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Fusion gene ID: 12938 |
FusionGeneSummary for FARP1_GPC6 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: FARP1_GPC6 | Fusion gene ID: 12938 | Hgene | Tgene | Gene symbol | FARP1 | GPC6 | Gene ID | 10160 | 10082 |
| Gene name | FERM, ARH/RhoGEF and pleckstrin domain protein 1 | glypican 6 | |
| Synonyms | CDEP|FARP1-IT1|PLEKHC2|PPP1R75 | OMIMD1 | |
| Cytomap | 13q32.2 | 13q31.3-q32.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | FERM, ARHGEF and pleckstrin domain-containing protein 1FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)FERM, RhoGEF and pleckstrin domain-containing protein 1PH domain-containing family C member 2chondrocyte-derived ezrin-li | glypican-6glypican proteoglycan 6 | |
| Modification date | 20180519 | 20180522 | |
| UniProtAcc | Q9Y4F1 | Q9Y625 | |
| Ensembl transtripts involved in fusion gene | ENST00000595437, ENST00000376586, ENST00000319562, ENST00000376581, ENST00000593990, | ENST00000377047, | |
| Fusion gene scores | * DoF score | 14 X 11 X 7=1078 | 5 X 6 X 4=120 |
| # samples | 13 | 6 | |
| ** MAII score | log2(13/1078*10)=-3.05177364972405 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(6/120*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: FARP1 [Title/Abstract] AND GPC6 [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 | FARP1 | GO:0010923 | negative regulation of phosphatase activity | 19389623 |
| Tgene | GPC6 | GO:0016477 | cell migration | 21871017 |
| 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 | LUSC | TCGA-60-2709-01A | FARP1 | chr13 | 99038068 | + | GPC6 | chr13 | 94482407 | + |
| * 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 |
| Frame-shift | ENST00000595437 | ENST00000377047 | FARP1 | chr13 | 99038068 | + | GPC6 | chr13 | 94482407 | + |
| Frame-shift | ENST00000376586 | ENST00000377047 | FARP1 | chr13 | 99038068 | + | GPC6 | chr13 | 94482407 | + |
| Frame-shift | ENST00000319562 | ENST00000377047 | FARP1 | chr13 | 99038068 | + | GPC6 | chr13 | 94482407 | + |
| intron-3CDS | ENST00000376581 | ENST00000377047 | FARP1 | chr13 | 99038068 | + | GPC6 | chr13 | 94482407 | + |
| intron-3CDS | ENST00000593990 | ENST00000377047 | FARP1 | chr13 | 99038068 | + | GPC6 | chr13 | 94482407 | + |
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FusionProtFeatures for FARP1_GPC6 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| FARP1 | GPC6 |
| Functions as guanine nucleotide exchange factor forRAC1. May play a role in semaphorin signaling. Plays a role in theassembly and disassembly of dendritic filopodia, the formation ofdendritic spines, regulation of dendrite length and ultimately theformation of synapses (By similarity). {ECO:0000250}. | 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}. |
| 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 FARP1_GPC6 |
| 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 FARP1_GPC6 |
| 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 |
| FARP1 | ELAVL1, NTRK1, CAPZA2, MYO1C, PDGFRA, AKAP1, SYNPO, GAR1, GEMIN7, BRD2, PTPRG, SNRPN, SDC1, SDC2, DCAF8, TRIM25 | GPC6 | FGF1, TMEM30A, GPR183, OGFOD3, ZACN, CHST8, PLTP, SCARA3, GPC4, CAMKV, DLX4, MRPS7 |
| - 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 FARP1_GPC6 |
| 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 FARP1_GPC6 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | FARP1 | C0236969 | Substance-Related Disorders | 1 | CTD_human |
| Tgene | GPC6 | C0206762 | Limb Deformities, Congenital | 1 | CTD_human |
| Tgene | GPC6 | C0376634 | Craniofacial Abnormalities | 1 | CTD_human |
| Tgene | GPC6 | C1850318 | Omodysplasia type 1 | 1 | CTD_human;ORPHANET |
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