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Fusion Protein:NOVA1-CHMP1A |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: NOVA1-CHMP1A | FusionPDB ID: 59795 | FusionGDB2.0 ID: 59795 | Hgene | Tgene | Gene symbol | NOVA1 | CHMP1A | Gene ID | 4857 | 5119 |
| Gene name | NOVA alternative splicing regulator 1 | charged multivesicular body protein 1A | |
| Synonyms | Nova-1 | CHMP1|PCH8|PCOLN3|PRSM1|VPS46-1|VPS46A | |
| Cytomap | 14q12 | 16q24.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | RNA-binding protein Nova-1neuro-oncological ventral antigen 1onconeural ventral antigen 1paraneoplastic Ri antigenventral neuron-specific protein 1 | charged multivesicular body protein 1acharged multivesicular body protein 1/chromatin modifying protein 1chromatin modifying protein 1Aprocollagen (type III) N-endopeptidaseprotease, metallo, 1, 33kDvacuolar protein sorting-associated protein 46-1 | |
| Modification date | 20200327 | 20200313 | |
| UniProtAcc | P51513 | Q9HD42 | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000267422, ENST00000344429, ENST00000539517, ENST00000465357, ENST00000547619, ENST00000551754, ENST00000574031, | ENST00000547614, ENST00000253475, ENST00000397901, ENST00000535997, ENST00000550102, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 7 X 5 X 5=175 | 45 X 11 X 21=10395 |
| # samples | 8 | 48 | |
| ** MAII score | log2(8/175*10)=-1.12928301694497 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(48/10395*10)=-4.43671154213721 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: NOVA1 [Title/Abstract] AND CHMP1A [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | NOVA1(26941526)-CHMP1A(89713739), # samples:3 | ||
| Anticipated loss of major functional domain due to fusion event. | NOVA1-CHMP1A 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. NOVA1-CHMP1A 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. NOVA1-CHMP1A 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. NOVA1-CHMP1A 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. NOVA1-CHMP1A seems lost the major protein functional domain in Hgene partner, which is a essential gene 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 | CHMP1A | GO:0007076 | mitotic chromosome condensation | 11559747 |
| Tgene | CHMP1A | GO:0016192 | vesicle-mediated transport | 11559748 |
| Tgene | CHMP1A | GO:0016458 | gene silencing | 11559747 |
| Tgene | CHMP1A | GO:0045892 | negative regulation of transcription, DNA-templated | 11559747 |
| Fusion gene breakpoints across NOVA1 (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 CHMP1A (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 | GBM | TCGA-02-2483-01A | NOVA1 | chr14 | 26941526 | - | CHMP1A | chr16 | 89713739 | - |
| ChimerDB4 | GBM | TCGA-06-0210-02A | NOVA1 | chr14 | 26941526 | - | CHMP1A | chr16 | 89713739 | - |
| ChimerDB4 | GBM | TCGA-12-0618-01A | NOVA1 | chr14 | 26941526 | - | CHMP1A | chr16 | 89713739 | - |
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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) |
| ENST00000539517 | NOVA1 | chr14 | 26941526 | - | ENST00000397901 | CHMP1A | chr16 | 89713739 | - | 2811 | 837 | 318 | 1175 | 285 |
| ENST00000539517 | NOVA1 | chr14 | 26941526 | - | ENST00000535997 | CHMP1A | chr16 | 89713739 | - | 2779 | 837 | 318 | 1175 | 285 |
| ENST00000539517 | NOVA1 | chr14 | 26941526 | - | ENST00000550102 | CHMP1A | chr16 | 89713739 | - | 1353 | 837 | 318 | 1175 | 285 |
| ENST00000344429 | NOVA1 | chr14 | 26941526 | - | ENST00000397901 | CHMP1A | chr16 | 89713739 | - | 2497 | 523 | 4 | 861 | 285 |
| ENST00000344429 | NOVA1 | chr14 | 26941526 | - | ENST00000535997 | CHMP1A | chr16 | 89713739 | - | 2465 | 523 | 4 | 861 | 285 |
| ENST00000344429 | NOVA1 | chr14 | 26941526 | - | ENST00000550102 | CHMP1A | chr16 | 89713739 | - | 1039 | 523 | 4 | 861 | 285 |
| 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 |
| ENST00000539517 | ENST00000397901 | NOVA1 | chr14 | 26941526 | - | CHMP1A | chr16 | 89713739 | - | 0.005644924 | 0.9943551 |
| ENST00000539517 | ENST00000535997 | NOVA1 | chr14 | 26941526 | - | CHMP1A | chr16 | 89713739 | - | 0.005858147 | 0.9941419 |
| ENST00000539517 | ENST00000550102 | NOVA1 | chr14 | 26941526 | - | CHMP1A | chr16 | 89713739 | - | 0.006304028 | 0.99369603 |
| ENST00000344429 | ENST00000397901 | NOVA1 | chr14 | 26941526 | - | CHMP1A | chr16 | 89713739 | - | 0.005849456 | 0.99415046 |
| ENST00000344429 | ENST00000535997 | NOVA1 | chr14 | 26941526 | - | CHMP1A | chr16 | 89713739 | - | 0.005955234 | 0.99404484 |
| ENST00000344429 | ENST00000550102 | NOVA1 | chr14 | 26941526 | - | CHMP1A | chr16 | 89713739 | - | 0.003256235 | 0.9967437 |
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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 >59795_59795_1_NOVA1-CHMP1A_NOVA1_chr14_26941526_ENST00000344429_CHMP1A_chr16_89713739_ENST00000397901_length(amino acids)=285AA_BP=172 MMAAAPIQQNGTHTGVPIDLDPPDSRKRPLEAPPEAGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKD FYPGTTERVCLIQGTVEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRIKQTLPSSPTTTKSSPSDPMTTSRANQVTKNMAQ VTKALDKALSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATTLTTPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVR -------------------------------------------------------------- >59795_59795_2_NOVA1-CHMP1A_NOVA1_chr14_26941526_ENST00000344429_CHMP1A_chr16_89713739_ENST00000535997_length(amino acids)=285AA_BP=172 MMAAAPIQQNGTHTGVPIDLDPPDSRKRPLEAPPEAGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKD FYPGTTERVCLIQGTVEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRIKQTLPSSPTTTKSSPSDPMTTSRANQVTKNMAQ VTKALDKALSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATTLTTPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVR -------------------------------------------------------------- >59795_59795_3_NOVA1-CHMP1A_NOVA1_chr14_26941526_ENST00000344429_CHMP1A_chr16_89713739_ENST00000550102_length(amino acids)=285AA_BP=172 MMAAAPIQQNGTHTGVPIDLDPPDSRKRPLEAPPEAGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKD FYPGTTERVCLIQGTVEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRIKQTLPSSPTTTKSSPSDPMTTSRANQVTKNMAQ VTKALDKALSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATTLTTPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVR -------------------------------------------------------------- >59795_59795_4_NOVA1-CHMP1A_NOVA1_chr14_26941526_ENST00000539517_CHMP1A_chr16_89713739_ENST00000397901_length(amino acids)=285AA_BP=172 MMAAAPIQQNGTHTGVPIDLDPPDSRKRPLEAPPEAGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKD FYPGTTERVCLIQGTVEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRIKQTLPSSPTTTKSSPSDPMTTSRANQVTKNMAQ VTKALDKALSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATTLTTPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVR -------------------------------------------------------------- >59795_59795_5_NOVA1-CHMP1A_NOVA1_chr14_26941526_ENST00000539517_CHMP1A_chr16_89713739_ENST00000535997_length(amino acids)=285AA_BP=172 MMAAAPIQQNGTHTGVPIDLDPPDSRKRPLEAPPEAGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKD FYPGTTERVCLIQGTVEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRIKQTLPSSPTTTKSSPSDPMTTSRANQVTKNMAQ VTKALDKALSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATTLTTPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVR -------------------------------------------------------------- >59795_59795_6_NOVA1-CHMP1A_NOVA1_chr14_26941526_ENST00000539517_CHMP1A_chr16_89713739_ENST00000550102_length(amino acids)=285AA_BP=172 MMAAAPIQQNGTHTGVPIDLDPPDSRKRPLEAPPEAGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKD FYPGTTERVCLIQGTVEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRIKQTLPSSPTTTKSSPSDPMTTSRANQVTKNMAQ VTKALDKALSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATTLTTPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVR -------------------------------------------------------------- |
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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/chr14:26941526/chr16:89713739) - 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 |
| NOVA1 | CHMP1A |
| FUNCTION: May regulate RNA splicing or metabolism in a specific subset of developing neurons. | FUNCTION: Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. Involved in cytokinesis. Involved in recruiting VPS4A and/or VPS4B to the midbody of dividing cells. May also be involved in chromosome condensation. Targets the Polycomb group (PcG) protein BMI1/PCGF4 to regions of condensed chromatin. May play a role in stable cell cycle progression and in PcG gene silencing. {ECO:0000269|PubMed:11559747, ECO:0000269|PubMed:11559748, ECO:0000269|PubMed:19129479, ECO:0000269|PubMed:23045692}. |
| 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 | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000344429 | - | 4 | 5 | 49_116 | 173.0 | 182.0 | Domain | KH 1 |
| Hgene | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000539517 | - | 4 | 5 | 49_116 | 173.0 | 508.0 | Domain | KH 1 |
| Hgene | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000344429 | - | 4 | 5 | 27_43 | 173.0 | 182.0 | Motif | Bipartite nuclear localization signal |
| Hgene | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000539517 | - | 4 | 5 | 27_43 | 173.0 | 508.0 | Motif | Bipartite nuclear localization signal |
| Tgene | CHMP1A | chr14:26941526 | chr16:89713739 | ENST00000397901 | 3 | 7 | 102_124 | 84.0 | 197.0 | Coiled coil | Ontology_term=ECO:0000255 | |
| Tgene | CHMP1A | chr14:26941526 | chr16:89713739 | ENST00000397901 | 3 | 7 | 185_195 | 84.0 | 197.0 | Motif | Note=MIT-interacting motif |
| - 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 | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000344429 | - | 4 | 5 | 273_409 | 173.0 | 182.0 | Compositional bias | Note=Ala-rich |
| Hgene | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000465357 | - | 1 | 4 | 273_409 | 0 | 484.0 | Compositional bias | Note=Ala-rich |
| Hgene | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000539517 | - | 4 | 5 | 273_409 | 173.0 | 508.0 | Compositional bias | Note=Ala-rich |
| Hgene | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000344429 | - | 4 | 5 | 171_237 | 173.0 | 182.0 | Domain | KH 2 |
| Hgene | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000344429 | - | 4 | 5 | 421_488 | 173.0 | 182.0 | Domain | KH 3 |
| Hgene | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000465357 | - | 1 | 4 | 171_237 | 0 | 484.0 | Domain | KH 2 |
| Hgene | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000465357 | - | 1 | 4 | 421_488 | 0 | 484.0 | Domain | KH 3 |
| Hgene | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000465357 | - | 1 | 4 | 49_116 | 0 | 484.0 | Domain | KH 1 |
| Hgene | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000539517 | - | 4 | 5 | 171_237 | 173.0 | 508.0 | Domain | KH 2 |
| Hgene | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000539517 | - | 4 | 5 | 421_488 | 173.0 | 508.0 | Domain | KH 3 |
| Hgene | NOVA1 | chr14:26941526 | chr16:89713739 | ENST00000465357 | - | 1 | 4 | 27_43 | 0 | 484.0 | Motif | Bipartite nuclear localization signal |
| Tgene | CHMP1A | chr14:26941526 | chr16:89713739 | ENST00000397901 | 3 | 7 | 5_47 | 84.0 | 197.0 | Coiled coil | Ontology_term=ECO:0000255 |
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Fusion Protein Structures |
| PDB and CIF files of the predicted 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. |
| Fusion protein PDB link (fusion AA seq ID in FusionPDB) | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | AA seq | Len(AA seq) |
| PDB file >>>498_NOVA1_26941526_CHMP1A_89713739_ranked_0.pdb | NOVA1 | 26941526 | 26941526 | ENST00000550102 | CHMP1A | chr16 | 89713739 | - | MMAAAPIQQNGTHTGVPIDLDPPDSRKRPLEAPPEAGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKD FYPGTTERVCLIQGTVEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRIKQTLPSSPTTTKSSPSDPMTTSRANQVTKNMAQ VTKALDKALSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATTLTTPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVR | 285 |
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pLDDT score distribution |
| pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
NOVA1_pLDDT.png  |
CHMP1A_pLDDT.png  |
| pLDDT score distribution of the predicted fusion protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
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Ramachandran Plot of 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. |
| Fusion AA seq ID in FusionPDB and their Ramachandran plots |
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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 |
| NOVA1 | |
| CHMP1A |
| - 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 NOVA1-CHMP1A |
| 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 NOVA1-CHMP1A |
| 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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