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Fusion gene ID: 41498 |
FusionGeneSummary for VMP1_SMARCD2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: VMP1_SMARCD2 | Fusion gene ID: 41498 | Hgene | Tgene | Gene symbol | VMP1 | SMARCD2 | Gene ID | 81671 | 6603 |
| Gene name | vacuole membrane protein 1 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 | |
| Synonyms | EPG3|TANGO5|TMEM49 | BAF60B|CRACD2|PRO2451|Rsc6p|SGD2 | |
| Cytomap | 17q23.1 | 17q23.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | vacuole membrane protein 1ectopic P-granules autophagy protein 3 homologtransmembrane protein 49transport and golgi organization 5 homolog | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 260 kDa BRG-1/Brm-associated factor subunit BBRG1-associated factor 60BSWI/SNF complex 60 kDa subunit BSwp73-like proteinchromatin remodeling complex BAF60B s | |
| Modification date | 20180523 | 20180519 | |
| UniProtAcc | Q96GC9 | Q92925 | |
| Ensembl transtripts involved in fusion gene | ENST00000262291, ENST00000537567, ENST00000539763, ENST00000536180, ENST00000545362, ENST00000588617, | ENST00000448276, ENST00000323347, ENST00000225742, | |
| Fusion gene scores | * DoF score | 19 X 10 X 9=1710 | 3 X 3 X 2=18 |
| # samples | 18 | 3 | |
| ** MAII score | log2(18/1710*10)=-3.24792751344359 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: VMP1 [Title/Abstract] AND SMARCD2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * 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 | SMARCD2 | GO:0006337 | nucleosome disassembly | 8895581 |
| Tgene | SMARCD2 | GO:0006338 | chromatin remodeling | 11726552 |
| 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 | LD | BRCA | TCGA-AO-A12C-01A | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| * 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 | ENST00000262291 | ENST00000448276 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| Frame-shift | ENST00000262291 | ENST00000323347 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| Frame-shift | ENST00000262291 | ENST00000225742 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| 5UTR-3CDS | ENST00000537567 | ENST00000448276 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| 5UTR-3CDS | ENST00000537567 | ENST00000323347 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| 5UTR-3CDS | ENST00000537567 | ENST00000225742 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| 5UTR-3CDS | ENST00000539763 | ENST00000448276 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| 5UTR-3CDS | ENST00000539763 | ENST00000323347 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| 5UTR-3CDS | ENST00000539763 | ENST00000225742 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| 5UTR-3CDS | ENST00000536180 | ENST00000448276 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| 5UTR-3CDS | ENST00000536180 | ENST00000323347 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| 5UTR-3CDS | ENST00000536180 | ENST00000225742 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| Frame-shift | ENST00000545362 | ENST00000448276 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| Frame-shift | ENST00000545362 | ENST00000323347 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| Frame-shift | ENST00000545362 | ENST00000225742 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| intron-3CDS | ENST00000588617 | ENST00000448276 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| intron-3CDS | ENST00000588617 | ENST00000323347 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
| intron-3CDS | ENST00000588617 | ENST00000225742 | VMP1 | chr17 | 57808883 | + | SMARCD2 | chr17 | 61910351 | - |
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FusionProtFeatures for VMP1_SMARCD2 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| VMP1 | SMARCD2 |
| Stress-induced protein that, when overexpressed,promotes formation of intracellular vacuoles followed by celldeath. May be involved in the cytoplasmic vacuolization of acinarcells during the early stage of acute pancreatitis. Plays a rolein the initial stages of the autophagic process through itsinteraction with BECN1 (By similarity). Involved in cell-celladhesion. Plays an essential role in formation of cell junctions.{ECO:0000250, ECO:0000269|PubMed:17724469}. | Involved in transcriptional activation and repression ofselect genes by chromatin remodeling (alteration of DNA-nucleosometopology). Component of SWI/SNF chromatin remodeling complexesthat carry out key enzymatic activities, changing chromatinstructure by altering DNA-histone contacts within a nucleosome inan ATP-dependent manner (PubMed:22952240, PubMed:26601204).Critical regulator of myeloid differentiation, controllinggranulocytopoiesis and the expression of genes involved inneutrophil granule formation (PubMed:28369036).{ECO:0000269|PubMed:28369036, ECO:0000303|PubMed:22952240,ECO:0000303|PubMed:26601204}. |
| 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 VMP1_SMARCD2 |
| 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 VMP1_SMARCD2 |
| 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 |
| VMP1 | HGS, ELAVL1, TJP1, KLK11, LPAR6, ERGIC3, FAF2, KRAS, TCTN2, TCTN3, TMEM216, DPEP1, CDH13, MAS1, LMNA | SMARCD2 | XRN1, BRCA1, TP53, TP63, TP73, SMARCA4, SMARCA2, UNKL, SMARCAD1, SMARCC2, SMARCE1, SMARCD1, CUL3, SMARCB1, ARID1A, SMARCC1, BAZ1B, TOP2B, KYNU, RBBP5, NUDCD2, BPTF, SIRT1, NOTCH2NL, RNF2, BMI1, QPRT, DPF3, NUP50, DPF2, SS18, NTRK1, ACTL6A, ARID1B, BCL7A, BCL7B, BCL7C, MDC1, TBL1X, TBL1XR1, UPF2, PCM1, KPNA1, PTPN1, NUP153, SAMHD1, NFATC1, NFATC2, RELB, TEX13A, FANCA, 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 VMP1_SMARCD2 |
| 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 VMP1_SMARCD2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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