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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:SMARCA2-YWHAH (FusionGDB2 ID:83882)

Fusion Gene Summary for SMARCA2-YWHAH

check button Fusion gene summary
Fusion gene informationFusion gene name: SMARCA2-YWHAH
Fusion gene ID: 83882
HgeneTgene
Gene symbol

SMARCA2

YWHAH

Gene ID

6595

7533

Gene nameSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein eta
SynonymsBAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2aYWHA1
Cytomap

9p24.3

22q12.3

Type of geneprotein-codingprotein-coding
Descriptionprobable global transcription activator SNF2L2ATP-dependent helicase SMARCA2BAF190BBRG1-associated factor 190BSNF2-alphaSNF2/SWI2-like protein 2SWI/SNF-related matrix-associated actin-dependent regulator of chromatin a2brahma homologglobal transcr14-3-3 protein eta14-3-3 etatyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide
Modification date2020031520200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000349721, ENST00000357248, 
ENST00000302401, ENST00000324954, 
ENST00000382185, ENST00000382186, 
ENST00000382194, ENST00000382203, 
ENST00000491574, 		ENST00000248975, 
ENST00000397492, ENST00000471374, 
Fusion gene scores* DoF score14 X 9 X 10=12609 X 7 X 6=378
# samples 1513
** MAII scorelog2(15/1260*10)=-3.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/378*10)=-1.53987461119262
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMARCA2 [Title/Abstract] AND YWHAH [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSMARCA2(2015404)-YWHAH(32352125), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneSMARCA2

GO:0008285

negative regulation of cell proliferation

14660596

HgeneSMARCA2

GO:0045892

negative regulation of transcription, DNA-templated

12065415

HgeneSMARCA2

GO:0045893

positive regulation of transcription, DNA-templated

17984088

HgeneSMARCA2

GO:0045944

positive regulation of transcription by RNA polymerase II

15774904

TgeneYWHAH

GO:0002028

regulation of sodium ion transport

16728661

TgeneYWHAH

GO:0006713

glucocorticoid catabolic process

15790729

TgeneYWHAH

GO:0042921

glucocorticoid receptor signaling pathway

15790729

TgeneYWHAH

GO:0045893

positive regulation of transcription, DNA-templated

15790729

TgeneYWHAH

GO:0086010

membrane depolarization during action potential

16728661

TgeneYWHAH

GO:2000649

regulation of sodium ion transmembrane transporter activity

16728661


check buttonFusion gene breakpoints across SMARCA2 (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 YWHAH (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
ChimerDB4LAMLTCGA-AB-2990SMARCA2chr9

2015404

+YWHAHchr22

32352125

+


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Fusion Gene ORF analysis for SMARCA2-YWHAH

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-3CDSENST00000349721ENST00000248975SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
5UTR-3CDSENST00000349721ENST00000397492SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
5UTR-3CDSENST00000357248ENST00000248975SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
5UTR-3CDSENST00000357248ENST00000397492SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
5UTR-3UTRENST00000349721ENST00000471374SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
5UTR-3UTRENST00000357248ENST00000471374SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000302401ENST00000248975SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000302401ENST00000397492SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000324954ENST00000248975SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000324954ENST00000397492SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000382185ENST00000248975SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000382185ENST00000397492SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000382186ENST00000248975SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000382186ENST00000397492SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000382194ENST00000248975SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000382194ENST00000397492SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000382203ENST00000248975SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000382203ENST00000397492SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000491574ENST00000248975SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3CDSENST00000491574ENST00000397492SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3UTRENST00000302401ENST00000471374SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3UTRENST00000324954ENST00000471374SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3UTRENST00000382185ENST00000471374SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3UTRENST00000382186ENST00000471374SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3UTRENST00000382194ENST00000471374SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3UTRENST00000382203ENST00000471374SMARCA2chr9

2015404

+YWHAHchr22

32352125

+
intron-3UTRENST00000491574ENST00000471374SMARCA2chr9

2015404

+YWHAHchr22

32352125

+

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 SMARCA2-YWHAH


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)
SMARCA2chr92015404+YWHAHchr2232352125+0.0001569850.999843
SMARCA2chr92015404+YWHAHchr2232352125+0.0001569850.999843

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 SMARCA2-YWHAH


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/:2015404/:32352125)
- 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 SMARCA2-YWHAH


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 SMARCA2-YWHAH


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 SMARCA2-YWHAH


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 SMARCA2-YWHAH


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