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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:CARM1-SMARCA4 (FusionGDB2 ID:HG10498TG6597)

Fusion Gene Summary for CARM1-SMARCA4

check button Fusion gene summary
Fusion gene informationFusion gene name: CARM1-SMARCA4
Fusion gene ID: hg10498tg6597
HgeneTgene
Gene symbol

CARM1

SMARCA4

Gene ID

10498

6597

Gene namecoactivator associated arginine methyltransferase 1SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
SynonymsPRMT4BAF190|BAF190A|BRG1|CSS4|MRD16|RTPS2|SNF2|SNF2-beta|SNF2L4|SNF2LB|SWI2|hSNF2b
Cytomap('CARM1')('SMARCA4')

19p13.2

19p13.2

Type of geneprotein-codingprotein-coding
Descriptionhistone-arginine methyltransferase CARM1protein arginine N-methyltransferase 4transcription activator BRG1ATP-dependent helicase SMARCA4BRG1-associated factor 190ABRM/SWI2-related gene 1SNF2-like 4brahma protein-like 1global transcription activator homologous sequencehomeotic gene regulatormitotic growth and transcription a
Modification date2020031320200315
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000327064, ENST00000344150, 
ENST00000327064, ENST00000344150, 
Fusion gene scores* DoF score14 X 10 X 10=140020 X 28 X 15=8400
# samples 2032
** MAII scorelog2(20/1400*10)=-2.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(32/8400*10)=-4.71424551766612
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]

Most frequent breakpointCARM1(11031803)-SMARCA4(11172460), # samples:2
Anticipated loss of major functional domain due to fusion event.SMARCA4-CARM1 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.
SMARCA4-CARM1 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.
SMARCA4-CARM1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
SMARCA4-CARM1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
SMARCA4-CARM1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
SMARCA4-CARM1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
SMARCA4-CARM1 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
SMARCA4-CARM1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
SMARCA4-CARM1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CARM1-SMARCA4 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
CARM1-SMARCA4 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CARM1-SMARCA4 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CARM1-SMARCA4 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
CARM1-SMARCA4 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
CARM1-SMARCA4 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CARM1-SMARCA4 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneCARM1

GO:0016571

histone methylation

19405910

TgeneSMARCA4

GO:0006337

nucleosome disassembly

8895581

TgeneSMARCA4

GO:0006338

chromatin remodeling

10943845|11726552

TgeneSMARCA4

GO:0045892

negative regulation of transcription, DNA-templated

12065415

TgeneSMARCA4

GO:0045944

positive regulation of transcription by RNA polymerase II

15774904|17938176

TgeneSMARCA4

GO:0051091

positive regulation of DNA-binding transcription factor activity

11950834|17938176

TgeneSMARCA4

GO:1902661

positive regulation of glucose mediated signaling pathway

22368283



check button Fusion gene information
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4BRCATCGA-AR-A0TU-01ACARM1chr19

11031803

+SMARCA4chr19

11172460

+
ChimerDB4ESCATCGA-LN-A49OCARM1chr19

11019883

+SMARCA4chr19

11094796

+


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Fusion Gene ORF analysis for CARM1-SMARCA4

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-5UTRENST00000327064ENST00000344626CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-5UTRENST00000327064ENST00000358026CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-5UTRENST00000327064ENST00000429416CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-5UTRENST00000327064ENST00000444061CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-5UTRENST00000327064ENST00000541122CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-5UTRENST00000327064ENST00000589677CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-5UTRENST00000327064ENST00000590574CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-5UTRENST00000344150ENST00000344626CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-5UTRENST00000344150ENST00000358026CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-5UTRENST00000344150ENST00000429416CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-5UTRENST00000344150ENST00000444061CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-5UTRENST00000344150ENST00000541122CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-5UTRENST00000344150ENST00000589677CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-5UTRENST00000344150ENST00000590574CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-intronENST00000327064ENST00000413806CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-intronENST00000327064ENST00000450717CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-intronENST00000327064ENST00000538456CARM1chr19

11031803

+SMARCA4chr19

11172460

+
5CDS-intronENST00000327064ENST00000538456CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-intronENST00000344150ENST00000413806CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-intronENST00000344150ENST00000450717CARM1chr19

11019883

+SMARCA4chr19

11094796

+
5CDS-intronENST00000344150ENST00000538456CARM1chr19

11031803

+SMARCA4chr19

11172460

+
5CDS-intronENST00000344150ENST00000538456CARM1chr19

11019883

+SMARCA4chr19

11094796

+
Frame-shiftENST00000327064ENST00000344626CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000327064ENST00000358026CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000327064ENST00000413806CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000327064ENST00000429416CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000327064ENST00000444061CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000327064ENST00000450717CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000327064ENST00000541122CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000327064ENST00000589677CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000327064ENST00000590574CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000344150ENST00000344626CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000344150ENST00000358026CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000344150ENST00000413806CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000344150ENST00000429416CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000344150ENST00000444061CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000344150ENST00000450717CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000344150ENST00000541122CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000344150ENST00000589677CARM1chr19

11031803

+SMARCA4chr19

11172460

+
Frame-shiftENST00000344150ENST00000590574CARM1chr19

11031803

+SMARCA4chr19

11172460

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for CARM1-SMARCA4


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
CARM1chr1911031803+SMARCA4chr1911172459+0.069222720.9307773
CARM1chr1911019883+SMARCA4chr1911094799+8.11E-121
CARM1chr1911031803+SMARCA4chr1911172459+0.069222720.9307773
CARM1chr1911019883+SMARCA4chr1911094799+8.11E-121


check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for CARM1-SMARCA4


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:11031803/:11172460)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is 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, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is 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, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

check buttonRetention 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

download page


* 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for CARM1-SMARCA4


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for CARM1-SMARCA4


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for CARM1-SMARCA4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for CARM1-SMARCA4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCARM1C0030246Pustulosis of Palms and Soles1CTD_human
HgeneCARM1C0033860Psoriasis1CTD_human
TgeneC2750074Rhabdoid Tumor Predisposition Syndrome 27CLINGEN;CTD_human;GENOMICS_ENGLAND
TgeneC0262584Carcinoma, Small Cell4CTD_human
TgeneC0919267ovarian neoplasm4CGI;CTD_human
TgeneC1140680Malignant neoplasm of ovary4CGI;CTD_human
TgeneC0009405Hereditary Nonpolyposis Colorectal Neoplasms2CLINGEN
TgeneC1112155Hereditary non-polyposis colorectal cancer syndrome2CLINGEN
TgeneC1333990Hereditary Nonpolyposis Colorectal Cancer2CLINGEN
TgeneC1333991Hereditary Non-Polyposis Colon Cancer Type 22CLINGEN
TgeneC2936783Colorectal cancer, hereditary nonpolyposis, type 12CLINGEN
TgeneC2985524Rhabdoid tumor predisposition syndrome2ORPHANET
TgeneC0006413Burkitt Lymphoma1CTD_human
TgeneC0009171Cocaine Abuse1CTD_human
TgeneC0036920Sezary Syndrome1CTD_human
TgeneC0039981Thoracic Neoplasms1CTD_human
TgeneC0149925Small cell carcinoma of lung1CTD_human
TgeneC0205944Sarcoma, Epithelioid1CTD_human
TgeneC0205945Sarcoma, Spindle Cell1CTD_human
TgeneC0236736Cocaine-Related Disorders1CTD_human
TgeneC0265338Coffin-Siris syndrome1CTD_human;GENOMICS_ENGLAND
TgeneC0343640African Burkitt's lymphoma1CTD_human
TgeneC0600427Cocaine Dependence1CTD_human
TgeneC1261473Sarcoma1CTD_human
TgeneC1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1CTD_human
TgeneC2239246Endometrial stromal sarcoma, high grade1GENOMICS_ENGLAND
TgeneC3281201MENTAL RETARDATION, AUTOSOMAL DOMINANT 121GENOMICS_ENGLAND
TgeneC3553249COFFIN-SIRIS SYNDROME 41GENOMICS_ENGLAND;UNIPROT
TgeneC4721444Burkitt Leukemia1CTD_human