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Kinase Fusion Gene:PAK3_TFG |
Kinase Fusion Protein Summary |
 Kinase Fusion gene summary |
| Kinase Fusion partner gene information | Kinase Fusion gene name: PAK3_TFG | KinaseFusionDB ID: KFG4446 | FusionGDB2.0 ID: KFG4446 | Hgene | Tgene | Gene symbol | PAK3 | TFG | Gene ID | 8874 | 10342 | |
| Gene name | Rho guanine nucleotide exchange factor 7 | trafficking from ER to golgi regulator | ||||||||||
| Synonyms | BETA-PIX|COOL-1|COOL1|Nbla10314|P50|P50BP|P85|P85COOL1|P85SPR|PAK3|PIXB | HMSNP|SPG57|TF6|TRKT3 | ||||||||||
| Cytomap | 13q34 | 3q12.2 | ||||||||||
| Type of gene | protein-coding | protein-coding | ||||||||||
| Description | rho guanine nucleotide exchange factor 7PAK-interacting exchange factor betaRho guanine nucleotide exchange factor (GEF) 7SH3 domain-containing proline-rich protein | protein TFGTRK-fusedTRK-fused gene proteinTRKT3 oncogene | ||||||||||
| Modification date | 20240407 | 20240407 | ||||||||||
| UniProtAcc | O75914 | Q92734 | ||||||||||
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000425146, ENST00000446737, ENST00000372010, ENST00000519681, ENST00000372007, ENST00000518291, ENST00000484442, ENST00000262836, ENST00000360648, ENST00000417227, | ENST00000418917, ENST00000490574, ENST00000240851, ENST00000476228, ENST00000481203, | |||||||||
| Context (manual curation of fusion genes in KinaseFusionDB) | PubMed: PAK3 [Title/Abstract] AND TFG [Title/Abstract] AND fusion [Title/Abstract] | |||||||||||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | ||||||||||||
| 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 | PAK3 | GO:0043547 | positive regulation of GTPase activity | 21048939 |
| Kinase Fusion gene breakpoints across PAK3 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Kinase Fusion gene breakpoints across TFG (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Kinase Fusion Gene Sample Information |
| Kinase Fusion gene information. |
| Kinase Fusion gene information from four resources (ChiTars 5.0, ChimerDB 4.0, COSMIC, and CCLE) * 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. |
| Source | Sample | Hgene | Hchr | Hbp | Tgene | Tchr | Tbp |
| CCLE | UO-31 | PAK3 | chrX | 110406955 | TFG | chr3 | 100455420 |
| CCLE | UO-31 | PAK3 | chrX | 110406274 | TFG | chr3 | 100455420 |
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Kinase Fusion ORF Analysis |
| Kinase Fusion information from ORFfinder translation from full-length transcript sequence from KinaseFusionDB. |
| Henst | Tenst | Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Seq length (transcript) | Seq length (amino acids) |
| ENST00000425146 | ENST00000418917 | PAK3 | chrX | 110406955 | TFG | chr3 | 100455420 | 2159 | 460 |
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Kinase Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from KinaseFusionDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >Henst_Tenst_Hgene_Hchr_Hbp_Tgene_Tchr_Tbp_length(fusion AA)_AAseq >ENST00000425146_ENST00000418917_PAK3_chrX_110406955_TFG_chr3_100455420_length(amino acids)=460 MKMSDGLDNEEKPPAPPLRMNSNNRDSSALNHSSKPLPMAPEEKNKKARLRSIFPGGGDKTNKKKEKERPEISLPSDFEHTIHVGFDAVT GEFTGIPEQWARLLQTSNITKLEQKKNPQAVLDVLKFYDSKETVNNQKYMSFTSGDKSAHGYIAAHPSSTKTASEPPLAPPVSEEEDEEE EEEEDENEPPPVIAPRPEHTKSIYTRSVVESIASPAVPNKEVTPPSAENANSSTLYRNTDRQRKKSKMTDEEILEKLRPPSAPAEDRSGT PDSIASSSSAAHPPGVQPQQPPYTGAQTQAGQMYQQYQQQAGYGAQQPQAPPQQPQQYGIQYSASYSQQTGPQQPQQFQGYGQQPTSQAP APAFSGQPQQLPAQPPQQYQASNYPAQTYTAQTSQPTNYTVAPASQPGMAPSQPGAYQPRPGFTSLPGSTMTPPPSGPNPYARNRPPFGQ -------------------------------------------------------------- |
Multiple Sequence Alignment of All Fusion Protein Isoforms |
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Kinase Fusion Protein Functional Features |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chrX:/chr3:) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| PAK3 | TFG |
| FUNCTION: Serine/threonine protein kinase that plays a role in a variety of different signaling pathways including cytoskeleton regulation, cell migration, or cell cycle regulation. Plays a role in dendrite spine morphogenesis as well as synapse formation and plasticity. Acts as a downstream effector of the small GTPases CDC42 and RAC1. Activation by the binding of active CDC42 and RAC1 results in a conformational change and a subsequent autophosphorylation on several serine and/or threonine residues. Phosphorylates MAPK4 and MAPK6 and activates the downstream target MAPKAPK5, a regulator of F-actin polymerization and cell migration. Additionally, phosphorylates TNNI3/troponin I to modulate calcium sensitivity and relaxation kinetics of thin myofilaments. May also be involved in early neuronal development. In hippocampal neurons, necessary for the formation of dendritic spines and excitatory synapses; this function is dependent on kinase activity and may be exerted by the regulation of actomyosin contractility through the phosphorylation of myosin II regulatory light chain (MLC) (By similarity). {ECO:0000250|UniProtKB:Q61036, ECO:0000269|PubMed:21177870}. | FUNCTION: Plays a role in the normal dynamic function of the endoplasmic reticulum (ER) and its associated microtubules (PubMed:23479643, PubMed:27813252). Required for secretory cargo traffic from the endoplasmic reticulum to the Golgi apparatus (PubMed:21478858). {ECO:0000269|PubMed:21478858, ECO:0000269|PubMed:23479643, ECO:0000269|PubMed:27813252}. |
| 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. |
| - Retained domain in the 5'-partner of fusion protein (protein functional feature from UniProt). |
| Partner | Hgeneene | Hbp | Tgeneene | Tbp | ENST | BPexon | TotalExon | Protein feature loci | BPloci | TotalLen | Feature | Note |
| Hgene | PAK3 | 110406955 | TFG | 100455420 | ENST00000425146 | 10 | 18 | 70_83 | 2551 | 545 | Domain | Note=CRIB;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00057 |
| Hgene | PAK3 | 110406955 | TFG | 100455420 | ENST00000425146 | 11 | 19 | 70_83 | 2701 | 560 | Domain | Note=CRIB;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00057 |
| Hgene | PAK3 | 110406955 | TFG | 100455420 | ENST00000425146 | 11 | 19 | 70_83 | 2761 | 566 | Domain | Note=CRIB;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00057 |
| Hgene | PAK3 | 110406955 | TFG | 100455420 | ENST00000425146 | 11 | 19 | 70_83 | 2911 | 581 | Domain | Note=CRIB;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00057 |
| Hgene | PAK3 | 110406955 | TFG | 100455420 | ENST00000425146 | 7 | 15 | 70_83 | 2551 | 545 | Domain | Note=CRIB;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00057 |
| Hgene | PAK3 | 110406955 | TFG | 100455420 | ENST00000425146 | 7 | 15 | 70_83 | 2701 | 560 | Domain | Note=CRIB;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00057 |
| Hgene | PAK3 | 110406955 | TFG | 100455420 | ENST00000425146 | 7 | 15 | 70_83 | 2761 | 566 | Domain | Note=CRIB;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00057 |
| Hgene | PAK3 | 110406955 | TFG | 100455420 | ENST00000425146 | 8 | 16 | 70_83 | 2551 | 545 | Domain | Note=CRIB;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00057 |
| Hgene | PAK3 | 110406955 | TFG | 100455420 | ENST00000425146 | 8 | 16 | 70_83 | 2911 | 581 | Domain | Note=CRIB;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00057 |
| - Retained domain in the 3'-partner of fusion protein (protein functional feature from UniProt). |
| Partner | Hgeneene | Hbp | Tgeneene | Tbp | ENST | BPexon | TotalExon | Protein feature loci | BPloci | TotalLen | Feature | Note |
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Kinase Fusion Protein Structures |
| CIF files of the predicted kinase fusion proteins * Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| Kinase Fusion protein CIF link (fusion AA seq ID in KinaseFusionDB) | Henst | Tenst | Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | AA seq | Len(AA seq) |
| PDB file >>>192_PAK3_TFG | ENST00000425146 | ENST00000418917 | PAK3 | chrX | 110406955 | TFG | chr3 | 100455420 | MKMSDGLDNEEKPPAPPLRMNSNNRDSSALNHSSKPLPMAPEEKNKKARLRSIFPGGGDKTNKKKEKERPEISLPSDFEHTIHVGFDAVT GEFTGIPEQWARLLQTSNITKLEQKKNPQAVLDVLKFYDSKETVNNQKYMSFTSGDKSAHGYIAAHPSSTKTASEPPLAPPVSEEEDEEE EEEEDENEPPPVIAPRPEHTKSIYTRSVVESIASPAVPNKEVTPPSAENANSSTLYRNTDRQRKKSKMTDEEILEKLRPPSAPAEDRSGT PDSIASSSSAAHPPGVQPQQPPYTGAQTQAGQMYQQYQQQAGYGAQQPQAPPQQPQQYGIQYSASYSQQTGPQQPQQFQGYGQQPTSQAP APAFSGQPQQLPAQPPQQYQASNYPAQTYTAQTSQPTNYTVAPASQPGMAPSQPGAYQPRPGFTSLPGSTMTPPPSGPNPYARNRPPFGQ | 460 |
| 3D view using mol* of 192_PAK3_TFG | ||||||||||
| PDB file >>>HKFP_279_PAK3_TFG | ENST00000425146 | ENST00000418917 | PAK3 | chrX | 110406955 | TFG | chr3 | 100455420 | MKMSDGLDNEEKPPAPPLRMNSNNRDSSALNHSSKPLPMAPEEKNKKARLRSIFPGGGDKTNKKKEKERPEISLPSDFEHTIHVGFDAVT GEFTGIPEQWARLLQTSNITKLEQKKNPQAVLDVLKFYDSKETVNNQKYMSFTSGDKSAHGYIAAHPSSTKTASEPPLAPPVSEEEDEEE EEEEDENEPPPVIAPRPEHTKSIYTRSVVESIASPAVPNKEVTPPSAENANSSTLYRNTDRQRKKSKMTDEEILEKLRPPSAPAEDRSGT PDSIASSSSAAHPPGVQPQQPPYTGAQTQAGQMYQQYQQQAGYGAQQPQAPPQQPQQYGIQYSASYSQQTGPQQPQQFQGYGQQPTSQAP APAFSGQPQQLPAQPPQQYQASNYPAQTYTAQTSQPTNYTVAPASQPGMAPSQPGAYQPRPGFTSLPGSTMTPPPSGPNPYARNRPPFGQ | 460_PAK3_TFG |
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Comparison of Fusion Protein Isoforms |
| Superimpose the 3D Structures Among All Fusion Protein Isoforms * Download the pdb file and open it from the molstar online viewer. |
| Comparison of the Secondary Structures of Fusion Protein Isoforms |
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Comparison of Fusion Protein Sequences/Structures with Known Sequences/Structures from PDB |
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pLDDT score distribution |
| pLDDT score distribution of the predicted fusion protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. * The blue color at the bottom marks the best active site residues. |
| 192_PAK3_TFG.png |
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| 192_PAK3_TFG.png |
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Potential Active Site Information |
| The potential binding sites of these fusion proteins were identified using SiteMap, a module of the Schrodinger suite. |
| Kinase Fusion AA seq ID in KinaseFusionDB | Site score | Size | Dscore | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
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Ramachandran Plot of Kinase Fusion Protein Structure |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide. |
| 192_PAK3_TFG_ramachandran.png |
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Virtual Screening Results |
| Distribution of the average docking score across all approved kinase inhibitors. Distribution of the number of occurrence across all approved kinase inhibitors. |
| 5'-kinase fusion protein case |
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| 3'-kinase fusion protein case |
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| Drug information from DrugBank of the top 20 interacting small molecules. * The detailed information of individual kinase inhibitors are available in the download page. |
| Fusion gene name info | Drug | Docking score | Glide g score | Glide energy |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Lapatinib | -5.25599 | -5.34479 | -51.7294 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Lenvatinib | -5.22851 | -5.22851 | -42.6904 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Larotrectinib | -5.16478 | -5.16478 | -44.6413 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Neratinib | -4.78498 | -4.967280000000001 | -44.4452 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Neratinib | -4.78498 | -4.967280000000001 | -44.4452 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Belumosudil | -4.71336 | -4.72106 | -43.4628 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Belumosudil | -4.698919999999999 | -4.70662 | -43.5074 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Acalabrutinib | -4.68369 | -4.69779 | -47.6719 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Acalabrutinib | -4.68369 | -4.69779 | -47.6719 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Cabozantinib | -4.51149 | -4.55649 | -49.8649 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Cabozantinib | -4.51149 | -4.55649 | -49.8649 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Acalabrutinib | -4.46321 | -4.47731 | -46.4818 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Acalabrutinib | -4.46321 | -4.47731 | -46.4818 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Ripretinib | -4.4348 | -4.4418 | -38.8689 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Ripretinib | -4.4348 | -4.4418 | -38.8689 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Zanubrutinib | -4.41589 | -4.41589 | -44.1322 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Larotrectinib | -4.36908 | -4.36908 | -38.2719 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Selumetinib | -4.36026 | -4.3689599999999995 | -39.8065 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Selumetinib | -4.36026 | -4.3689599999999995 | -39.8065 |
| 192_PAK3_TFG-DOCK_HTVS_1-001 | Osimertinib | -4.28761 | -4.29531 | -49.0274 |
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Kinase-Substrate Information of PAK3_TFG |
| Phosphorylation target of the kinase (phosphosite, 03-17-2024) |
| Kinase | Kinase UniProt Acc | Kinase species | Substrate | Substrate UniProt Acc | Substrate phosphorylated residues | Substrate phosphorylated sites (+/-7AA) | Domain |
| Biological Network Integration of This Kinase and Substrates (GeneMANIA website) |
| Enriched GO biological processes of the phosphorylation target genes of the kinase |
| Kinase | GOID | GO term | P.adjust |
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Related Drugs to PAK3_TFG |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
| Distribution of the number of studies mentioning PAK3-TFG and kinase inhibitors the PubMed Abstract (04-01-2024) |
| Fusion gene - drug pair 1 | Fusion gene - drug pair 2 | PMID | Publication date | DOI | Study title |
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Related Diseases to PAK3_TFG |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Related diseases from the literature mentioned this fusion gene and drug. (PubMed, 04-01-2024) |
| MeSH ID | MeSH term |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | TFG | C3714897 | SPASTIC PARAPLEGIA 57, AUTOSOMAL RECESSIVE | 5 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Tgene | TFG | C1858338 | Neuropathy, hereditary motor and sensory, Okinawa type | 4 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Tgene | TFG | C0238463 | Papillary thyroid carcinoma | 2 | ORPHANET |
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Clinical Trials of the Found Drugs/Small Molecules |
| Statistics of the Clinical Trials of the Found Kinase Inibitors from clinicaltrials.gov (06-17-2024) |
| Clinical Trials from clinicaltrials.gov (06-17-2024) |
| Fusion Gene | Kinase Inhibitor | NCT ID | Study Status | Phases | Disease | # Enrolment | Date |
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