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Fusion Protein:KCNN3-LAPTM4B |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: KCNN3-LAPTM4B | FusionPDB ID: 41527 | FusionGDB2.0 ID: 41527 | Hgene | Tgene | Gene symbol | KCNN3 | LAPTM4B | Gene ID | 3782 | 55353 |
| Gene name | potassium calcium-activated channel subfamily N member 3 | lysosomal protein transmembrane 4 beta | |
| Synonyms | KCa2.3|SK3|SKCA3|ZLS3|hSK3 | LAPTM4beta|LC27 | |
| Cytomap | 1q21.3 | 8q22.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | small conductance calcium-activated potassium channel protein 3SKCa 3potassium channel, calcium activated intermediate/small conductance subfamily N alpha, member 3potassium intermediate/small conductance calcium-activated channel, subfamily N, member | lysosomal-associated transmembrane protein 4Blysosomal associated protein transmembrane 4 betalysosome-associated transmembrane protein 4-beta | |
| Modification date | 20200329 | 20200313 | |
| UniProtAcc | Q9UGI6 | Q86VI4 | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000358505, ENST00000271915, ENST00000361147, ENST00000515643, | ENST00000445593, ENST00000521545, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 6 X 6 X 5=180 | 14 X 8 X 8=896 |
| # samples | 8 | 16 | |
| ** MAII score | log2(8/180*10)=-1.16992500144231 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(16/896*10)=-2.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: KCNN3 [Title/Abstract] AND LAPTM4B [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | KCNN3(154794565)-LAPTM4B(98817581), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | KCNN3-LAPTM4B 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. KCNN3-LAPTM4B 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. KCNN3-LAPTM4B 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. KCNN3-LAPTM4B 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. KCNN3-LAPTM4B seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted 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 | LAPTM4B | GO:0032509 | endosome transport via multivesicular body sorting pathway | 25588945 |
| Tgene | LAPTM4B | GO:0032911 | negative regulation of transforming growth factor beta1 production | 26126825 |
| Fusion gene breakpoints across KCNN3 (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 LAPTM4B (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 Gene Sample Information |
| Fusion gene information from FusionGDB2.0. |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * 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 | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | STAD | TCGA-CG-4449-01A | KCNN3 | chr1 | 154794565 | - | LAPTM4B | chr8 | 98817581 | + |
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Fusion ORF Analysis |
| 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) |
| ENST00000271915 | KCNN3 | chr1 | 154794565 | - | ENST00000445593 | LAPTM4B | chr8 | 98817581 | + | 3466 | 1345 | 58 | 1926 | 622 |
| ENST00000271915 | KCNN3 | chr1 | 154794565 | - | ENST00000521545 | LAPTM4B | chr8 | 98817581 | + | 1927 | 1345 | 58 | 1926 | 623 |
| ENST00000361147 | KCNN3 | chr1 | 154794565 | - | ENST00000445593 | LAPTM4B | chr8 | 98817581 | + | 2366 | 245 | 131 | 826 | 231 |
| ENST00000361147 | KCNN3 | chr1 | 154794565 | - | ENST00000521545 | LAPTM4B | chr8 | 98817581 | + | 827 | 245 | 131 | 826 | 232 |
| 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 |
| ENST00000271915 | ENST00000445593 | KCNN3 | chr1 | 154794565 | - | LAPTM4B | chr8 | 98817581 | + | 0.009146508 | 0.9908535 |
| ENST00000271915 | ENST00000521545 | KCNN3 | chr1 | 154794565 | - | LAPTM4B | chr8 | 98817581 | + | 0.03907387 | 0.9609261 |
| ENST00000361147 | ENST00000445593 | KCNN3 | chr1 | 154794565 | - | LAPTM4B | chr8 | 98817581 | + | 0.000399952 | 0.9996001 |
| ENST00000361147 | ENST00000521545 | KCNN3 | chr1 | 154794565 | - | LAPTM4B | chr8 | 98817581 | + | 0.000518649 | 0.9994814 |
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Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP >41527_41527_1_KCNN3-LAPTM4B_KCNN3_chr1_154794565_ENST00000271915_LAPTM4B_chr8_98817581_ENST00000445593_length(amino acids)=622AA_BP=428 MREFFHPLFFLQAPLLLSLPAQYNAFLSGSVWTPGSPREPKQAKERTGAKILVGEIGCLAFFEDIFGARVALGWGLVLQGIQPGPKMDTS GHFHDSGVGDLDEDPKCPCPSSGDEQQQQQQQQQQQQPPPPAPPAAPQQPLGPSLQPQPPQLQQQQQQQQQQQQQQPPHPLSQLAQLQSQ PVHPGLLHSSPTAFRAPPSSNSTAILHPSSRQGSQLNLNDHLLGHSPSSTATSGPGGGSRHRQASPLVHRRDSNPFTEIAMSSCKYSGGV MKPLSRLSASRRNLIEAETEGQPLQLFSPSNPPEIVISSREDNHAHQTLLHHPNATHNHQHAGTTASSTTFPKANKRKNQNIGYKLGHRR ALFEKRKRLSDYALIFGMFGIVVMVIETELSWGLYSKDSMFSLALKCLISLSTIILLGLIIAYHTREVQIINAVVLLILLSALADPDQYN FSSSELGGDFEFMDDANMCIAIAISLLMILICAMATYGAYKQRAAWIIPFFCYQIFDFALNMLVAITVLIYPNSIQEYIRQLPPNFPYRD -------------------------------------------------------------- >41527_41527_2_KCNN3-LAPTM4B_KCNN3_chr1_154794565_ENST00000271915_LAPTM4B_chr8_98817581_ENST00000521545_length(amino acids)=623AA_BP=428 MREFFHPLFFLQAPLLLSLPAQYNAFLSGSVWTPGSPREPKQAKERTGAKILVGEIGCLAFFEDIFGARVALGWGLVLQGIQPGPKMDTS GHFHDSGVGDLDEDPKCPCPSSGDEQQQQQQQQQQQQPPPPAPPAAPQQPLGPSLQPQPPQLQQQQQQQQQQQQQQPPHPLSQLAQLQSQ PVHPGLLHSSPTAFRAPPSSNSTAILHPSSRQGSQLNLNDHLLGHSPSSTATSGPGGGSRHRQASPLVHRRDSNPFTEIAMSSCKYSGGV MKPLSRLSASRRNLIEAETEGQPLQLFSPSNPPEIVISSREDNHAHQTLLHHPNATHNHQHAGTTASSTTFPKANKRKNQNIGYKLGHRR ALFEKRKRLSDYALIFGMFGIVVMVIETELSWGLYSKDSMFSLALKCLISLSTIILLGLIIAYHTREVQIINAVVLLILLSALADPDQYN FSSSELGGDFEFMDDANMCIAIAISLLMILICAMATYGAYKQRAAWIIPFFCYQIFDFALNMLVAITVLIYPNSIQEYIRQLPPNFPYRD -------------------------------------------------------------- >41527_41527_3_KCNN3-LAPTM4B_KCNN3_chr1_154794565_ENST00000361147_LAPTM4B_chr8_98817581_ENST00000445593_length(amino acids)=231AA_BP=37 MERPIKDSMFSLALKCLISLSTIILLGLIIAYHTREVQIINAVVLLILLSALADPDQYNFSSSELGGDFEFMDDANMCIAIAISLLMILI CAMATYGAYKQRAAWIIPFFCYQIFDFALNMLVAITVLIYPNSIQEYIRQLPPNFPYRDDVMSVNPTCLVLIILLFISIILTFKGYLISC -------------------------------------------------------------- >41527_41527_4_KCNN3-LAPTM4B_KCNN3_chr1_154794565_ENST00000361147_LAPTM4B_chr8_98817581_ENST00000521545_length(amino acids)=232AA_BP=37 MERPIKDSMFSLALKCLISLSTIILLGLIIAYHTREVQIINAVVLLILLSALADPDQYNFSSSELGGDFEFMDDANMCIAIAISLLMILI CAMATYGAYKQRAAWIIPFFCYQIFDFALNMLVAITVLIYPNSIQEYIRQLPPNFPYRDDVMSVNPTCLVLIILLFISIILTFKGYLISC -------------------------------------------------------------- |
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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/chr1:154794565/chr8:98817581) - 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 |
| KCNN3 | LAPTM4B |
| FUNCTION: Forms a voltage-independent potassium channel activated by intracellular calcium (PubMed:31155282). Activation is followed by membrane hyperpolarization. Thought to regulate neuronal excitability by contributing to the slow component of synaptic afterhyperpolarization. The channel is blocked by apamin. {ECO:0000269|PubMed:31155282}. | FUNCTION: Required for optimal lysosomal function (PubMed:21224396). Blocks EGF-stimulated EGFR intraluminal sorting and degradation. Conversely by binding with the phosphatidylinositol 4,5-bisphosphate, regulates its PIP5K1C interaction, inhibits HGS ubiquitination and relieves LAPTM4B inhibition of EGFR degradation (PubMed:25588945). Recruits SLC3A2 and SLC7A5 (the Leu transporter) to the lysosome, promoting entry of leucine and other essential amino acid (EAA) into the lysosome, stimulating activation of proton-transporting vacuolar (V)-ATPase protein pump (V-ATPase) and hence mTORC1 activation (PubMed:25998567). Plays a role as negative regulator of TGFB1 production in regulatory T cells (PubMed:26126825). Binds ceramide and facilitates its exit from late endosome in order to control cell death pathways (PubMed:26280656). {ECO:0000269|PubMed:21224396, ECO:0000269|PubMed:25588945, ECO:0000269|PubMed:25998567, ECO:0000269|PubMed:26126825, ECO:0000269|PubMed:26280656}. |
| 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 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 |
| Tgene | LAPTM4B | chr1:154794565 | chr8:98817581 | ENST00000445593 | 0 | 7 | 163_183 | 124.0 | 318.0 | Transmembrane | Helical | |
| Tgene | LAPTM4B | chr1:154794565 | chr8:98817581 | ENST00000445593 | 0 | 7 | 191_211 | 124.0 | 318.0 | Transmembrane | Helical | |
| Tgene | LAPTM4B | chr1:154794565 | chr8:98817581 | ENST00000445593 | 0 | 7 | 244_264 | 124.0 | 318.0 | Transmembrane | Helical | |
| Tgene | LAPTM4B | chr1:154794565 | chr8:98817581 | ENST00000521545 | 0 | 7 | 117_137 | 33.0 | 227.0 | Transmembrane | Helical | |
| Tgene | LAPTM4B | chr1:154794565 | chr8:98817581 | ENST00000521545 | 0 | 7 | 163_183 | 33.0 | 227.0 | Transmembrane | Helical | |
| Tgene | LAPTM4B | chr1:154794565 | chr8:98817581 | ENST00000521545 | 0 | 7 | 191_211 | 33.0 | 227.0 | Transmembrane | Helical | |
| Tgene | LAPTM4B | chr1:154794565 | chr8:98817581 | ENST00000521545 | 0 | 7 | 244_264 | 33.0 | 227.0 | Transmembrane | Helical |
| - 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 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000358505 | - | 2 | 8 | 30_94 | 30.0 | 419.0 | Compositional bias | Note=Gln-rich |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000358505 | - | 2 | 8 | 42_64 | 30.0 | 419.0 | Compositional bias | Note=Pro-rich |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000358505 | - | 2 | 8 | 683_687 | 30.0 | 419.0 | Compositional bias | Note=Poly-Gln |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000358505 | - | 2 | 8 | 727_730 | 30.0 | 419.0 | Compositional bias | Note=Poly-Ser |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000361147 | - | 2 | 8 | 30_94 | 38.0 | 427.0 | Compositional bias | Note=Gln-rich |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000361147 | - | 2 | 8 | 42_64 | 38.0 | 427.0 | Compositional bias | Note=Pro-rich |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000361147 | - | 2 | 8 | 683_687 | 38.0 | 427.0 | Compositional bias | Note=Poly-Gln |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000361147 | - | 2 | 8 | 727_730 | 38.0 | 427.0 | Compositional bias | Note=Poly-Ser |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000358505 | - | 2 | 8 | 494_514 | 30.0 | 419.0 | Intramembrane | Pore-forming%3B Name%3DSegment H5 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000361147 | - | 2 | 8 | 494_514 | 38.0 | 427.0 | Intramembrane | Pore-forming%3B Name%3DSegment H5 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000358505 | - | 2 | 8 | 561_637 | 30.0 | 419.0 | Region | Calmodulin-binding |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000361147 | - | 2 | 8 | 561_637 | 38.0 | 427.0 | Region | Calmodulin-binding |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000358505 | - | 2 | 8 | 288_308 | 30.0 | 419.0 | Transmembrane | Helical%3B Name%3DSegment S1 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000358505 | - | 2 | 8 | 315_335 | 30.0 | 419.0 | Transmembrane | Helical%3B Name%3DSegment S2 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000358505 | - | 2 | 8 | 366_386 | 30.0 | 419.0 | Transmembrane | Helical%3B Name%3DSegment S3 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000358505 | - | 2 | 8 | 405_425 | 30.0 | 419.0 | Transmembrane | Helical%3B Name%3DSegment S4 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000358505 | - | 2 | 8 | 454_474 | 30.0 | 419.0 | Transmembrane | Helical%3B Name%3DSegment S5 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000358505 | - | 2 | 8 | 523_543 | 30.0 | 419.0 | Transmembrane | Helical%3B Name%3DSegment S6 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000361147 | - | 2 | 8 | 288_308 | 38.0 | 427.0 | Transmembrane | Helical%3B Name%3DSegment S1 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000361147 | - | 2 | 8 | 315_335 | 38.0 | 427.0 | Transmembrane | Helical%3B Name%3DSegment S2 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000361147 | - | 2 | 8 | 366_386 | 38.0 | 427.0 | Transmembrane | Helical%3B Name%3DSegment S3 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000361147 | - | 2 | 8 | 405_425 | 38.0 | 427.0 | Transmembrane | Helical%3B Name%3DSegment S4 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000361147 | - | 2 | 8 | 454_474 | 38.0 | 427.0 | Transmembrane | Helical%3B Name%3DSegment S5 |
| Hgene | KCNN3 | chr1:154794565 | chr8:98817581 | ENST00000361147 | - | 2 | 8 | 523_543 | 38.0 | 427.0 | Transmembrane | Helical%3B Name%3DSegment S6 |
| Tgene | LAPTM4B | chr1:154794565 | chr8:98817581 | ENST00000445593 | 0 | 7 | 117_137 | 124.0 | 318.0 | Transmembrane | Helical |
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Fusion Protein-Protein Interaction |
| 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 from validated records (BIOGRID-3.4.160) |
| Gene | PPI interactors |
| Protein-protein interactors based on sequence similarity (STRING) |
| Gene | STRING network |
| KCNN3 | |
| LAPTM4B |
| - Retained interactions in fusion protein (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost interactions due to fusion (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs to KCNN3-LAPTM4B |
| 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 KCNN3-LAPTM4B |
| 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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