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Fusion gene ID: 41609 |
FusionGeneSummary for VPS41_KLF12 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: VPS41_KLF12 | Fusion gene ID: 41609 | Hgene | Tgene | Gene symbol | VPS41 | KLF12 | Gene ID | 27072 | 11278 |
| Gene name | VPS41, HOPS complex subunit | Kruppel like factor 12 | |
| Synonyms | HVPS41|HVSP41|hVps41p | AP-2rep|AP2REP|HSPC122 | |
| Cytomap | 7p14.1 | 13q22.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | vacuolar protein sorting-associated protein 41 homologS53vacuolar assembly protein 41vacuolar protein sorting 41 homolog | Krueppel-like factor 12AP-2 repressorAP-2rep transcription factorKLF12 zinc finger transcriptional repressortranscriptional repressor AP-2rep | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | P49754 | Q9Y4X4 | |
| Ensembl transtripts involved in fusion gene | ENST00000310301, ENST00000395969, ENST00000466017, | ENST00000377669, ENST00000377666, ENST00000472022, | |
| Fusion gene scores | * DoF score | 9 X 7 X 8=504 | 9 X 10 X 4=360 |
| # samples | 9 | 11 | |
| ** MAII score | log2(9/504*10)=-2.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(11/360*10)=-1.71049338280502 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: VPS41 [Title/Abstract] AND KLF12 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Tgene | KLF12 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 16615998 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChiTaRS3.1 | BF821492 | VPS41 | chr7 | 38764628 | - | KLF12 | chr13 | 74663171 | - |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| intron-intron | ENST00000310301 | ENST00000377669 | VPS41 | chr7 | 38764628 | - | KLF12 | chr13 | 74663171 | - |
| intron-intron | ENST00000310301 | ENST00000377666 | VPS41 | chr7 | 38764628 | - | KLF12 | chr13 | 74663171 | - |
| intron-intron | ENST00000310301 | ENST00000472022 | VPS41 | chr7 | 38764628 | - | KLF12 | chr13 | 74663171 | - |
| intron-intron | ENST00000395969 | ENST00000377669 | VPS41 | chr7 | 38764628 | - | KLF12 | chr13 | 74663171 | - |
| intron-intron | ENST00000395969 | ENST00000377666 | VPS41 | chr7 | 38764628 | - | KLF12 | chr13 | 74663171 | - |
| intron-intron | ENST00000395969 | ENST00000472022 | VPS41 | chr7 | 38764628 | - | KLF12 | chr13 | 74663171 | - |
| intron-intron | ENST00000466017 | ENST00000377669 | VPS41 | chr7 | 38764628 | - | KLF12 | chr13 | 74663171 | - |
| intron-intron | ENST00000466017 | ENST00000377666 | VPS41 | chr7 | 38764628 | - | KLF12 | chr13 | 74663171 | - |
| intron-intron | ENST00000466017 | ENST00000472022 | VPS41 | chr7 | 38764628 | - | KLF12 | chr13 | 74663171 | - |
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FusionProtFeatures for VPS41_KLF12 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| VPS41 | KLF12 |
| Plays a role in vesicle-mediated protein trafficking tolysosomal compartments including the endocytic membrane transportand autophagic pathways. Believed to act in part as a corecomponent of the putative HOPS endosomal tethering complex isproposed to be involved in the Rab5-to-Rab7 endosome conversionprobably implicating MON1A/B, and via binding SNAREs and SNAREcomplexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The HOPS complex is proposed to berecruited to Rab7 on the late endosomal membrane and to regulatelate endocytic, phagocytic and autophagic traffic towardslysosomes (PubMed:23351085). Involved in homotypic vesicle fusionsbetween late endosomes and in heterotypic fusions between lateendosomes and lysosomes implicated in degradation of endocytosedcargo (PubMed:9159129, PubMed:23167963, PubMed:25445562,PubMed:25908847). Required for fusion of autophagosomes withlysosomes (PubMed:25783203). May link the HOPS complex toendosomal Rab7 via its association with RILP and to lysosomalmembranes via its association with ARL8B, suggesting that theseinteractions may bring the compartments to close proximity forfusion (PubMed:25445562, PubMed:25908847). Involved in the directtrans-Golgi network to late endosomes transport of lysosomalmembrane proteins independently of HOPS (PubMed:23322049).Involved in sorting to the regulated secretory pathway presumablyimplicating the AP-3 adaptor complex (By similarity). May play arole in HOPS-independent function in the regulated secretorypathway (PubMed:24210660). {ECO:0000250|UniProtKB:D3ZVH6,ECO:0000269|PubMed:23167963, ECO:0000269|PubMed:23322049,ECO:0000269|PubMed:25445562, ECO:0000269|PubMed:25783203,ECO:0000269|PubMed:25908847, ECO:0000269|PubMed:9159129,ECO:0000305|PubMed:23167963, ECO:0000305|PubMed:23351085,ECO:0000305|PubMed:24210660, ECO:0000305|PubMed:25445562}. | Confers strong transcriptional repression to the AP-2-alpha gene. Binds to a regulatory element (A32) in the AP-2-alphagene promoter. |
| Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at . * Minus value of BPloci means that the break pointn is located before the CDS. |
| - In-frame and retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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FusionGeneSequence for VPS41_KLF12 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for VPS41_KLF12 |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for VPS41_KLF12 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for VPS41_KLF12 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | KLF12 | C0036341 | Schizophrenia | 1 | CTD_human |
| Tgene | KLF12 | C0236969 | Substance-Related Disorders | 1 | CTD_human |
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