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Fusion Protein:SLC12A9-EGFR |
Fusion Gene and Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: SLC12A9-EGFR | FusionPDB ID: 82259 | FusionGDB2.0 ID: 82259 | Hgene | Tgene | Gene symbol | SLC12A9 | EGFR | Gene ID | 56996 | 1956 |
| Gene name | solute carrier family 12 member 9 | epidermal growth factor receptor | |
| Synonyms | CCC6|CIP1|WO3.3|hCCC6 | ERBB|ERBB1|HER1|NISBD2|PIG61|mENA | |
| Cytomap | 7q22.1 | 7p11.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | solute carrier family 12 member 9CCC-interacting protein 1cation-chloride cotransporter 6cation-chloride cotransporter-interacting protein 1potassium-chloride transporter 9solute carrier family 12 (potassium/chloride transporters), member 9 | epidermal growth factor receptoravian erythroblastic leukemia viral (v-erb-b) oncogene homologcell growth inhibiting protein 40cell proliferation-inducing protein 61epidermal growth factor receptor tyrosine kinase domainerb-b2 receptor tyrosine kinas | |
| Modification date | 20200313 | 20200329 | |
| UniProtAcc | . | P00533 Main function of 5'-partner protein: FUNCTION: Receptor tyrosine kinase binding ligands of the EGF family and activating several signaling cascades to convert extracellular cues into appropriate cellular responses (PubMed:2790960, PubMed:10805725, PubMed:27153536). Known ligands include EGF, TGFA/TGF-alpha, AREG, epigen/EPGN, BTC/betacellulin, epiregulin/EREG and HBEGF/heparin-binding EGF (PubMed:2790960, PubMed:7679104, PubMed:8144591, PubMed:9419975, PubMed:15611079, PubMed:12297049, PubMed:27153536, PubMed:20837704, PubMed:17909029). Ligand binding triggers receptor homo- and/or heterodimerization and autophosphorylation on key cytoplasmic residues. The phosphorylated receptor recruits adapter proteins like GRB2 which in turn activates complex downstream signaling cascades. Activates at least 4 major downstream signaling cascades including the RAS-RAF-MEK-ERK, PI3 kinase-AKT, PLCgamma-PKC and STATs modules (PubMed:27153536). May also activate the NF-kappa-B signaling cascade (PubMed:11116146). Also directly phosphorylates other proteins like RGS16, activating its GTPase activity and probably coupling the EGF receptor signaling to the G protein-coupled receptor signaling (PubMed:11602604). Also phosphorylates MUC1 and increases its interaction with SRC and CTNNB1/beta-catenin (PubMed:11483589). Positively regulates cell migration via interaction with CCDC88A/GIV which retains EGFR at the cell membrane following ligand stimulation, promoting EGFR signaling which triggers cell migration (PubMed:20462955). Plays a role in enhancing learning and memory performance (By similarity). {ECO:0000250|UniProtKB:Q01279, ECO:0000269|PubMed:10805725, ECO:0000269|PubMed:11116146, ECO:0000269|PubMed:11483589, ECO:0000269|PubMed:11602604, ECO:0000269|PubMed:12297049, ECO:0000269|PubMed:12297050, ECO:0000269|PubMed:12620237, ECO:0000269|PubMed:12873986, ECO:0000269|PubMed:15374980, ECO:0000269|PubMed:15590694, ECO:0000269|PubMed:15611079, ECO:0000269|PubMed:17115032, ECO:0000269|PubMed:17909029, ECO:0000269|PubMed:19560417, ECO:0000269|PubMed:20462955, ECO:0000269|PubMed:20837704, ECO:0000269|PubMed:21258366, ECO:0000269|PubMed:27153536, ECO:0000269|PubMed:2790960, ECO:0000269|PubMed:7679104, ECO:0000269|PubMed:8144591, ECO:0000269|PubMed:9419975}.; FUNCTION: Isoform 2 may act as an antagonist of EGF action.; FUNCTION: (Microbial infection) Acts as a receptor for hepatitis C virus (HCV) in hepatocytes and facilitates its cell entry. Mediates HCV entry by promoting the formation of the CD81-CLDN1 receptor complexes that are essential for HCV entry and by enhancing membrane fusion of cells expressing HCV envelope glycoproteins. {ECO:0000269|PubMed:21516087}. | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000354161, ENST00000275729, ENST00000415287, ENST00000428758, ENST00000475623, ENST00000540482, | ENST00000275493, ENST00000342916, ENST00000344576, ENST00000420316, ENST00000442591, ENST00000454757, ENST00000463948, ENST00000455089, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 4 X 4 X 2=32 | 17 X 20 X 8=2720 |
| # samples | 4 | 22 | |
| ** MAII score | log2(4/32*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(22/2720*10)=-3.62803122261304 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Fusion gene context | PubMed: SLC12A9 [Title/Abstract] AND EGFR [Title/Abstract] AND fusion [Title/Abstract] | ||
| Fusion neoantigen context | PubMed: SLC12A9 [Title/Abstract] AND EGFR [Title/Abstract] AND neoantigen [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | SLC12A9(100463764)-EGFR(55270275), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | SLC12A9-EGFR seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. SLC12A9-EGFR seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. | ||
| * 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 | EGFR | GO:0001934 | positive regulation of protein phosphorylation | 20551055 |
| Tgene | EGFR | GO:0007165 | signal transduction | 10572067 |
| Tgene | EGFR | GO:0007166 | cell surface receptor signaling pathway | 7736574 |
| Tgene | EGFR | GO:0007173 | epidermal growth factor receptor signaling pathway | 7736574|12435727 |
| Tgene | EGFR | GO:0008283 | cell proliferation | 17115032 |
| Tgene | EGFR | GO:0008284 | positive regulation of cell proliferation | 7736574 |
| Tgene | EGFR | GO:0010750 | positive regulation of nitric oxide mediated signal transduction | 12828935 |
| Tgene | EGFR | GO:0018108 | peptidyl-tyrosine phosphorylation | 22732145 |
| Tgene | EGFR | GO:0030307 | positive regulation of cell growth | 15467833 |
| Tgene | EGFR | GO:0042177 | negative regulation of protein catabolic process | 17115032 |
| Tgene | EGFR | GO:0042327 | positive regulation of phosphorylation | 15082764 |
| Tgene | EGFR | GO:0043406 | positive regulation of MAP kinase activity | 10572067 |
| Tgene | EGFR | GO:0045739 | positive regulation of DNA repair | 17115032 |
| Tgene | EGFR | GO:0045740 | positive regulation of DNA replication | 17115032 |
| Tgene | EGFR | GO:0045944 | positive regulation of transcription by RNA polymerase II | 20551055 |
| Tgene | EGFR | GO:0050679 | positive regulation of epithelial cell proliferation | 10572067 |
| Tgene | EGFR | GO:0050999 | regulation of nitric-oxide synthase activity | 12828935 |
| Tgene | EGFR | GO:0070141 | response to UV-A | 18483258 |
| Tgene | EGFR | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 20551055 |
| Tgene | EGFR | GO:0071392 | cellular response to estradiol stimulus | 20551055 |
| Tgene | EGFR | GO:1900020 | positive regulation of protein kinase C activity | 22732145 |
| Tgene | EGFR | GO:1903078 | positive regulation of protein localization to plasma membrane | 22732145 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr7:100463764/chr7:55270275) - 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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| Retention analysis results 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, are available here. |
| Fusion gene breakpoints across SLC12A9 (5'-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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| Fusion gene breakpoints across EGFR (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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Fusion Amino Acid Sequences |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| ENST00000354161 | SLC12A9 | chr7 | 100463764 | + | ENST00000455089 | EGFR | chr7 | 55270275 | + | 3343 | 2849 | 113 | 2068 | 651 |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
| ENST00000354161 | ENST00000455089 | SLC12A9 | chr7 | 100463764 | + | EGFR | chr7 | 55270275 | + | 0.007304164 | 0.9926958 |
| Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones. |
Get the fusion protein sequences from here. |
| Fusion protein sequence information is available in the fasta format. >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP |
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Fusion Protein Breakpoint Sequences for SLC12A9-EGFR |
| +/-13 AA sequence from the breakpoints of the fusion protein sequences. |
| Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
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Potential FusionNeoAntigen Information of SLC12A9-EGFR in HLA I |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| Potential FusionNeoAntigen Information * We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5) |
| Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA I | FusionNeoAntigen peptide | Binding score | Immunogenic score | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Potential FusionNeoAntigen Information of SLC12A9-EGFR in HLA II |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| Potential FusionNeoAntigen Information * We used NetMHCIIpan v4.1 (%rank<0.5). |
| Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA II | FusionNeoAntigen peptide | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Fusion breakpoint peptide structures of SLC12A9-EGFR |
| 3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens * The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA. |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SLC12A9-EGFR |
| Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens * We used Glide to predict the interaction between HLAs and neoantigens. |
| HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
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Vaccine Design for the FusionNeoAntigens of SLC12A9-EGFR |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
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Information of the samples that have these potential fusion neoantigens of SLC12A9-EGFR |
| These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens. |
| Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
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Potential target of CAR-T therapy development for SLC12A9-EGFR |
| Predicted 3D structure. We used RoseTTAFold. |
| 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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features * Minus value of BPloci means that the break point is located before the CDS. |
| - In-frame and retained 'Transmembrane'. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| Tgene | EGFR | chr7:100463764 | chr7:55270275 | ENST00000275493 | 0 | 28 | 646_668 | 0 | 1211.0 | Transmembrane | Helical | |
| Tgene | EGFR | chr7:100463764 | chr7:55270275 | ENST00000342916 | 0 | 16 | 646_668 | 0 | 629.0 | Transmembrane | Helical | |
| Tgene | EGFR | chr7:100463764 | chr7:55270275 | ENST00000344576 | 0 | 16 | 646_668 | 0 | 706.0 | Transmembrane | Helical | |
| Tgene | EGFR | chr7:100463764 | chr7:55270275 | ENST00000420316 | 0 | 10 | 646_668 | 0 | 406.0 | Transmembrane | Helical |
| Subcellular localization prediction of the transmembrane domain retained fusion proteins * We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image. |
| Hgene | Hchr | Hbp | Henst | Tgene | Tchr | Tbp | Tenst | DeepLoc result |
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Related Drugs to SLC12A9-EGFR |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to SLC12A9-EGFR |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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