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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:CABIN1-SMARCB1 (FusionGDB2 ID:12239)

Fusion Gene Summary for CABIN1-SMARCB1

check button Fusion gene summary
Fusion gene informationFusion gene name: CABIN1-SMARCB1
Fusion gene ID: 12239
HgeneTgene
Gene symbol

CABIN1

SMARCB1

Gene ID

23523

6598

Gene namecalcineurin binding protein 1SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1
SynonymsCAIN|KB-318B8.7|PPP3INBAF47|CSS3|INI1|MRD15|PPP1R144|RDT|RTPS1|SNF5|SNF5L1|SWNTS1|Sfh1p|Snr1|hSNFS
Cytomap

22q11.23

22q11.23|22q11

Type of geneprotein-codingprotein-coding
Descriptioncalcineurin-binding protein cabin-1calcineurin binding protein cabin 1calcineurin inhibitorSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1BRG1-associated factor 47SNF5 homologSWI/SNF-related matrix-associated proteinhSNF5integrase interactor 1 proteinmalignant rhabdoid tumor suppressorprotein
Modification date2020031320200313
UniProtAcc

Q9Y6J0

.
Ensembl transtripts involved in fusion geneENST00000263119, ENST00000398319, 
ENST00000405822, ENST00000337989, 
ENST00000485008, 		ENST00000263121, 
ENST00000344921, ENST00000407082, 
ENST00000407422, ENST00000477836, 
Fusion gene scores* DoF score16 X 15 X 8=192011 X 12 X 6=792
# samples 1817
** MAII scorelog2(18/1920*10)=-3.41503749927884
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/792*10)=-2.21996568394191
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CABIN1 [Title/Abstract] AND SMARCB1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCABIN1(24408178)-SMARCB1(24175759), # samples:2
SMARCB1(24135875)-CABIN1(24560368), # samples:1
Anticipated loss of major functional domain due to fusion event.SMARCB1-CABIN1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
SMARCB1-CABIN1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
SMARCB1-CABIN1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
SMARCB1-CABIN1 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneCABIN1

GO:0006336

DNA replication-independent nucleosome assembly

14718166

TgeneSMARCB1

GO:0006337

nucleosome disassembly

8895581

TgeneSMARCB1

GO:0006338

chromatin remodeling

11726552

TgeneSMARCB1

GO:0039692

single stranded viral RNA replication via double stranded DNA intermediate

14963118

TgeneSMARCB1

GO:0045944

positive regulation of transcription by RNA polymerase II

11950834

TgeneSMARCB1

GO:0051091

positive regulation of DNA-binding transcription factor activity

11950834

TgeneSMARCB1

GO:1902661

positive regulation of glucose mediated signaling pathway

22368283


check buttonFusion gene breakpoints across CABIN1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across SMARCB1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChimerDB4OVTCGA-13-1405-01ACABIN1chr22

24407817

+SMARCB1chr22

24175759

+
ChimerDB4OVTCGA-13-1405-01ACABIN1chr22

24408178

-SMARCB1chr22

24175759

+
ChimerDB4OVTCGA-13-1405-01ACABIN1chr22

24408178

+SMARCB1chr22

24175759

+


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Fusion Gene ORF analysis for CABIN1-SMARCB1

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
5UTR-3CDSENST00000263119ENST00000263121CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
5UTR-3CDSENST00000263119ENST00000344921CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
5UTR-3CDSENST00000263119ENST00000407082CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
5UTR-3CDSENST00000263119ENST00000407422CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
5UTR-3CDSENST00000398319ENST00000263121CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
5UTR-3CDSENST00000398319ENST00000344921CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
5UTR-3CDSENST00000398319ENST00000407082CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
5UTR-3CDSENST00000398319ENST00000407422CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
5UTR-3CDSENST00000405822ENST00000263121CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
5UTR-3CDSENST00000405822ENST00000344921CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
5UTR-3CDSENST00000405822ENST00000407082CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
5UTR-3CDSENST00000405822ENST00000407422CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
5UTR-intronENST00000263119ENST00000477836CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
5UTR-intronENST00000398319ENST00000477836CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
5UTR-intronENST00000405822ENST00000477836CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-3CDSENST00000263119ENST00000263121CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000263119ENST00000344921CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000263119ENST00000407082CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000263119ENST00000407422CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000337989ENST00000263121CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-3CDSENST00000337989ENST00000263121CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000337989ENST00000344921CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-3CDSENST00000337989ENST00000344921CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000337989ENST00000407082CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-3CDSENST00000337989ENST00000407082CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000337989ENST00000407422CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-3CDSENST00000337989ENST00000407422CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000398319ENST00000263121CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-3CDSENST00000398319ENST00000344921CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-3CDSENST00000398319ENST00000407082CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-3CDSENST00000398319ENST00000407422CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-3CDSENST00000405822ENST00000263121CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000405822ENST00000344921CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000405822ENST00000407082CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000405822ENST00000407422CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000485008ENST00000263121CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-3CDSENST00000485008ENST00000263121CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000485008ENST00000344921CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-3CDSENST00000485008ENST00000344921CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000485008ENST00000407082CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-3CDSENST00000485008ENST00000407082CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-3CDSENST00000485008ENST00000407422CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-3CDSENST00000485008ENST00000407422CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-intronENST00000263119ENST00000477836CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-intronENST00000337989ENST00000477836CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-intronENST00000337989ENST00000477836CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-intronENST00000398319ENST00000477836CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-intronENST00000405822ENST00000477836CABIN1chr22

24408178

+SMARCB1chr22

24175759

+
intron-intronENST00000485008ENST00000477836CABIN1chr22

24407817

+SMARCB1chr22

24175759

+
intron-intronENST00000485008ENST00000477836CABIN1chr22

24408178

+SMARCB1chr22

24175759

+

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 CABIN1-SMARCB1


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)
CABIN1chr2224408178+SMARCB1chr2224175758+0.063360320.9366397
CABIN1chr2224407817+SMARCB1chr2224175758+5.41E-070.9999994
CABIN1chr2224408178+SMARCB1chr2224175758+0.063360320.9366397
CABIN1chr2224407817+SMARCB1chr2224175758+5.41E-070.9999994

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

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 CABIN1-SMARCB1


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/:24408178/:24175759)
- 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
CABIN1

Q9Y6J0

.
FUNCTION: May be required for replication-independent chromatin assembly. May serve as a negative regulator of T-cell receptor (TCR) signaling via inhibition of calcineurin. Inhibition of activated calcineurin is dependent on both PKC and calcium signals. Acts as a negative regulator of p53/TP53 by keeping p53 in an inactive state on chromatin at promoters of a subset of it's target genes. {ECO:0000269|PubMed:14718166, ECO:0000269|PubMed:9655484}.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 CABIN1-SMARCB1


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 CABIN1-SMARCB1


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 CABIN1-SMARCB1


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 CABIN1-SMARCB1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource