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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 VPS52 |
 Gene summary |
| Gene information | Gene symbol | VPS52 | Gene ID | 6293 |
| Gene name | VPS52, GARP complex subunit | |
| Synonyms | ARE1|SAC2|SACM2L|dJ1033B10.5 | |
| Cytomap | 6p21.32 | |
| Type of gene | protein-coding | |
| Description | vacuolar protein sorting-associated protein 52 homologSAC2 suppressor of actin mutations 2-like proteinvacuolar protein sorting 52 homolog | |
| Modification date | 20180523 | |
| UniProtAcc | Q8N1B4 | |
| Context | PubMed: VPS52 [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 |
| VPS52 | GO:0007041 | lysosomal transport | 25799061 |
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Exon skipping events across known transcript of Ensembl for VPS52 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 VPS52 |
| 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 VPS52 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_458436 | 6 | 33218587:33218764:33219294:33219413:33219636:33219748 | 33219294:33219413 | ENSG00000223501.4 | ENST00000482399.1,ENST00000436044.2,ENST00000478934.1,ENST00000495981.1,ENST00000445902.2,ENST00000493674.1 |
| exon_skip_458442 | 6 | 33231855:33231880:33232150:33232274:33232558:33232677 | 33232150:33232274 | ENSG00000223501.4 | ENST00000482399.1,ENST00000436044.2,ENST00000478934.1,ENST00000445902.2 |
| exon_skip_458453 | 6 | 33236275:33236426:33236790:33236966:33237266:33237334 | 33236790:33236966 | ENSG00000223501.4 | ENST00000482399.1,ENST00000436044.2,ENST00000463486.1,ENST00000478934.1,ENST00000445902.2 |
| exon_skip_458454 | 6 | 33236275:33236426:33236790:33236995:33237266:33237334 | 33236790:33236995 | ENSG00000223501.4 | ENST00000464425.1 |
| exon_skip_458456 | 6 | 33237520:33237596:33237775:33237828:33237975:33238060 | 33237775:33237828 | ENSG00000223501.4 | ENST00000464425.1,ENST00000436044.2,ENST00000463486.1,ENST00000478934.1,ENST00000445902.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for VPS52 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_458436 | 6 | 33218587:33218764:33219294:33219413:33219636:33219748 | 33219294:33219413 | ENSG00000223501.4 | ENST00000482399.1,ENST00000445902.2,ENST00000478934.1,ENST00000436044.2,ENST00000495981.1,ENST00000493674.1 |
| exon_skip_458442 | 6 | 33231855:33231880:33232150:33232274:33232558:33232677 | 33232150:33232274 | ENSG00000223501.4 | ENST00000482399.1,ENST00000445902.2,ENST00000478934.1,ENST00000436044.2 |
| exon_skip_458453 | 6 | 33236275:33236426:33236790:33236966:33237266:33237334 | 33236790:33236966 | ENSG00000223501.4 | ENST00000482399.1,ENST00000445902.2,ENST00000478934.1,ENST00000436044.2,ENST00000463486.1 |
| exon_skip_458454 | 6 | 33236275:33236426:33236790:33236995:33237266:33237334 | 33236790:33236995 | ENSG00000223501.4 | ENST00000464425.1 |
| exon_skip_458456 | 6 | 33237520:33237596:33237775:33237828:33237975:33238060 | 33237775:33237828 | ENSG00000223501.4 | ENST00000445902.2,ENST00000478934.1,ENST00000436044.2,ENST00000463486.1,ENST00000464425.1 |
| 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 VPS52 |
| 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 |
| 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 |
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Infer the effects of exon skipping event on protein functional features for VPS52 |
| 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 |
| 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 |
| 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 |
| 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 |
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SNVs in the skipped exons for VPS52 |
| - 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 |
| COAD | TCGA-CM-5861-01 | exon_skip_458442 | 33232151 | 33232274 | 33232172 | 33232172 | Frame_Shift_Del | C | - | p.L502fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_458442 | 33232151 | 33232274 | 33232172 | 33232172 | Frame_Shift_Del | C | - | p.G501fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_458453 | 33236791 | 33236966 | 33236841 | 33236841 | Frame_Shift_Del | C | - | p.G166fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_458454 | 33236791 | 33236995 | 33236841 | 33236841 | Frame_Shift_Del | C | - | p.G166fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_458453 | 33236791 | 33236966 | 33236841 | 33236841 | Frame_Shift_Del | C | - | p.G166fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_458454 | 33236791 | 33236995 | 33236841 | 33236841 | Frame_Shift_Del | C | - | p.G166fs |
| UCEC | TCGA-AX-A0J1-01 | exon_skip_458442 | 33232151 | 33232274 | 33232201 | 33232201 | Nonsense_Mutation | G | A | p.R492* |
| CHOL | TCGA-W5-AA38-01 | exon_skip_458453 | 33236791 | 33236966 | 33236870 | 33236870 | Nonsense_Mutation | G | A | p.R157* |
| CHOL | TCGA-W5-AA38-01 | exon_skip_458453 | 33236791 | 33236966 | 33236870 | 33236870 | Nonsense_Mutation | G | A | p.R157X |
| CHOL | TCGA-W5-AA38-01 | exon_skip_458454 | 33236791 | 33236995 | 33236870 | 33236870 | Nonsense_Mutation | G | A | p.R157* |
| CHOL | TCGA-W5-AA38-01 | exon_skip_458454 | 33236791 | 33236995 | 33236870 | 33236870 | Nonsense_Mutation | G | A | p.R157X |
| PRAD | TCGA-J9-A52C-01 | exon_skip_458453 | 33236791 | 33236966 | 33236870 | 33236870 | Nonsense_Mutation | G | A | p.R157* |
| PRAD | TCGA-J9-A52C-01 | exon_skip_458453 | 33236791 | 33236966 | 33236870 | 33236870 | Nonsense_Mutation | G | A | p.R157X |
| PRAD | TCGA-J9-A52C-01 | exon_skip_458454 | 33236791 | 33236995 | 33236870 | 33236870 | Nonsense_Mutation | G | A | p.R157* |
| PRAD | TCGA-J9-A52C-01 | exon_skip_458454 | 33236791 | 33236995 | 33236870 | 33236870 | Nonsense_Mutation | G | A | p.R157X |
| HNSC | TCGA-CN-6019-01 | exon_skip_458453 | 33236791 | 33236966 | 33236966 | 33236966 | Nonsense_Mutation | G | A | p.R125* |
| HNSC | TCGA-CN-6019-01 | exon_skip_458454 | 33236791 | 33236995 | 33236966 | 33236966 | Nonsense_Mutation | G | A | p.R125* |
| - 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 |
| KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 33219295 | 33219413 | 33219322 | 33219322 | Missense_Mutation | G | T | p.N666K |
| HCC2450_LUNG | 33232151 | 33232274 | 33232210 | 33232210 | Missense_Mutation | G | C | p.Q489E |
| COLO679_SKIN | 33232151 | 33232274 | 33232226 | 33232226 | Missense_Mutation | G | C | p.I483M |
| ESS1_ENDOMETRIUM | 33236791 | 33236995 | 33236882 | 33236882 | Missense_Mutation | C | T | p.A153T |
| ESS1_ENDOMETRIUM | 33236791 | 33236966 | 33236882 | 33236882 | Missense_Mutation | C | T | p.A153T |
| HCC2998_LARGE_INTESTINE | 33236791 | 33236995 | 33236864 | 33236864 | Nonsense_Mutation | G | A | p.R159* |
| HCC2998_LARGE_INTESTINE | 33236791 | 33236966 | 33236864 | 33236864 | Nonsense_Mutation | G | A | p.R159* |
| SNUC4_LARGE_INTESTINE | 33237776 | 33237828 | 33237777 | 33237777 | Splice_Site | G | A | p.T76M |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for VPS52 |
| 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 VPS52 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for VPS52 |
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RelatedDrugs for VPS52 |
| 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 VPS52 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| VPS52 | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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