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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 PIK3C3 |
 Gene summary |
| Gene information | Gene symbol | PIK3C3 | Gene ID | 5289 |
| Gene name | phosphatidylinositol 3-kinase catalytic subunit type 3 | |
| Synonyms | VPS34|Vps34|hVps34 | |
| Cytomap | 18q12.3 | |
| Type of gene | protein-coding | |
| Description | phosphatidylinositol 3-kinase catalytic subunit type 3PI3-kinase type 3PI3K type 3PtdIns-3-kinase type 3phosphatidylinositol 3-kinase p100 subunitphosphoinositide-3-kinase, class 3 | |
| Modification date | 20180523 | |
| UniProtAcc | Q8NEB9 | |
| Context | PubMed: PIK3C3 [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 |
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Exon skipping events across known transcript of Ensembl for PIK3C3 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 PIK3C3 |
| 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 PIK3C3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_296610 | 18 | 39535226:39535324:39537534:39537723:39542453:39542597 | 39537534:39537723 | ENSG00000078142.7 | ENST00000586545.1 |
| exon_skip_296612 | 18 | 39550290:39550420:39564843:39565071:39567775:39567839 | 39564843:39565071 | ENSG00000078142.7 | ENST00000591011.1 |
| exon_skip_296617 | 18 | 39600601:39600669:39607406:39607512:39609288:39609395 | 39607406:39607512 | ENSG00000078142.7 | ENST00000262039.4,ENST00000398870.3 |
| exon_skip_296620 | 18 | 39609288:39609405:39613789:39613921:39617655:39617781 | 39613789:39613921 | ENSG00000078142.7 | ENST00000593098.1,ENST00000262039.4,ENST00000590013.1,ENST00000398870.3 |
| exon_skip_296622 | 18 | 39618744:39618814:39620640:39620705:39623696:39623781 | 39620640:39620705 | ENSG00000078142.7 | ENST00000589056.1,ENST00000593098.1,ENST00000587402.1,ENST00000597477.1,ENST00000262039.4,ENST00000398870.3 |
| exon_skip_296624 | 18 | 39623696:39623781:39629494:39629569:39637846:39638015 | 39629494:39629569 | ENSG00000078142.7 | ENST00000593098.1,ENST00000262039.4,ENST00000398870.3 |
| exon_skip_296625 | 18 | 39629494:39629569:39637846:39638015:39644703:39644794 | 39637846:39638015 | ENSG00000078142.7 | ENST00000593098.1,ENST00000262039.4,ENST00000398870.3 |
| exon_skip_296629 | 18 | 39629494:39629569:39644703:39644794:39647351:39647374 | 39644703:39644794 | ENSG00000078142.7 | ENST00000588631.1 |
| exon_skip_296632 | 18 | 39637846:39638015:39639758:39639858:39644703:39644794 | 39639758:39639858 | ENSG00000078142.7 | ENST00000587261.1 |
| exon_skip_296633 | 18 | 39637846:39638015:39644703:39644794:39647351:39647374 | 39644703:39644794 | ENSG00000078142.7 | ENST00000588156.1,ENST00000593098.1,ENST00000262039.4,ENST00000398870.3 |
| exon_skip_296637 | 18 | 39644703:39644794:39647351:39647477:39661086:39661148 | 39647351:39647477 | ENSG00000078142.7 | ENST00000588156.1,ENST00000587328.1,ENST00000593098.1,ENST00000588631.1,ENST00000262039.4,ENST00000398870.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PIK3C3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_296610 | 18 | 39535226:39535324:39537534:39537723:39542453:39542597 | 39537534:39537723 | ENSG00000078142.7 | ENST00000586545.1 |
| exon_skip_296612 | 18 | 39550290:39550420:39564843:39565071:39567775:39567839 | 39564843:39565071 | ENSG00000078142.7 | ENST00000591011.1 |
| exon_skip_296617 | 18 | 39600601:39600669:39607406:39607512:39609288:39609395 | 39607406:39607512 | ENSG00000078142.7 | ENST00000262039.4,ENST00000398870.3 |
| exon_skip_296620 | 18 | 39609288:39609405:39613789:39613921:39617655:39617781 | 39613789:39613921 | ENSG00000078142.7 | ENST00000262039.4,ENST00000398870.3,ENST00000593098.1,ENST00000590013.1 |
| exon_skip_296622 | 18 | 39618744:39618814:39620640:39620705:39623696:39623781 | 39620640:39620705 | ENSG00000078142.7 | ENST00000262039.4,ENST00000398870.3,ENST00000593098.1,ENST00000597477.1,ENST00000589056.1,ENST00000587402.1 |
| exon_skip_296624 | 18 | 39623696:39623781:39629494:39629569:39637846:39638015 | 39629494:39629569 | ENSG00000078142.7 | ENST00000262039.4,ENST00000398870.3,ENST00000593098.1 |
| exon_skip_296625 | 18 | 39629494:39629569:39637846:39638015:39644703:39644794 | 39637846:39638015 | ENSG00000078142.7 | ENST00000262039.4,ENST00000398870.3,ENST00000593098.1 |
| exon_skip_296629 | 18 | 39629494:39629569:39644703:39644794:39647351:39647374 | 39644703:39644794 | ENSG00000078142.7 | ENST00000588631.1 |
| exon_skip_296632 | 18 | 39637846:39638015:39639758:39639858:39644703:39644794 | 39639758:39639858 | ENSG00000078142.7 | ENST00000587261.1 |
| exon_skip_296633 | 18 | 39637846:39638015:39644703:39644794:39647351:39647374 | 39644703:39644794 | ENSG00000078142.7 | ENST00000262039.4,ENST00000398870.3,ENST00000593098.1,ENST00000588156.1 |
| exon_skip_296637 | 18 | 39644703:39644794:39647351:39647477:39661086:39661148 | 39647351:39647477 | ENSG00000078142.7 | ENST00000262039.4,ENST00000398870.3,ENST00000593098.1,ENST00000588631.1,ENST00000588156.1,ENST00000587328.1 |
| 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 PIK3C3 |
| 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 |
| ENST00000262039 | 39607406 | 39607512 | Frame-shift |
| ENST00000262039 | 39620640 | 39620705 | Frame-shift |
| ENST00000262039 | 39637846 | 39638015 | Frame-shift |
| ENST00000262039 | 39644703 | 39644794 | Frame-shift |
| ENST00000262039 | 39613789 | 39613921 | In-frame |
| ENST00000262039 | 39629494 | 39629569 | In-frame |
| ENST00000262039 | 39647351 | 39647477 | 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 |
| ENST00000262039 | 39607406 | 39607512 | Frame-shift |
| ENST00000262039 | 39620640 | 39620705 | Frame-shift |
| ENST00000262039 | 39637846 | 39638015 | Frame-shift |
| ENST00000262039 | 39644703 | 39644794 | Frame-shift |
| ENST00000262039 | 39613789 | 39613921 | In-frame |
| ENST00000262039 | 39629494 | 39629569 | In-frame |
| ENST00000262039 | 39647351 | 39647477 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PIK3C3 |
| 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 |
| ENST00000262039 | 9460 | 887 | 39613789 | 39613921 | 1794 | 1925 | 569 | 613 |
| ENST00000262039 | 9460 | 887 | 39629494 | 39629569 | 2275 | 2349 | 729 | 754 |
| ENST00000262039 | 9460 | 887 | 39647351 | 39647477 | 2610 | 2735 | 841 | 883 |
| 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 |
| ENST00000262039 | 9460 | 887 | 39613789 | 39613921 | 1794 | 1925 | 569 | 613 |
| ENST00000262039 | 9460 | 887 | 39629494 | 39629569 | 2275 | 2349 | 729 | 754 |
| ENST00000262039 | 9460 | 887 | 39647351 | 39647477 | 2610 | 2735 | 841 | 883 |
| 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 |
| Q8NEB9 | 569 | 613 | 591 | 593 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 569 | 613 | 596 | 604 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 569 | 613 | 613 | 616 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PH4 |
| Q8NEB9 | 569 | 613 | 1 | 887 | Chain | ID=PRO_0000088802;Note=Phosphatidylinositol 3-kinase catalytic subunit type 3 |
| Q8NEB9 | 569 | 613 | 566 | 578 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 569 | 613 | 580 | 583 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 569 | 613 | 606 | 608 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 729 | 754 | 748 | 751 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 729 | 754 | 1 | 887 | Chain | ID=PRO_0000088802;Note=Phosphatidylinositol 3-kinase catalytic subunit type 3 |
| Q8NEB9 | 729 | 754 | 631 | 885 | Domain | Note=PI3K/PI4K;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00269 |
| Q8NEB9 | 729 | 754 | 719 | 738 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 729 | 754 | 750 | 750 | Sequence conflict | Note=L->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q8NEB9 | 841 | 883 | 1 | 887 | Chain | ID=PRO_0000088802;Note=Phosphatidylinositol 3-kinase catalytic subunit type 3 |
| Q8NEB9 | 841 | 883 | 631 | 885 | Domain | Note=PI3K/PI4K;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00269 |
| Q8NEB9 | 841 | 883 | 838 | 845 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 841 | 883 | 852 | 872 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 841 | 883 | 846 | 849 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| 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 |
| Q8NEB9 | 569 | 613 | 591 | 593 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 569 | 613 | 596 | 604 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 569 | 613 | 613 | 616 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PH4 |
| Q8NEB9 | 569 | 613 | 1 | 887 | Chain | ID=PRO_0000088802;Note=Phosphatidylinositol 3-kinase catalytic subunit type 3 |
| Q8NEB9 | 569 | 613 | 566 | 578 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 569 | 613 | 580 | 583 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 569 | 613 | 606 | 608 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 729 | 754 | 748 | 751 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 729 | 754 | 1 | 887 | Chain | ID=PRO_0000088802;Note=Phosphatidylinositol 3-kinase catalytic subunit type 3 |
| Q8NEB9 | 729 | 754 | 631 | 885 | Domain | Note=PI3K/PI4K;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00269 |
| Q8NEB9 | 729 | 754 | 719 | 738 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 729 | 754 | 750 | 750 | Sequence conflict | Note=L->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q8NEB9 | 841 | 883 | 1 | 887 | Chain | ID=PRO_0000088802;Note=Phosphatidylinositol 3-kinase catalytic subunit type 3 |
| Q8NEB9 | 841 | 883 | 631 | 885 | Domain | Note=PI3K/PI4K;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00269 |
| Q8NEB9 | 841 | 883 | 838 | 845 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 841 | 883 | 852 | 872 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
| Q8NEB9 | 841 | 883 | 846 | 849 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UWH |
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SNVs in the skipped exons for PIK3C3 |
| - 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-DD-A3A0-01 | exon_skip_296610 | 39537535 | 39537723 | 39537654 | 39537654 | Frame_Shift_Del | T | - | p.V63fs |
| LIHC | TCGA-BC-A3KG-01 | exon_skip_296620 | 39613790 | 39613921 | 39613864 | 39613864 | Frame_Shift_Del | T | - | p.P594fs |
| STAD | TCGA-CD-A4MJ-01 | exon_skip_296624 | 39629495 | 39629569 | 39629562 | 39629562 | Frame_Shift_Del | A | - | p.T752fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_296625 | 39637847 | 39638015 | 39637944 | 39637944 | Frame_Shift_Del | G | - | p.M787fs |
| STAD | TCGA-HU-A4G8-01 | exon_skip_296629 exon_skip_296633 | 39644704 | 39644794 | 39644789 | 39644789 | Frame_Shift_Del | A | - | p.K840fs |
| STAD | TCGA-HU-A4G8-01 | exon_skip_296629 exon_skip_296633 | 39644704 | 39644794 | 39644789 | 39644789 | Frame_Shift_Del | A | - | p.V839fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_296637 | 39647352 | 39647477 | 39647437 | 39647437 | Frame_Shift_Del | T | - | p.L870fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_296624 | 39629495 | 39629569 | 39629551 | 39629552 | Frame_Shift_Ins | - | T | p.F749fs |
| ACC | TCGA-OR-A5J7-01 | exon_skip_296625 | 39637847 | 39638015 | 39637866 | 39637867 | Frame_Shift_Ins | - | T | p.D761fs |
| ACC | TCGA-OR-A5J7-01 | exon_skip_296625 | 39637847 | 39638015 | 39637866 | 39637867 | Frame_Shift_Ins | - | T | p.W762fs |
| CHOL | TCGA-ZH-A8Y6-01 | exon_skip_296624 | 39629495 | 39629569 | 39629497 | 39629497 | Nonsense_Mutation | G | T | p.G731X |
| - 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 |
| OSC19_UPPER_AERODIGESTIVE_TRACT | 39613790 | 39613921 | 39613864 | 39613865 | Frame_Shift_Del | TT | - | p.L595fs |
| CORL51_LUNG | 39644704 | 39644794 | 39644711 | 39644711 | Frame_Shift_Del | A | - | p.N814fs |
| HCC515_LUNG | 39537535 | 39537723 | 39537657 | 39537657 | Missense_Mutation | T | C | p.F64S |
| HCC366_LUNG | 39537535 | 39537723 | 39537657 | 39537657 | Missense_Mutation | T | C | p.F64S |
| SNU520_STOMACH | 39607407 | 39607512 | 39607492 | 39607492 | Missense_Mutation | T | C | p.F524L |
| LNCAPCLONEFGC_PROSTATE | 39607407 | 39607512 | 39607493 | 39607493 | Missense_Mutation | T | G | p.F524C |
| NCIH2286_LUNG | 39607407 | 39607512 | 39607500 | 39607500 | Missense_Mutation | A | T | p.Q526H |
| TUHR4TKB_KIDNEY | 39613790 | 39613921 | 39613911 | 39613911 | Missense_Mutation | C | T | p.T610I |
| SKUT1_SOFT_TISSUE | 39620641 | 39620705 | 39620664 | 39620664 | Missense_Mutation | G | T | p.V688F |
| TE4_OESOPHAGUS | 39629495 | 39629569 | 39629544 | 39629545 | Missense_Mutation | GG | TT | p.D747Y |
| SQ1_LUNG | 39629495 | 39629569 | 39629545 | 39629545 | Missense_Mutation | G | T | p.D747Y |
| TE4_OESOPHAGUS | 39629495 | 39629569 | 39629545 | 39629545 | Missense_Mutation | G | T | p.D747Y |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 39637847 | 39638015 | 39637863 | 39637863 | Missense_Mutation | A | G | p.I760M |
| NCIH510_LUNG | 39637847 | 39638015 | 39637929 | 39637929 | Missense_Mutation | A | T | p.E782D |
| MM386_SKIN | 39644704 | 39644794 | 39644733 | 39644733 | Missense_Mutation | C | T | p.S821F |
| BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 39647352 | 39647477 | 39647362 | 39647362 | Missense_Mutation | A | C | p.K845T |
| DU145_PROSTATE | 39647352 | 39647477 | 39647368 | 39647368 | Missense_Mutation | G | A | p.R847H |
| CAL54_KIDNEY | 39647352 | 39647477 | 39647413 | 39647413 | Missense_Mutation | T | A | p.L862Q |
| NCIH1573_LUNG | 39607407 | 39607512 | 39607512 | 39607512 | Splice_Site | G | T | p.K530N |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PIK3C3 |
| 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 |
| exon_skip_296612 | 18 | 39550290:39550420:39564843:39565071:39567775:39567839 | 39564843:39565071 | ENST00000591011.1 | LGG | rs9956832 | chr18:39564876 | A/C | 4.15e-04 |
| exon_skip_296612 | 18 | 39550290:39550420:39564843:39565071:39567775:39567839 | 39564843:39565071 | ENST00000591011.1 | LGG | rs9956832 | chr18:39564876 | A/C | 5.02e-04 |
| exon_skip_296612 | 18 | 39550290:39550420:39564843:39565071:39567775:39567839 | 39564843:39565071 | ENST00000591011.1 | KIRC | rs9956832 | chr18:39564876 | A/C | 1.55e-04 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PIK3C3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PIK3C3 |
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RelatedDrugs for PIK3C3 |
| 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 PIK3C3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PIK3C3 | C0036341 | Schizophrenia | 3 | PSYGENET |
| PIK3C3 | C0005586 | Bipolar Disorder | 1 | PSYGENET |
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