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Fusion gene ID: 20445 |
FusionGeneSummary for LYN_VPS13B |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LYN_VPS13B | Fusion gene ID: 20445 | Hgene | Tgene | Gene symbol | LYN | VPS13B | Gene ID | 4067 | 157680 |
| Gene name | LYN proto-oncogene, Src family tyrosine kinase | vacuolar protein sorting 13 homolog B | |
| Synonyms | JTK8|p53Lyn|p56Lyn | CHS1|COH1 | |
| Cytomap | 8q12.1 | 8q22.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | tyrosine-protein kinase Lynlck/Yes-related novel protein tyrosine kinasev-yes-1 Yamaguchi sarcoma viral related oncogene homolog | vacuolar protein sorting-associated protein 13B | |
| Modification date | 20180523 | 20180519 | |
| UniProtAcc | P07948 | Q7Z7G8 | |
| Ensembl transtripts involved in fusion gene | ENST00000519728, ENST00000520220, ENST00000420292, | ENST00000395996, ENST00000358544, ENST00000357162, ENST00000355155, ENST00000441350, ENST00000521932, | |
| Fusion gene scores | * DoF score | 3 X 3 X 3=27 | 10 X 10 X 7=700 |
| # samples | 3 | 10 | |
| ** MAII score | log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(10/700*10)=-2.8073549220576 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: LYN [Title/Abstract] AND VPS13B [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 |
| Hgene | LYN | GO:0006468 | protein phosphorylation | 11517336 |
| Hgene | LYN | GO:0006974 | cellular response to DNA damage stimulus | 10891478|11517336 |
| Hgene | LYN | GO:0018108 | peptidyl-tyrosine phosphorylation | 7682714|11782428 |
| Hgene | LYN | GO:0046777 | protein autophosphorylation | 7682714 |
| Hgene | LYN | GO:0051272 | positive regulation of cellular component movement | 16467205 |
| Hgene | LYN | GO:0070304 | positive regulation of stress-activated protein kinase signaling cascade | 10891478 |
| 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 | RV | COAD | TCGA-A6-5666-01A | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| * 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 |
| 5UTR-3CDS | ENST00000519728 | ENST00000395996 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| 5UTR-3CDS | ENST00000519728 | ENST00000358544 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| 5UTR-3CDS | ENST00000519728 | ENST00000357162 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| 5UTR-intron | ENST00000519728 | ENST00000355155 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| 5UTR-intron | ENST00000519728 | ENST00000441350 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| 5UTR-intron | ENST00000519728 | ENST00000521932 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| 5UTR-3CDS | ENST00000520220 | ENST00000395996 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| 5UTR-3CDS | ENST00000520220 | ENST00000358544 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| 5UTR-3CDS | ENST00000520220 | ENST00000357162 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| 5UTR-intron | ENST00000520220 | ENST00000355155 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| 5UTR-intron | ENST00000520220 | ENST00000441350 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| 5UTR-intron | ENST00000520220 | ENST00000521932 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| intron-3CDS | ENST00000420292 | ENST00000395996 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| intron-3CDS | ENST00000420292 | ENST00000358544 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| intron-3CDS | ENST00000420292 | ENST00000357162 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| intron-intron | ENST00000420292 | ENST00000355155 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| intron-intron | ENST00000420292 | ENST00000441350 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
| intron-intron | ENST00000420292 | ENST00000521932 | LYN | chr8 | 56792662 | + | VPS13B | chr8 | 100513915 | + |
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FusionProtFeatures for LYN_VPS13B |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LYN | VPS13B |
| Non-receptor tyrosine-protein kinase that transmitssignals from cell surface receptors and plays an important role inthe regulation of innate and adaptive immune responses,hematopoiesis, responses to growth factors and cytokines, integrinsignaling, but also responses to DNA damage and genotoxic agents.Functions primarily as negative regulator, but can also functionas activator, depending on the context. Required for theinitiation of the B-cell response, but also for its down-regulation and termination. Plays an important role in theregulation of B-cell differentiation, proliferation, survival andapoptosis, and is important for immune self-tolerance. Actsdownstream of several immune receptors, including the B-cellreceptor, CD79A, CD79B, CD5, CD19, CD22, FCER1, FCGR2, FCGR1A,TLR2 and TLR4. Plays a role in the inflammatory response tobacterial lipopolysaccharide. Mediates the responses to cytokinesand growth factors in hematopoietic progenitors, platelets,erythrocytes, and in mature myeloid cells, such as dendriticcells, neutrophils and eosinophils. Acts downstream of EPOR, KIT,MPL, the chemokine receptor CXCR4, as well as the receptors forIL3, IL5 and CSF2. Plays an important role in integrin signaling.Regulates cell proliferation, survival, differentiation,migration, adhesion, degranulation, and cytokine release. Down-regulates signaling pathways by phosphorylation of immunoreceptortyrosine-based inhibitory motifs (ITIM), that then serve asbinding sites for phosphatases, such as PTPN6/SHP-1, PTPN11/SHP-2and INPP5D/SHIP-1, that modulate signaling by dephosphorylation ofkinases and their substrates. Phosphorylates LIME1 in response toCD22 activation. Phosphorylates BTK, CBL, CD5, CD19, CD72, CD79A,CD79B, CSF2RB, DOK1, HCLS1, LILRB3/PIR-B, MS4A2/FCER1B, SYK andTEC. Promotes phosphorylation of SIRPA, PTPN6/SHP-1, PTPN11/SHP-2and INPP5D/SHIP-1. Mediates phosphorylation of the BCR-ABL fusionprotein. Required for rapid phosphorylation of FER in response toFCER1 activation. Mediates KIT phosphorylation. Acts as aneffector of EPOR (erythropoietin receptor) in controlling KITexpression and may play a role in erythroid differentiation duringthe switch between proliferation and maturation. Depending on thecontext, activates or inhibits several signaling cascades.Regulates phosphatidylinositol 3-kinase activity and AKT1activation. Regulates activation of the MAP kinase signalingcascade, including activation of MAP2K1/MEK1, MAPK1/ERK2,MAPK3/ERK1, MAPK8/JNK1 and MAPK9/JNK2. Mediates activation ofSTAT5A and/or STAT5B. Phosphorylates LPXN on 'Tyr-72'. Kinaseactivity facilitates TLR4-TLR6 heterodimerization and signalinitiation. {ECO:0000269|PubMed:10574931,ECO:0000269|PubMed:10748115, ECO:0000269|PubMed:10891478,ECO:0000269|PubMed:11435302, ECO:0000269|PubMed:11517336,ECO:0000269|PubMed:11825908, ECO:0000269|PubMed:14726379,ECO:0000269|PubMed:15795233, ECO:0000269|PubMed:16467205,ECO:0000269|PubMed:17640867, ECO:0000269|PubMed:17977829,ECO:0000269|PubMed:18056483, ECO:0000269|PubMed:18070987,ECO:0000269|PubMed:18235045, ECO:0000269|PubMed:18577747,ECO:0000269|PubMed:18802065, ECO:0000269|PubMed:19290919,ECO:0000269|PubMed:20037584, ECO:0000269|PubMed:7687428}. |
| 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 LYN_VPS13B |
| 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 LYN_VPS13B |
| 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 |
| LYN | CSNK2B, CDK4, MUC1, INPP5D, PDE4A, PRAM1, CD22, PTPN6, CDK1, UNC119, GAB2, TEC, DOK1, SRC, PTK2B, SYK, CD36, MME, NEDD9, BCAR1, PLCG2, LCP2, MAPK3, GAB3, JAK2, EPOR, SKAP2, RPS6KB1, RPS6KB2, KIT, SKAP1, FCGR2A, CSF2RB, BTK, PRKDC, EVL, PPP1R15A, PECAM1, PAG1, TRAT1, BANK1, CBL, NMT1, TYK2, CD72, PTK2, RPL10, CD24, SHC1, HCLS1, PPP1R8, PIK3CG, PTPRC, CTLA4, CBLC, TRPV4, GP6, CSF3R, CSF1R, CDK2, FCAR, FASLG, CENPV, NDFIP2, UHRF2, ELAVL1, KHDRBS1, BLNK, SH3KBP1, FGFR2, TP53, CEP97, CCP110, CREBBP, LYN, TNK2, GP1BB, ADAM15, PDE4D, ACSL3, HSP90AA1, STAT3, SVIL, PAN2, SH2D1A, ANKRD54, HNRNPK, RNF180, KHDRBS2, LNP1, PIK3R3, PAK1, SH2D3C, HBS1L, RDX, SH2D4A, MAATS1, DTX3, HOXC4, CBX6, ZNF189, FRS2, PLAUR, PRKCB, HTR2A, SLITRK4, ANGPT2, YEATS4, LAMP2, TPTE2, TYW1, RIMS2, OSBPL11, CYP4V2, TGDS, DVL2, UGP2, ZNF423, TTYH3, NKAPL, ERO1L, FSD1L, HSP90B1, NFYB, OCLN, RBM11, TADA2A, DNA2, LRRIQ3, DENND2C, CNOT10, HDGFRP3, TNFSF12, PRUNE2, CPT1A, TMX1, TUBB4A, GTPBP3, MCL1, ZCCHC7, ZNF577, TFDP3, SCIMP, ADAM22, DUOXA1, E2F6, C21orf59, PLEKHH2, SLC12A4, FBXO28, ARHGAP19, DTL, DDX21, SPESP1, SCG3, SLC22A16, DKFZP434K028, KYNU, C2orf47, RASSF8, CDH23, CDKN1B, TNF, IL1B, RGS16, EGFR, TRIM28, IKBKG, CCDC8, ABCE1, SLC25A41, HOXB5, TMEM185A, CCNL2, NTRK1, TMEM17, MYH9, TSNAX, FGFR1OP, LIMA1, ANLN, KLC2, TRIM25 | VPS13B | CSNK1E, SPACA1, FAM177A1, DNAJC7, CSNK1D, SNX20, SNX21, LGALS7, DOCK5, LYPD4, FUZ |
| - 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 LYN_VPS13B |
| 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 |
| Hgene | LYN | P07948 | DB06616 | Bosutinib | Tyrosine-protein kinase Lyn | small molecule | approved |
| Hgene | LYN | P07948 | DB09079 | Nintedanib | Tyrosine-protein kinase Lyn | small molecule | approved |
| Hgene | LYN | P07948 | DB01254 | Dasatinib | Tyrosine-protein kinase Lyn | small molecule | approved|investigational |
| Hgene | LYN | P07948 | DB08901 | Ponatinib | Tyrosine-protein kinase Lyn | small molecule | approved|investigational |
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RelatedDiseases for LYN_VPS13B |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | LYN | C0019693 | HIV Infections | 1 | CTD_human |
| Tgene | VPS13B | C0265223 | Cohen syndrome | 6 | CTD_human;ORPHANET;UNIPROT |
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