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Fusion Protein:KDM5B-KLHL12 |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: KDM5B-KLHL12 | FusionPDB ID: 41862 | FusionGDB2.0 ID: 41862 | Hgene | Tgene | Gene symbol | KDM5B | KLHL12 | Gene ID | 10765 | 59349 |
| Gene name | lysine demethylase 5B | kelch like family member 12 | |
| Synonyms | CT31|JARID1B|MRT65|PLU-1|PLU1|PPP1R98|PUT1|RBBP2H1A|RBP2-H1 | C3IP1|DKIR | |
| Cytomap | 1q32.1 | 1q32.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | lysine-specific demethylase 5Bcancer/testis antigen 31histone demethylase JARID1Bjumonji, AT rich interactive domain 1Bjumonji/ARID domain-containing protein 1Blysine (K)-specific demethylase 5Bprotein phosphatase 1, regulatory subunit 98putative D | kelch-like protein 12CUL3-interacting protein 1DKIR homologkelch-like protein C3IP1 | |
| Modification date | 20200320 | 20200327 | |
| UniProtAcc | Q9UGL1 | Q53G59 | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000367264, ENST00000367265, ENST00000456180, | ENST00000367259, ENST00000435533, ENST00000367261, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 14 X 13 X 9=1638 | 5 X 5 X 3=75 |
| # samples | 17 | 5 | |
| ** MAII score | log2(17/1638*10)=-3.26832870550331 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/75*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: KDM5B [Title/Abstract] AND KLHL12 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | KDM5B(202742246)-KLHL12(202880331), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | KDM5B-KLHL12 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. KDM5B-KLHL12 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. KDM5B-KLHL12 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. KDM5B-KLHL12 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 |
| Hgene | KDM5B | GO:0034720 | histone H3-K4 demethylation | 20228790 |
| Tgene | KLHL12 | GO:0006513 | protein monoubiquitination | 22358839|27716508 |
| Tgene | KLHL12 | GO:0006888 | ER to Golgi vesicle-mediated transport | 22358839 |
| Fusion gene breakpoints across KDM5B (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 KLHL12 (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-5717-01A | KDM5B | chr1 | 202742246 | - | KLHL12 | chr1 | 202880331 | - |
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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) |
| ENST00000367265 | KDM5B | chr1 | 202742246 | - | ENST00000367261 | KLHL12 | chr1 | 202880331 | - | 4314 | 1741 | 934 | 2880 | 648 |
| ENST00000367264 | KDM5B | chr1 | 202742246 | - | ENST00000367261 | KLHL12 | chr1 | 202880331 | - | 3262 | 689 | 113 | 1828 | 571 |
| 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 |
| ENST00000367265 | ENST00000367261 | KDM5B | chr1 | 202742246 | - | KLHL12 | chr1 | 202880331 | - | 0.001224299 | 0.99877566 |
| ENST00000367264 | ENST00000367261 | KDM5B | chr1 | 202742246 | - | KLHL12 | chr1 | 202880331 | - | 0.001006995 | 0.998993 |
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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 >41862_41862_1_KDM5B-KLHL12_KDM5B_chr1_202742246_ENST00000367264_KLHL12_chr1_202880331_ENST00000367261_length(amino acids)=571AA_BP=183 MEAATTLHPGPRPALPLGGPGPLGEFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRL NELEAQTRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHYERILN PYNLFLSGDSLRVDSEEPVFEAVINWVKHAKKEREESLPNLLQYVRMPLLTPRYITDVIDAEPFIRCSLQCRDLVDEAKKFHLRPELRSQ MQGPRTRARLGANEVLLVVGGFGSQQSPIDVVEKYDPKTQEWSFLPSITRKRRYVASVSLHDRIYVIGGYDGRSRLSSVECLDYTADEDG VWYSVAPMNVRRGLAGATTLGDMIYVSGGFDGSRRHTSMERYDPNIDQWSMLGDMQTAREGAGLVVASGVIYCLGGYDGLNILNSVEKYD PHTGHWTNVTPMATKRSGAGVALLNDHIYVVGGFDGTAHLSSVEAYNIRTDSWTTVTSMTTPRCYVGATVLRGRLYAIAGYDGNSLLSSI -------------------------------------------------------------- >41862_41862_2_KDM5B-KLHL12_KDM5B_chr1_202742246_ENST00000367265_KLHL12_chr1_202880331_ENST00000367261_length(amino acids)=648AA_BP=260 MGVGWDSFSSPWRRRRTAWACGETSSSEAEKAQGAAVARTTRTCCCSSRVCTGLGPSGARSLGPGAHLRLALAQPAVMEAATTLHPGPRP ALPLGGPGPLGEFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLNF LDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHYERILNPYNLFLSGDSLRV DSEEPVFEAVINWVKHAKKEREESLPNLLQYVRMPLLTPRYITDVIDAEPFIRCSLQCRDLVDEAKKFHLRPELRSQMQGPRTRARLGAN EVLLVVGGFGSQQSPIDVVEKYDPKTQEWSFLPSITRKRRYVASVSLHDRIYVIGGYDGRSRLSSVECLDYTADEDGVWYSVAPMNVRRG LAGATTLGDMIYVSGGFDGSRRHTSMERYDPNIDQWSMLGDMQTAREGAGLVVASGVIYCLGGYDGLNILNSVEKYDPHTGHWTNVTPMA TKRSGAGVALLNDHIYVVGGFDGTAHLSSVEAYNIRTDSWTTVTSMTTPRCYVGATVLRGRLYAIAGYDGNSLLSSIECYDPIIDSWEVV -------------------------------------------------------------- |
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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/chr1:202742246/chr1:202880331) - 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 |
| KDM5B | KLHL12 |
| FUNCTION: Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code (PubMed:24952722, PubMed:27214403, PubMed:28262558). Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor suppressor genes such as BRCA1 and HOXA5 (PubMed:24952722). In contrast, may act as a tumor suppressor for melanoma. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 (By similarity). {ECO:0000250|UniProtKB:Q80Y84, ECO:0000269|PubMed:12657635, ECO:0000269|PubMed:16645588, ECO:0000269|PubMed:17320161, ECO:0000269|PubMed:17363312, ECO:0000269|PubMed:24952722, ECO:0000269|PubMed:26645689, ECO:0000269|PubMed:26741168, ECO:0000269|PubMed:27214403, ECO:0000269|PubMed:28262558}. | FUNCTION: Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that acts as a negative regulator of Wnt signaling pathway and ER-Golgi transport (PubMed:22358839, PubMed:27565346). The BCR(KLHL12) complex is involved in ER-Golgi transport by regulating the size of COPII coats, thereby playing a key role in collagen export, which is required for embryonic stem (ES) cells division: BCR(KLHL12) acts by mediating monoubiquitination of SEC31 (SEC31A or SEC31B) (PubMed:22358839, PubMed:27565346). The BCR(KLHL12) complex is also involved in neural crest specification: in response to cytosolic calcium increase, interacts with the heterodimer formed with PEF1 and PDCD6/ALG-2, leading to bridge together the BCR(KLHL12) complex and SEC31 (SEC31A or SEC31B), promoting monoubiquitination of SEC31 and subsequent collagen export (PubMed:27716508). As part of the BCR(KLHL12) complex, also acts as a negative regulator of the Wnt signaling pathway by mediating ubiquitination and subsequent proteolysis of DVL3 (PubMed:16547521). The BCR(KLHL12) complex also mediates polyubiquitination of DRD4 and PEF1, without leading to degradation of these proteins (PubMed:18303015, PubMed:20100572, PubMed:27716508). {ECO:0000269|PubMed:16547521, ECO:0000269|PubMed:18303015, ECO:0000269|PubMed:20100572, ECO:0000269|PubMed:22358839, ECO:0000269|PubMed:27565346, ECO:0000269|PubMed:27716508}. |
| 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 |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367264 | - | 4 | 28 | 32_73 | 192.0 | 1581.0 | Domain | JmjN |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367264 | - | 4 | 28 | 97_187 | 192.0 | 1581.0 | Domain | ARID |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367265 | - | 4 | 27 | 32_73 | 192.0 | 1545.0 | Domain | JmjN |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367265 | - | 4 | 27 | 97_187 | 192.0 | 1545.0 | Domain | ARID |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000367261 | 3 | 12 | 282_329 | 189.0 | 569.0 | Repeat | Note=Kelch 1 | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000367261 | 3 | 12 | 331_379 | 189.0 | 569.0 | Repeat | Note=Kelch 2 | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000367261 | 3 | 12 | 380_426 | 189.0 | 569.0 | Repeat | Note=Kelch 3 | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000367261 | 3 | 12 | 427_473 | 189.0 | 569.0 | Repeat | Note=Kelch 4 | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000367261 | 3 | 12 | 475_520 | 189.0 | 569.0 | Repeat | Note=Kelch 5 | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000367261 | 3 | 12 | 522_567 | 189.0 | 569.0 | Repeat | Note=Kelch 6 | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000435533 | 3 | 12 | 282_329 | 227.0 | 607.0 | Repeat | Note=Kelch 1 | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000435533 | 3 | 12 | 331_379 | 227.0 | 607.0 | Repeat | Note=Kelch 2 | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000435533 | 3 | 12 | 380_426 | 227.0 | 607.0 | Repeat | Note=Kelch 3 | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000435533 | 3 | 12 | 427_473 | 227.0 | 607.0 | Repeat | Note=Kelch 4 | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000435533 | 3 | 12 | 475_520 | 227.0 | 607.0 | Repeat | Note=Kelch 5 | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000435533 | 3 | 12 | 522_567 | 227.0 | 607.0 | Repeat | Note=Kelch 6 |
| - 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 | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367264 | - | 4 | 28 | 1434_1439 | 192.0 | 1581.0 | Compositional bias | Note=Poly-Lys |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367265 | - | 4 | 27 | 1434_1439 | 192.0 | 1545.0 | Compositional bias | Note=Poly-Lys |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367264 | - | 4 | 28 | 453_619 | 192.0 | 1581.0 | Domain | JmjC |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367265 | - | 4 | 27 | 453_619 | 192.0 | 1545.0 | Domain | JmjC |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367264 | - | 4 | 28 | 1176_1224 | 192.0 | 1581.0 | Zinc finger | PHD-type 2 |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367264 | - | 4 | 28 | 1484_1538 | 192.0 | 1581.0 | Zinc finger | PHD-type 3 |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367264 | - | 4 | 28 | 309_359 | 192.0 | 1581.0 | Zinc finger | PHD-type 1 |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367264 | - | 4 | 28 | 692_744 | 192.0 | 1581.0 | Zinc finger | C5HC2 |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367265 | - | 4 | 27 | 1176_1224 | 192.0 | 1545.0 | Zinc finger | PHD-type 2 |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367265 | - | 4 | 27 | 1484_1538 | 192.0 | 1545.0 | Zinc finger | PHD-type 3 |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367265 | - | 4 | 27 | 309_359 | 192.0 | 1545.0 | Zinc finger | PHD-type 1 |
| Hgene | KDM5B | chr1:202742246 | chr1:202880331 | ENST00000367265 | - | 4 | 27 | 692_744 | 192.0 | 1545.0 | Zinc finger | C5HC2 |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000367261 | 3 | 12 | 135_236 | 189.0 | 569.0 | Domain | Note=BACK | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000367261 | 3 | 12 | 33_100 | 189.0 | 569.0 | Domain | BTB | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000435533 | 3 | 12 | 135_236 | 227.0 | 607.0 | Domain | Note=BACK | |
| Tgene | KLHL12 | chr1:202742246 | chr1:202880331 | ENST00000435533 | 3 | 12 | 33_100 | 227.0 | 607.0 | Domain | BTB |
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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 |
| KDM5B | |
| KLHL12 |
| - 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 KDM5B-KLHL12 |
| 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 KDM5B-KLHL12 |
| 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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