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Fusion gene ID: 22612 |
FusionGeneSummary for MSH3_RASGEF1C |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: MSH3_RASGEF1C | Fusion gene ID: 22612 | Hgene | Tgene | Gene symbol | MSH3 | RASGEF1C | Gene ID | 4437 | 255426 |
| Gene name | mutS homolog 3 | RasGEF domain family member 1C | |
| Synonyms | DUP|FAP4|MRP1 | - | |
| Cytomap | 5q14.1 | 5q35.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | DNA mismatch repair protein Msh3divergent upstream proteinhMSH3mismatch repair protein 1 | ras-GEF domain-containing family member 1C | |
| Modification date | 20180523 | 20180519 | |
| UniProtAcc | P20585 | Q8N431 | |
| Ensembl transtripts involved in fusion gene | ENST00000265081, ENST00000512258, | ENST00000361132, ENST00000393371, ENST00000522500, ENST00000519883, | |
| Fusion gene scores | * DoF score | 2 X 3 X 2=12 | 5 X 3 X 4=60 |
| # samples | 3 | 5 | |
| ** MAII score | log2(3/12*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(5/60*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: MSH3 [Title/Abstract] AND RASGEF1C [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | DDR (DNA damage repair) gene involved fusion gene, retained protein feature but frameshift. | ||
| * 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 | MSH3 | GO:0006281 | DNA repair | 8942985 |
| Hgene | MSH3 | GO:0045910 | negative regulation of DNA recombination | 17715146 |
| Hgene | MSH3 | GO:0051096 | positive regulation of helicase activity | 17715146 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * 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. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| TCGA | RV | LGG | TCGA-HT-A614-01A | MSH3 | chr5 | 79952350 | + | RASGEF1C | chr5 | 179555610 | - |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| Frame-shift | ENST00000265081 | ENST00000361132 | MSH3 | chr5 | 79952350 | + | RASGEF1C | chr5 | 179555610 | - |
| Frame-shift | ENST00000265081 | ENST00000393371 | MSH3 | chr5 | 79952350 | + | RASGEF1C | chr5 | 179555610 | - |
| 5CDS-5UTR | ENST00000265081 | ENST00000522500 | MSH3 | chr5 | 79952350 | + | RASGEF1C | chr5 | 179555610 | - |
| 5CDS-5UTR | ENST00000265081 | ENST00000519883 | MSH3 | chr5 | 79952350 | + | RASGEF1C | chr5 | 179555610 | - |
| intron-3CDS | ENST00000512258 | ENST00000361132 | MSH3 | chr5 | 79952350 | + | RASGEF1C | chr5 | 179555610 | - |
| intron-3CDS | ENST00000512258 | ENST00000393371 | MSH3 | chr5 | 79952350 | + | RASGEF1C | chr5 | 179555610 | - |
| intron-5UTR | ENST00000512258 | ENST00000522500 | MSH3 | chr5 | 79952350 | + | RASGEF1C | chr5 | 179555610 | - |
| intron-5UTR | ENST00000512258 | ENST00000519883 | MSH3 | chr5 | 79952350 | + | RASGEF1C | chr5 | 179555610 | - |
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FusionProtFeatures for MSH3_RASGEF1C |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| MSH3 | RASGEF1C |
| Component of the post-replicative DNA mismatch repairsystem (MMR). Heterodimerizes with MSH2 to form MutS beta whichbinds to DNA mismatches thereby initiating DNA repair. When bound,the MutS beta heterodimer bends the DNA helix and shieldsapproximately 20 base pairs. MutS beta recognizes large insertion-deletion loops (IDL) up to 13 nucleotides long. After mismatchbinding, forms a ternary complex with the MutL alpha heterodimer,which is thought to be responsible for directing the downstreamMMR events, including strand discrimination, excision, andresynthesis. | Guanine nucleotide exchange factor (GEF). {ECO:0000250}. |
| 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. |
| - In-frame and 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 |
| - In-frame and 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 |
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FusionGeneSequence for MSH3_RASGEF1C |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for MSH3_RASGEF1C |
| 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 (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| MSH3 | BRCA1, BARD1, MSH2, PCNA, EXO1, SLX4, MLH1, PMS2, XPA, RPA4, MYC, SMARCAD1, HUS1, RAD1, RAD9A, MSH6, KATNB1, OTUD7B, ORAOV1, RPA1, RCHY1, RPA2, RPA3, KARS, SNX8, NTRK1, CDC42, IKBKG, ZSCAN26, FOXA1, TSC22D2, APLF, LMO2, SLC39A9, HDAC6, UHRF2, MCM9 | RASGEF1C | TERF1, TERF2, POT1, S100A7A, TRIM25 |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for MSH3_RASGEF1C |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for MSH3_RASGEF1C |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | MSH3 | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
| Hgene | MSH3 | C0152013 | Adenocarcinoma of lung (disorder) | 1 | CTD_human |
| Hgene | MSH3 | C0920269 | Microsatellite Instability | 1 | CTD_human |
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