305921.3 |
| exon_skip_155004 | 17 | 58725252:58725443:58733959:58734202:58740355:58741834 | 58733959:58734202 | ENSG00000170836.7 | ENST00000305921.3 |
| exon_skip_155005 | 17 | 58733959:58734202:58734292:58734403:58740355:58741834 | 58734292:58734403 | ENSG00000170836.7 | ENST00000392995.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PPM1D |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_154999 | 17 | 58677629:58678247:58700881:58701110:58711213:58711318 | 58700881:58701110 | ENSG00000170836.7 | ENST00000392995.3 |
| exon_skip_155003 | 17 | 58700881:58701110:58711213:58711338:58725252:58725443 | 58711213:58711338 | ENSG00000170836.7 | ENST00000305921.3,ENST00000392995.3 |
| exon_skip_155004 | 17 | 58725252:58725443:58733959:58734202:58740355:58741834 | 58733959:58734202 | ENSG00000170836.7 | ENST00000305921.3 |
| exon_skip_155005 | 17 | 58733959:58734202:58734292:58734403:58740355:58741834 | 58734292:58734403 | ENSG00000170836.7 | ENST00000392995.3 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for PPM1D |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000305921 | 58711213 | 58711338 | Frame-shift |
| ENST00000305921 | 58733959 | 58734202 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000305921 | 58711213 | 58711338 | Frame-shift |
| ENST00000305921 | 58733959 | 58734202 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PPM1D |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000305921 | 3003 | 605 | 58733959 | 58734202 | 1250 | 1492 | 339 | 420 |
| Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000305921 | 3003 | 605 | 58733959 | 58734202 | 1250 | 1492 | 339 | 420 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| O15297 | 339 | 420 | 1 | 605 | Chain | ID=PRO_0000057752;Note=Protein phosphatase 1D |
| O15297 | 339 | 420 | 8 | 375 | Domain | Note=PPM-type phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01082 |
| O15297 | 339 | 420 | 366 | 366 | Metal binding | Note=Manganese 2;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| O15297 | 339 | 420 | 404 | 605 | Natural variant | ID=VAR_080081;Note=In IDDGIP. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:28343630;Dbxref=PMID:28343630 |
| O15297 | 339 | 420 | 407 | 605 | Natural variant | ID=VAR_080082;Note=In IDDGIP. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:28343630;Dbxref=PMID:28343630 |
| Lost protein functional features of individual exon skipping events in GTEx. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| O15297 | 339 | 420 | 1 | 605 | Chain | ID=PRO_0000057752;Note=Protein phosphatase 1D |
| O15297 | 339 | 420 | 8 | 375 | Domain | Note=PPM-type phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01082 |
| O15297 | 339 | 420 | 366 | 366 | Metal binding | Note=Manganese 2;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| O15297 | 339 | 420 | 404 | 605 | Natural variant | ID=VAR_080081;Note=In IDDGIP. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:28343630;Dbxref=PMID:28343630 |
| O15297 | 339 | 420 | 407 | 605 | Natural variant | ID=VAR_080082;Note=In IDDGIP. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:28343630;Dbxref=PMID:28343630 |
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SNVs in the skipped exons for PPM1D |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_155003 | 58711214 | 58711338 | 58711282 | 58711282 | Frame_Shift_Del | T | - | p.V257fs |
| THCA | TCGA-ET-A3BW-01 | exon_skip_155004 | 58733960 | 58734202 | 58734159 | 58734159 | Frame_Shift_Del | C | - | p.T406fs |
| COAD | TCGA-AA-3713-01 | exon_skip_155004 | 58733960 | 58734202 | 58733983 | 58733984 | Frame_Shift_Ins | - | A | p.A347fs |
| SKCM | TCGA-QB-AA9O-06 | exon_skip_155004 | 58733960 | 58734202 | 58734155 | 58734155 | Nonsense_Mutation | G | T | p.E405* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| DOV13_OVARY | 58700882 | 58701110 | 58700939 | 58700939 | Missense_Mutation | T | C | p.V177A |
| HS294T_SKIN | 58700882 | 58701110 | 58700939 | 58700939 | Missense_Mutation | T | C | p.V177A |
| MM415_SKIN | 58700882 | 58701110 | 58700987 | 58700987 | Missense_Mutation | C | T | p.S193L |
| NCIH2135_LUNG | 58711214 | 58711338 | 58711239 | 58711239 | Missense_Mutation | C | T | p.R243C |
| HCC2279_LUNG | 58711214 | 58711338 | 58711273 | 58711273 | Missense_Mutation | A | G | p.N254S |
| C32_SKIN | 58711214 | 58711338 | 58711311 | 58711311 | Missense_Mutation | C | T | p.P267S |
| NCIH1048_LUNG | 58733960 | 58734202 | 58733966 | 58733966 | Missense_Mutation | C | T | p.H342Y |
| DJM1_SKIN | 58733960 | 58734202 | 58733979 | 58733979 | Missense_Mutation | G | T | p.C346F |
| HCC56_LARGE_INTESTINE | 58733960 | 58734202 | 58733979 | 58733979 | Missense_Mutation | G | T | p.C346F |
| HSC2_UPPER_AERODIGESTIVE_TRACT | 58733960 | 58734202 | 58733979 | 58733979 | Missense_Mutation | G | T | p.C346F |
| KYAE1_OESOPHAGUS | 58733960 | 58734202 | 58733979 | 58733979 | Missense_Mutation | G | T | p.C346F |
| OVISE_OVARY | 58733960 | 58734202 | 58733979 | 58733979 | Missense_Mutation | G | T | p.C346F |
| TE8_OESOPHAGUS | 58733960 | 58734202 | 58733979 | 58733979 | Missense_Mutation | G | T | p.C346F |
| KYSE450_OESOPHAGUS | 58733960 | 58734202 | 58734117 | 58734117 | Missense_Mutation | A | G | p.Y392C |
| HEC1A_ENDOMETRIUM | 58733960 | 58734202 | 58734162 | 58734162 | Missense_Mutation | G | A | p.C407Y |
| SW982_SOFT_TISSUE | 58733960 | 58734202 | 58734173 | 58734174 | Missense_Mutation | CC | TT | p.P411F |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 58700882 | 58701110 | 58700883 | 58700883 | Splice_Site | G | A | p.A158A |
| TE5_OESOPHAGUS | 58733960 | 58734202 | 58733961 | 58733961 | Splice_Site | G | A | p.G340D |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PPM1D |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PPM1D |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PPM1D |
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RelatedDrugs for PPM1D |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for PPM1D |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PPM1D | C0017638 | Glioma | 1 | CTD_human |
| PPM1D | C0677866 | Brain Stem Neoplasms | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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