|
||||||
|
 | |
| |
| |
| |
| |
|
Fusion gene ID: 34838 |
FusionGeneSummary for SMARCD1_ATP2C2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SMARCD1_ATP2C2 | Fusion gene ID: 34838 | Hgene | Tgene | Gene symbol | SMARCD1 | ATP2C2 | Gene ID | 6602 | 9914 |
| Gene name | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 | ATPase secretory pathway Ca2+ transporting 2 | |
| Synonyms | BAF60A|CRACD1|Rsc6p | SPCA2 | |
| Cytomap | 12q13.12 | 16q24.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 160 kDa BRG-1/Brm-associated factor subunit ABRG1-associated factor 60ASWI/SNF complex 60 kDa subunit ASwp73-like proteinchromatin remodeling complex BAF60A s | calcium-transporting ATPase type 2C member 2ATPase 2C2ATPase, Ca++ transporting, type 2C, member 2secretory pathway Ca(2+)-ATPase 2secretory pathway calcium ATPase 2 | |
| Modification date | 20180522 | 20180523 | |
| UniProtAcc | Q96GM5 | O75185 | |
| Ensembl transtripts involved in fusion gene | ENST00000394963, ENST00000381513, ENST00000548573, ENST00000549526, | ENST00000262429, ENST00000416219, ENST00000420010, | |
| Fusion gene scores | * DoF score | 1 X 1 X 1=1 | 3 X 5 X 2=30 |
| # samples | 1 | 5 | |
| ** MAII score | log2(1/1*10)=3.32192809488736 | log2(5/30*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: SMARCD1 [Title/Abstract] AND ATP2C2 [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 |
| Hgene | SMARCD1 | GO:0006337 | nucleosome disassembly | 8895581 |
| Hgene | SMARCD1 | 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 |
| ChiTaRS3.1 | AW389291 | SMARCD1 | chr12 | 50484310 | + | ATP2C2 | chr16 | 84456272 | + |
| * 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-shit | ENST00000394963 | ENST00000262429 | SMARCD1 | chr12 | 50484310 | + | ATP2C2 | chr16 | 84456272 | + |
| Frame-shit | ENST00000394963 | ENST00000416219 | SMARCD1 | chr12 | 50484310 | + | ATP2C2 | chr16 | 84456272 | + |
| 5CDS-3UTR | ENST00000394963 | ENST00000420010 | SMARCD1 | chr12 | 50484310 | + | ATP2C2 | chr16 | 84456272 | + |
| Frame-shit | ENST00000381513 | ENST00000262429 | SMARCD1 | chr12 | 50484310 | + | ATP2C2 | chr16 | 84456272 | + |
| Frame-shit | ENST00000381513 | ENST00000416219 | SMARCD1 | chr12 | 50484310 | + | ATP2C2 | chr16 | 84456272 | + |
| 5CDS-3UTR | ENST00000381513 | ENST00000420010 | SMARCD1 | chr12 | 50484310 | + | ATP2C2 | chr16 | 84456272 | + |
| Frame-shit | ENST00000548573 | ENST00000262429 | SMARCD1 | chr12 | 50484310 | + | ATP2C2 | chr16 | 84456272 | + |
| Frame-shit | ENST00000548573 | ENST00000416219 | SMARCD1 | chr12 | 50484310 | + | ATP2C2 | chr16 | 84456272 | + |
| 5CDS-3UTR | ENST00000548573 | ENST00000420010 | SMARCD1 | chr12 | 50484310 | + | ATP2C2 | chr16 | 84456272 | + |
| intron-3CDS | ENST00000549526 | ENST00000262429 | SMARCD1 | chr12 | 50484310 | + | ATP2C2 | chr16 | 84456272 | + |
| intron-3CDS | ENST00000549526 | ENST00000416219 | SMARCD1 | chr12 | 50484310 | + | ATP2C2 | chr16 | 84456272 | + |
| intron-3UTR | ENST00000549526 | ENST00000420010 | SMARCD1 | chr12 | 50484310 | + | ATP2C2 | chr16 | 84456272 | + |
Top |
FusionProtFeatures for SMARCD1_ATP2C2 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SMARCD1 | ATP2C2 |
| 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:8804307). Belongs to the neuralprogenitors-specific chromatin remodeling complex (npBAF complex)and the neuron-specific chromatin remodeling complex (nBAFcomplex). During neural development a switch from astem/progenitor to a postmitotic chromatin remodeling mechanismoccurs as neurons exit the cell cycle and become committed totheir adult state. The transition from proliferating neuralstem/progenitor cells to postmitotic neurons requires a switch insubunit composition of the npBAF and nBAF complexes. As neuralprogenitors exit mitosis and differentiate into neurons, npBAFcomplexes which contain ACTL6A/BAF53A and PHF10/BAF45A, areexchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45Bor DPF3/BAF45C subunits in neuron-specific complexes (nBAF). ThenpBAF complex is essential for the self-renewal/proliferativecapacity of the multipotent neural stem cells. The nBAF complexalong with CREST plays a role regulating the activity of genesessential for dendrite growth (By similarity). Has a stronginfluence on vitamin D-mediated transcriptional activity from anenhancer vitamin D receptor element (VDRE). May be a link betweenmammalian SWI-SNF-like chromatin remodeling complexes and thevitamin D receptor (VDR) heterodimer (PubMed:14698202). Mediatescritical interactions between nuclear receptors and theBRG1/SMARCA4 chromatin-remodeling complex for transactivation(PubMed:12917342). {ECO:0000250|UniProtKB:Q61466,ECO:0000269|PubMed:12917342, ECO:0000269|PubMed:14698202,ECO:0000269|PubMed:8804307, ECO:0000303|PubMed:22952240,ECO:0000303|PubMed:26601204}. | This magnesium-dependent enzyme catalyzes the hydrolysisof ATP coupled with the transport of calcium. {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 |
Top |
FusionGeneSequence for SMARCD1_ATP2C2 |
| 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). |
Top |
FusionGenePPI for SMARCD1_ATP2C2 |
| 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 |
| - 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 |
Top |
RelatedDrugs for SMARCD1_ATP2C2 |
| 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 |
Top |
RelatedDiseases for SMARCD1_ATP2C2 |
| 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)
|