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Fusion gene ID: 5547 |
FusionGeneSummary for CARM1_SMARCA4 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CARM1_SMARCA4 | Fusion gene ID: 5547 | Hgene | Tgene | Gene symbol | CARM1 | SMARCA4 | Gene ID | 10498 | 6597 |
| Gene name | coactivator associated arginine methyltransferase 1 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 | |
| Synonyms | PRMT4 | BAF190|BAF190A|BRG1|CSS4|MRD16|RTPS2|SNF2|SNF2L4|SNF2LB|SWI2|hSNF2b | |
| Cytomap | 19p13.2 | 19p13.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | histone-arginine methyltransferase CARM1protein arginine N-methyltransferase 4 | transcription activator BRG1ATP-dependent helicase SMARCA4BRG1-associated factor 190ABRM/SWI2-related gene 1SNF2-betaSNF2-like 4brahma protein-like 1global transcription activator homologous sequencehomeotic gene regulatormitotic growth and trans | |
| Modification date | 20180527 | 20180523 | |
| UniProtAcc | Q86X55 | P51532 | |
| Ensembl transtripts involved in fusion gene | ENST00000327064, ENST00000344150, | ENST00000358026, ENST00000344626, ENST00000429416, ENST00000541122, ENST00000589677, ENST00000444061, ENST00000590574, ENST00000413806, ENST00000450717, ENST00000538456, | |
| Fusion gene scores | * DoF score | 9 X 5 X 9=405 | 12 X 14 X 8=1344 |
| # samples | 11 | 15 | |
| ** MAII score | log2(11/405*10)=-1.88041838424733 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(15/1344*10)=-3.16349873228288 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: CARM1 [Title/Abstract] AND SMARCA4 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | Tumor suppressor gene involved fusion gene, in-frame but not retained their domain. Tumor suppressor gene involved fusion gene, retained protein feature but frameshift. DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain. DDR (DNA damage repair) gene involved fusion gene, retained protein feature but frameshift. Transcription factor involved fusion gene, inframe and retained DNA-binding domain. | ||
| * 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 | CARM1 | GO:0016571 | histone methylation | 19405910 |
| Tgene | SMARCA4 | GO:0006337 | nucleosome disassembly | 8895581 |
| Tgene | SMARCA4 | GO:0006338 | chromatin remodeling | 10943845|11726552 |
| Tgene | SMARCA4 | GO:0045892 | negative regulation of transcription, DNA-templated | 12065415 |
| Tgene | SMARCA4 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 15774904|17938176 |
| Tgene | SMARCA4 | GO:0051091 | positive regulation of DNA binding transcription factor activity | 11950834|17938176 |
| Tgene | SMARCA4 | GO:1902661 | positive regulation of glucose mediated signaling pathway | 22368283 |
| 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-AR-A0TU-01A | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| * 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 | ENST00000327064 | ENST00000358026 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000327064 | ENST00000344626 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000327064 | ENST00000429416 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000327064 | ENST00000541122 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000327064 | ENST00000589677 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000327064 | ENST00000444061 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000327064 | ENST00000590574 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000327064 | ENST00000413806 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000327064 | ENST00000450717 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| 5CDS-intron | ENST00000327064 | ENST00000538456 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000344150 | ENST00000358026 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000344150 | ENST00000344626 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000344150 | ENST00000429416 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000344150 | ENST00000541122 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000344150 | ENST00000589677 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000344150 | ENST00000444061 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000344150 | ENST00000590574 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000344150 | ENST00000413806 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| Frame-shift | ENST00000344150 | ENST00000450717 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
| 5CDS-intron | ENST00000344150 | ENST00000538456 | CARM1 | chr19 | 11031803 | + | SMARCA4 | chr19 | 11172460 | + |
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FusionProtFeatures for CARM1_SMARCA4 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| CARM1 | SMARCA4 |
| Methylates (mono- and asymmetric dimethylation) theguanidino nitrogens of arginyl residues in several proteinsinvolved in DNA packaging, transcription regulation, pre-mRNAsplicing, and mRNA stability. Recruited to promoters upon geneactivation together with histone acetyltransferases fromEP300/P300 and p160 families, methylates histone H3 at 'Arg-17'(H3R17me), forming mainly asymmetric dimethylarginine (H3R17me2a),leading to activate transcription via chromatin remodeling. Duringnuclear hormone receptor activation and TCF7L2/TCF4 activation,acts synergically with EP300/P300 and either one of the p160histone acetyltransferases NCOA1/SRC1, NCOA2/GRIP1 and NCOA3/ACTRor CTNNB1/beta-catenin to activate transcription. During myogenictranscriptional activation, acts together with NCOA3/ACTR as acoactivator for MEF2C. During monocyte inflammatory stimulation,acts together with EP300/P300 as a coactivator for NF-kappa-B.Acts as coactivator for PPARG, promotes adipocyte differentiationand the accumulation of brown fat tissue. Plays a role in theregulation of pre-mRNA alternative splicing by methylation ofsplicing factors. Also seems to be involved in p53/TP53transcriptional activation. Methylates EP300/P300, both at 'Arg-2142', which may loosen its interaction with NCOA2/GRIP1, and at'Arg-580' and 'Arg-604' in the KIX domain, which impairs itsinteraction with CREB and inhibits CREB-dependent transcriptionalactivation. Also methylates arginine residues in RNA-bindingproteins PABPC1, ELAVL1 and ELAV4, which may affect their mRNA-stabilizing properties and the half-life of their target mRNAs.{ECO:0000269|PubMed:16497732, ECO:0000269|PubMed:19405910}. | 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. Component of the CREST-BRG1 complex, amultiprotein complex that regulates promoter activation byorchestrating the calcium-dependent release of a repressor complexand the recruitment of an activator complex. In resting neurons,transcription of the c-FOS promoter is inhibited by SMARCA4-dependent recruitment of a phospho-RB1-HDAC repressor complex.Upon calcium influx, RB1 is dephosphorylated by calcineurin, whichleads to release of the repressor complex. At the same time, thereis increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation.The CREST-BRG1 complex also binds to the NR2B promoter, andactivity-dependent induction of NR2B expression involves therelease of HDAC1 and recruitment of CREBBP. 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. SMARCA4/BAF190A may promote neuralstem cell self-renewal/proliferation by enhancing Notch-dependentproliferative signals, while concurrently making the neural stemcell insensitive to SHH-dependent differentiating cues (Bysimilarity). Acts as a corepressor of ZEB1 to regulate E-cadherintranscription and is required for induction of epithelial-mesenchymal transition (EMT) by ZEB1. Binds via DLX1 to enhancerslocated in the intergenic region between DLX5 and DLX6 and thisbinding is stabilized by the long non-coding RNA (lncRNA) Evf2 (Bysimilarity). Binds to RNA in a promiscuous manner (By similarity).Binding to RNAs including lncRNA Evf2 leads to inhibition ofSMARCA4 ATPase and chromatin remodeling activities (Bysimilarity). {ECO:0000250|UniProtKB:Q3TKT4,ECO:0000269|PubMed:19571879, ECO:0000269|PubMed:20418909,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 CARM1_SMARCA4 |
| 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 CARM1_SMARCA4 |
| 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 |
| CARM1 | TP53, PRMT1, PABPN1, MEF2D, MYOD1, MYOG, NRIP1, NCOA3, CREBBP, HIST1H3A, EP300, NCOA2, RELA, SRCAP, CREB1, FOS, NCOA1, GRIP1, CTNNB1, MYC, STAT5A, PARP1, NR1H4, ARID1A, SMARCA4, SMARCC2, SMARCC1, NFKB1, SMARCE1, SMARCB1, ACTB, SMARCD1, H3F3A, CEBPB, TERF2, WDR5, AXIN1, AFF1, IRF4, ELAVL1, CUL3, CUL5, CUL2, CUL1, COPS5, CAND1, RABGAP1, TP63, METTL21C, HNRNPA1, DNAJA3, NUDT21, QKI, DAXX, MALT1, PYGO1, SPAG8, UBE2I, FAF1, SUPT5H, HSPH1, ILK, PARVA, PPAT, UGP2, XPO7, DROSHA, TNRC6B, CACYBP, NUDCD3, KAT2B, KIAA1191, NECAP2, HEY2, CNN3, FOSL2, TICAM1, IL36A, TEX33, FASN, HNRNPK, PXDNL, SNRPC, CTBP1, NTRK1, KRAS, IFI16, DZIP3, MTMR14, MTMR6, MTMR8, HRSP12, CEP170B, KIAA1683, ALDOA, GTSE1, SH3BP5L, KIF16B, MED9, RBM4, HN1L, ETV4, WDR4, ARFGAP1, PRCC, DGCR14, C1orf94, RAB39B, RAB11A, ATP6V1G1, VASN, BRCA1, ESR1 | SMARCA4 | ESR1, FANCA, ARID1B, RELB, MYC, BRCA1, CTNNB1, NR3C1, SMARCD1, SMARCB1, POLR2A, SMARCC1, SIN3A, HDAC2, RBBP4, KLF1, GATA1, SP1, CCNE1, TP53, HSF1, PHB, RB1, AHR, STAT2, ARID1A, SMARCC2, SMARCE1, ACTL6A, STK11, CBX5, MED17, HSP90B1, NCOR2, NCOR1, ACTB, CREBBP, NCOA1, ING1, PABPN1, AR, ZMYND8, TAF10, PMS2, MYOD1, SMARCA2, JUNB, LMNB1, SRF, MYOCD, CDKN2A, SS18L1, HDAC1, HDAC3, CDYL, ADD1, NR4A2, MCPH1, REST, DDX5, H2AFX, NFE2L2, BCL7C, BRD7, PAX6, CREB1, HSF4, CEBPA, CDX2, MYOG, MYEF2, ATF3, PRMT5, SMARCD2, SIN3B, CHD4, BRWD1, HNRNPC, STAT1, USF1, IRF1, RCOR1, CIITA, ZMIZ2, GMNN, NEUROG2, NEUROD1, NF1, PBX1, NR1H2, RXRA, HIF1A, STAT3, NONO, SMAD2, SMAD3, CARM1, ADNP, STAT5A, CEBPB, PML, MKL1, DPF2, NPM1, KPNA2, BCL7A, ZEB1, HDAC9, TOPBP1, TRIM28, RUNX1, WDR77, HIST1H3A, BCL6, CHD7, PBRM1, ARID2, MARK4, BRD4, WHSC1L1, SMARCAD1, MBD3, KLF4, CDK19, CDK8, MED6, SIRT7, ANGPTL4, ACTC1, SETD7, DPF3, PHF10, DPF1, CHFR, KDM6A, TBX5, SMARCD3, NR2C1, CUL3, COPS5, CAND1, HIST1H4F, HIST2H3C, HIST2H2BE, CHMP5, IKZF1, RBL1, RBL2, RPS6KA5, BAZ1B, TOP2B, CPSF2, SMARCA1, CAD, NOTCH1, RBPJ, MAML1, EPAS1, PPARG, MPP6, FBXO6, WWOX, OBSL1, EED, RNF2, BMI1, SS18, HSPB1, NTRK1, BYSL, EP400, HMGB1, MDC1, MYO18A, PELO, BCL7B, GTF3C3, NOP56, POLR3A, POLR3C, POLR3F, SMC3, UPF1, SCARNA22, MDM2, HIST1H3E, CAT, KPNA1, RAB5C, REEP5, VAPA, PARD6A, NEIL3, ATL2, PAPD5, GLI1, NFATC1, FOXE1, FOXO1, CDC5L, NFATC2, CHEK1, NCL, SPTA1, TRIM25, YAP1 |
| - 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 CARM1_SMARCA4 |
| 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 CARM1_SMARCA4 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | CARM1 | C0033860 | Psoriasis | 1 | CTD_human |
| Tgene | SMARCA4 | C0262584 | Carcinoma, Small Cell | 4 | CTD_human |
| Tgene | SMARCA4 | C0919267 | ovarian neoplasm | 4 | CTD_human |
| Tgene | SMARCA4 | C0006413 | Burkitt Lymphoma | 1 | CTD_human |
| Tgene | SMARCA4 | C0036920 | Sezary Syndrome | 1 | CTD_human |
| Tgene | SMARCA4 | C0039981 | Thoracic Neoplasms | 1 | CTD_human |
| Tgene | SMARCA4 | C0149925 | Small cell carcinoma of lung | 1 | CTD_human |
| Tgene | SMARCA4 | C0265338 | Coffin-Siris syndrome | 1 | CTD_human;ORPHANET |
| Tgene | SMARCA4 | C1261473 | Sarcoma | 1 | CTD_human |
| Tgene | SMARCA4 | C3553249 | MENTAL RETARDATION, AUTOSOMAL DOMINANT 16 | 1 | UNIPROT |
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