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Fusion gene ID: 15188 |
FusionGeneSummary for GPC6_SMG1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: GPC6_SMG1 | Fusion gene ID: 15188 | Hgene | Tgene | Gene symbol | GPC6 | SMG1 | Gene ID | 10082 | 23049 |
| Gene name | glypican 6 | SMG1, nonsense mediated mRNA decay associated PI3K related kinase | |
| Synonyms | OMIMD1 | 61E3.4|ATX|LIP | |
| Cytomap | 13q31.3-q32.1 | 16p12.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | glypican-6glypican proteoglycan 6 | serine/threonine-protein kinase SMG1PI-3-kinase-related kinase SMG-1SMG1 phosphatidylinositol 3-kinase-related kinaselambda-interacting proteinlambda/iota protein kinase C-interacting proteinsmg-1 homolog, phosphatidylinositol 3-kinase-related kinase | |
| Modification date | 20180522 | 20180523 | |
| UniProtAcc | Q9Y625 | Q96Q15 | |
| Ensembl transtripts involved in fusion gene | ENST00000377047, | ENST00000389467, ENST00000446231, ENST00000565224, ENST00000567737, | |
| Fusion gene scores | * DoF score | 5 X 7 X 8=280 | 7 X 8 X 4=224 |
| # samples | 12 | 8 | |
| ** MAII score | log2(12/280*10)=-1.22239242133645 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(8/224*10)=-1.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: GPC6 [Title/Abstract] AND SMG1 [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 | GPC6 | GO:0016477 | cell migration | 21871017 |
| Tgene | SMG1 | GO:0000184 | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 11544179 |
| Tgene | SMG1 | GO:0018105 | peptidyl-serine phosphorylation | 11544179|15175154 |
| Tgene | SMG1 | GO:0046777 | protein autophosphorylation | 11331269|11544179 |
| Tgene | SMG1 | GO:0046854 | phosphatidylinositol phosphorylation | 11331269 |
| Tgene | SMG1 | GO:2001020 | regulation of response to DNA damage stimulus | 15175154 |
| 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-46-3769-01A | GPC6 | chr13 | 95055810 | + | SMG1 | chr16 | 18816264 | - |
| * 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 |
| 3UTR-3UTR | ENST00000377047 | ENST00000389467 | GPC6 | chr13 | 95055810 | + | SMG1 | chr16 | 18816264 | - |
| 3UTR-3UTR | ENST00000377047 | ENST00000446231 | GPC6 | chr13 | 95055810 | + | SMG1 | chr16 | 18816264 | - |
| 3UTR-intron | ENST00000377047 | ENST00000565224 | GPC6 | chr13 | 95055810 | + | SMG1 | chr16 | 18816264 | - |
| 3UTR-intron | ENST00000377047 | ENST00000567737 | GPC6 | chr13 | 95055810 | + | SMG1 | chr16 | 18816264 | - |
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FusionProtFeatures for GPC6_SMG1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| GPC6 | SMG1 |
| Cell surface proteoglycan that bears heparan sulfate.Putative cell surface coreceptor for growth factors, extracellularmatrix proteins, proteases and anti-proteases (By similarity).Enhances migration and invasion of cancer cells through WNT5Asignaling. {ECO:0000250, ECO:0000269|PubMed:21871017}. | Serine/threonine protein kinase involved in both mRNAsurveillance and genotoxic stress response pathways. Recognizesthe substrate consensus sequence [ST]-Q. Plays a central role innonsense-mediated decay (NMD) of mRNAs containing premature stopcodons by phosphorylating UPF1/RENT1. Recruited by release factorsto stalled ribosomes together with SMG8 and SMG9 (forming theSMG1C protein kinase complex), and UPF1 to form the transient SURF(SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURFcomplex associates with the exon junction complex (EJC) throughUPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillancecomplex which is believed to activate NMD. Also acts as agenotoxic stress-activated protein kinase that displays somefunctional overlap with ATM. Can phosphorylate p53/TP53 and isrequired for optimal p53/TP53 activation after cellular exposureto genotoxic stress. Its depletion leads to spontaneous DNA damageand increased sensitivity to ionizing radiation (IR). May activatePRKCI but not PRKCZ. {ECO:0000269|PubMed:11331269,ECO:0000269|PubMed:11544179, ECO:0000269|PubMed:15175154,ECO:0000269|PubMed:16452507}. |
| 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 GPC6_SMG1 |
| 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 GPC6_SMG1 |
| 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 |
| GPC6 | FGF1, TMEM30A, GPR183, OGFOD3, ZACN, CHST8, PLTP, SCARA3, GPC4, CAMKV, DLX4, MRPS7 | SMG1 | PRKCI, SMG1, UPF1, UPF2, UPF3A, TTI1, TELO2, ELAVL1, SMG8, SMG9, RBM8A, UPF3B, NCBP2, PABPC1, SMG7, EIF4A3, MAGOH, GSPT2, GSPT1, EEF2, HSP90AA1, HSPA4, RUVBL1, RUVBL2, POLR2E, TUBA1A, TUBG1, HAUS2, HTR6, HSP90B1, EGFR, EPHA1 |
| - 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 GPC6_SMG1 |
| 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 GPC6_SMG1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | GPC6 | C0206762 | Limb Deformities, Congenital | 1 | CTD_human |
| Hgene | GPC6 | C0376634 | Craniofacial Abnormalities | 1 | CTD_human |
| Hgene | GPC6 | C1850318 | Omodysplasia type 1 | 1 | CTD_human;ORPHANET |
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