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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:BCAS3-CYTH1 (FusionGDB2 ID:9204)

Fusion Gene Summary for BCAS3-CYTH1

check button Fusion gene summary
Fusion gene informationFusion gene name: BCAS3-CYTH1
Fusion gene ID: 9204
HgeneTgene
Gene symbol

BCAS3

CYTH1

Gene ID

54828

9267

Gene nameBCAS3 microtubule associated cell migration factorcytohesin 1
SynonymsGAOB1|MAABB2-1|CYTOHESIN-1|D17S811E|PSCD1|SEC7
Cytomap

17q23.2

17q25.3

Type of geneprotein-codingprotein-coding
Descriptionbreast carcinoma-amplified sequence 3BCAS4/BCAS3 fusionRudhirabreast carcinoma amplified sequence 4/3 fusion proteinmetastasis associated antigen of breast cancerprotein Maab1cytohesin-1PH, SEC7 and coiled-coil domain-containing protein 1SEC7 homolog B2-1cytoadhesin 1homolog of secretory protein SEC7pleckstrin homology, Sec7 and coiled-coil domains 1
Modification date2020031320200313
UniProtAcc.

Q15438

Ensembl transtripts involved in fusion geneENST00000390652, ENST00000407086, 
ENST00000408905, ENST00000585744, 
ENST00000588462, ENST00000588874, 
ENST00000589222, ENST00000585812, 
ENST00000361101, ENST00000446868, 
ENST00000585509, ENST00000589296, 
ENST00000589297, ENST00000591455, 
ENST00000586175, 
Fusion gene scores* DoF score53 X 35 X 17=315356 X 5 X 2=60
# samples 616
** MAII scorelog2(61/31535*10)=-5.69200088030826
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/60*10)=0
Context

PubMed: BCAS3 [Title/Abstract] AND CYTH1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBCAS3(59001861)-CYTH1(76705814), # samples:3
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
HgeneBCAS3

GO:0043085

positive regulation of catalytic activity

17505058

HgeneBCAS3

GO:0045944

positive regulation of transcription by RNA polymerase II

17505058

HgeneBCAS3

GO:0071391

cellular response to estrogen stimulus

17505058

TgeneCYTH1

GO:0030155

regulation of cell adhesion

12606567


check buttonFusion gene breakpoints across BCAS3 (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 CYTH1 (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
ChimerDB4BRCATCGA-AR-A0TQ-01ABCAS3chr17

59001861

-CYTH1chr17

76705814

-
ChimerDB4BRCATCGA-AR-A0TQ-01ABCAS3chr17

59001861

+CYTH1chr17

76705814

-


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Fusion Gene ORF analysis for BCAS3-CYTH1

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-5UTRENST00000390652ENST00000361101BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000390652ENST00000446868BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000390652ENST00000585509BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000390652ENST00000589296BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000390652ENST00000589297BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000390652ENST00000591455BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000407086ENST00000361101BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000407086ENST00000446868BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000407086ENST00000585509BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000407086ENST00000589296BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000407086ENST00000589297BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000407086ENST00000591455BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000408905ENST00000361101BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000408905ENST00000446868BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000408905ENST00000585509BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000408905ENST00000589296BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000408905ENST00000589297BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000408905ENST00000591455BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000585744ENST00000361101BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000585744ENST00000446868BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000585744ENST00000585509BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000585744ENST00000589296BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000585744ENST00000589297BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000585744ENST00000591455BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000588462ENST00000361101BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000588462ENST00000446868BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000588462ENST00000585509BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000588462ENST00000589296BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000588462ENST00000589297BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000588462ENST00000591455BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000588874ENST00000361101BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000588874ENST00000446868BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000588874ENST00000585509BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000588874ENST00000589296BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000588874ENST00000589297BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000588874ENST00000591455BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000589222ENST00000361101BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000589222ENST00000446868BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000589222ENST00000585509BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000589222ENST00000589296BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000589222ENST00000589297BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-5UTRENST00000589222ENST00000591455BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-intronENST00000390652ENST00000586175BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-intronENST00000407086ENST00000586175BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-intronENST00000408905ENST00000586175BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-intronENST00000585744ENST00000586175BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-intronENST00000588462ENST00000586175BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-intronENST00000588874ENST00000586175BCAS3chr17

59001861

+CYTH1chr17

76705814

-
5CDS-intronENST00000589222ENST00000586175BCAS3chr17

59001861

+CYTH1chr17

76705814

-
intron-5UTRENST00000585812ENST00000361101BCAS3chr17

59001861

+CYTH1chr17

76705814

-
intron-5UTRENST00000585812ENST00000446868BCAS3chr17

59001861

+CYTH1chr17

76705814

-
intron-5UTRENST00000585812ENST00000585509BCAS3chr17

59001861

+CYTH1chr17

76705814

-
intron-5UTRENST00000585812ENST00000589296BCAS3chr17

59001861

+CYTH1chr17

76705814

-
intron-5UTRENST00000585812ENST00000589297BCAS3chr17

59001861

+CYTH1chr17

76705814

-
intron-5UTRENST00000585812ENST00000591455BCAS3chr17

59001861

+CYTH1chr17

76705814

-
intron-intronENST00000585812ENST00000586175BCAS3chr17

59001861

+CYTH1chr17

76705814

-

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 BCAS3-CYTH1


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)

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.

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Fusion Protein Features for BCAS3-CYTH1


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/:59001861/:76705814)
- 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
.CYTH1

Q15438

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: Promotes guanine-nucleotide exchange on ARF1, ARF5 and ARF6. Promotes the activation of ARF factors through replacement of GDP with GTP. Plays an important role in membrane trafficking, during junctional remodeling and epithelial polarization, through regulation of ARF6 activity. {ECO:0000250|UniProtKB:Q9QX11, ECO:0000269|PubMed:10652308, ECO:0000269|PubMed:29420262, ECO:0000269|PubMed:9653114}.

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 BCAS3-CYTH1


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 BCAS3-CYTH1


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 BCAS3-CYTH1


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 BCAS3-CYTH1


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