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Fusion gene ID: 19424 |
FusionGeneSummary for LAMTOR4_AP4M1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LAMTOR4_AP4M1 | Fusion gene ID: 19424 | Hgene | Tgene | Gene symbol | LAMTOR4 | AP4M1 | Gene ID | 389541 | 9179 |
| Gene name | late endosomal/lysosomal adaptor, MAPK and MTOR activator 4 | adaptor related protein complex 4 subunit mu 1 | |
| Synonyms | C7orf59 | CPSQ3|MU-4|MU-ARP2|SPG50 | |
| Cytomap | 7q22.1 | 7q22.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | ragulator complex protein LAMTOR4UPF0539 protein C7orf59late endosomal/lysosomal adaptor and MAPK and MTOR activator 4 | AP-4 complex subunit mu-1AP-4 adaptor complex mu subunitadapter-related protein complex 4 mu-1 subunitadapter-related protein complex 4 subunit mu-1adaptor related protein complex 4 mu 1 subunitadaptor-related protein complex AP-4 mu4 subunitmu subu | |
| Modification date | 20180523 | 20180529 | |
| UniProtAcc | Q0VGL1 | O00189 | |
| Ensembl transtripts involved in fusion gene | ENST00000341942, ENST00000441173, ENST00000468582, | ENST00000429084, ENST00000359593, ENST00000478501, ENST00000421755, ENST00000422582, | |
| Fusion gene scores | * DoF score | 5 X 6 X 2=60 | 6 X 6 X 3=108 |
| # samples | 6 | 6 | |
| ** MAII score | log2(6/60*10)=0 | log2(6/108*10)=-0.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: LAMTOR4 [Title/Abstract] AND AP4M1 [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 | AP4M1 | GO:0006605 | protein targeting | 20230749 |
| Tgene | AP4M1 | GO:0006622 | protein targeting to lysosome | 11139587 |
| Tgene | AP4M1 | GO:0090160 | Golgi to lysosome transport | 11139587 |
| 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 |
| TCGA | LD | LUSC | TCGA-18-3415-01A | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| TCGA | LD | LUSC | TCGA-85-A53L-01A | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| * 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 |
| 5CDS-5UTR | ENST00000341942 | ENST00000429084 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 5CDS-5UTR | ENST00000341942 | ENST00000359593 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 5CDS-3UTR | ENST00000341942 | ENST00000478501 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 5CDS-5UTR | ENST00000341942 | ENST00000421755 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 5CDS-intron | ENST00000341942 | ENST00000422582 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 5CDS-5UTR | ENST00000441173 | ENST00000429084 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 5CDS-5UTR | ENST00000441173 | ENST00000359593 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 5CDS-3UTR | ENST00000441173 | ENST00000478501 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 5CDS-5UTR | ENST00000441173 | ENST00000421755 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 5CDS-intron | ENST00000441173 | ENST00000422582 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 3UTR-5UTR | ENST00000468582 | ENST00000429084 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 3UTR-5UTR | ENST00000468582 | ENST00000359593 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 3UTR-3UTR | ENST00000468582 | ENST00000478501 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 3UTR-5UTR | ENST00000468582 | ENST00000421755 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 3UTR-intron | ENST00000468582 | ENST00000422582 | LAMTOR4 | chr7 | 99747202 | + | AP4M1 | chr7 | 99699331 | + |
| 5CDS-intron | ENST00000341942 | ENST00000429084 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 5CDS-intron | ENST00000341942 | ENST00000359593 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 5CDS-intron | ENST00000341942 | ENST00000478501 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 5CDS-3UTR | ENST00000341942 | ENST00000421755 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 5CDS-intron | ENST00000341942 | ENST00000422582 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 5CDS-intron | ENST00000441173 | ENST00000429084 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 5CDS-intron | ENST00000441173 | ENST00000359593 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 5CDS-intron | ENST00000441173 | ENST00000478501 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 5CDS-3UTR | ENST00000441173 | ENST00000421755 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 5CDS-intron | ENST00000441173 | ENST00000422582 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 3UTR-intron | ENST00000468582 | ENST00000429084 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 3UTR-intron | ENST00000468582 | ENST00000359593 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 3UTR-intron | ENST00000468582 | ENST00000478501 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 3UTR-3UTR | ENST00000468582 | ENST00000421755 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
| 3UTR-intron | ENST00000468582 | ENST00000422582 | LAMTOR4 | chr7 | 99747188 | + | AP4M1 | chr7 | 99707814 | + |
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FusionProtFeatures for LAMTOR4_AP4M1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LAMTOR4 | AP4M1 |
| As part of the Ragulator complex it is involved in aminoacid sensing and activation of mTORC1, a signaling complexpromoting cell growth in response to growth factors, energylevels, and amino acids. Activated by amino acids through amechanism involving the lysosomal V-ATPase, the Ragulatorfunctions as a guanine nucleotide exchange factor activating thesmall GTPases Rag. Activated Ragulator and Rag GTPases function asa scaffold recruiting mTORC1 to lysosomes where it is in turnactivated. {ECO:0000269|PubMed:22980980}. | Component of the adaptor protein complex 4 (AP-4).Adaptor protein complexes are vesicle coat components involvedboth in vesicle formation and cargo selection. They control thevesicular transport of proteins in different trafficking pathways(PubMed:10436028, PubMed:11139587, PubMed:10066790,PubMed:11802162, PubMed:20230749). AP-4 forms a non clathrin-associated coat on vesicles departing the trans-Golgi network(TGN) and may be involved in the targeting of proteins from thetrans-Golgi network (TGN) to the endosomal-lysosomal system(PubMed:11139587, PubMed:20230749). It is also involved in proteinsorting to the basolateral membrane in epithelial cells and theproper asymmetric localization of somatodendritic proteins inneurons (By similarity). Within AP-4, the mu-type subunit AP4M1 isdirectly involved in the recognition and binding of tyrosine-basedsorting signals found in the cytoplasmic part of cargos(PubMed:10436028, PubMed:11139587, PubMed:26544806,PubMed:20230749). The adaptor protein complex 4 (AP-4) may alsorecognize other types of sorting signal (By similarity).{ECO:0000250|UniProtKB:E2RED8, ECO:0000250|UniProtKB:Q2PWT8,ECO:0000250|UniProtKB:Q9JKC7, ECO:0000269|PubMed:10066790,ECO:0000269|PubMed:10436028, ECO:0000269|PubMed:11139587,ECO:0000269|PubMed:11802162, ECO:0000269|PubMed:20230749,ECO:0000269|PubMed:26544806}. |
| 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 LAMTOR4_AP4M1 |
| 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 LAMTOR4_AP4M1 |
| 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 |
| LAMTOR4 | USP19, LAMTOR1, LAMTOR2, RRAGB, LAMTOR5, CDCA3, CCR1, C17orf59, SNCA, BIRC5, DUSP22, SLC38A9 | AP4M1 | ARF1, AP4E1, AP4B1, DDX52, ZBTB22, CHTF8, USP47, XPO1, ACY1, AKT2, GALNT2, H3F3A, HMGA1, IMPDH2, NPAT, RALA, CBX4, AP4S1, ENTHD2, LCMT2, SF3B2, ZNF318, MED31, TFB1M, MRPL48, MRPS23, WDR76, C19orf52, ARID2, ARPIN, CDK11A, SUV39H2 |
| - 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 LAMTOR4_AP4M1 |
| 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 LAMTOR4_AP4M1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | AP4M1 | C3714756 | Intellectual Disability | 1 | CTD_human |
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