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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-RNFT1 (FusionGDB2 ID:HG54828TG51136)

Fusion Gene Summary for BCAS3-RNFT1

check button Fusion gene summary
Fusion gene informationFusion gene name: BCAS3-RNFT1
Fusion gene ID: hg54828tg51136
HgeneTgene
Gene symbol

BCAS3

RNFT1

Gene ID

54828

51136

Gene nameBCAS3 microtubule associated cell migration factorring finger protein, transmembrane 1
SynonymsGAOB1|MAABPTD016
Cytomap('BCAS3')('RNFT1')

17q23.2

17q23.1

Type of geneprotein-codingprotein-coding
Descriptionbreast carcinoma-amplified sequence 3BCAS4/BCAS3 fusionRudhirabreast carcinoma amplified sequence 4/3 fusion proteinmetastasis associated antigen of breast cancerprotein Maab1E3 ubiquitin-protein ligase RNFT1RING finger and transmembrane domain-containing protein 1
Modification date2020031320200313
UniProtAcc

Q9H6U6

.
Ensembl transtripts involved in fusion geneENST00000390652, ENST00000407086, 
ENST00000408905, ENST00000585744, 
ENST00000588462, ENST00000588874, 
ENST00000589222, ENST00000585812, 
Fusion gene scores* DoF score53 X 35 X 17=315358 X 7 X 6=336
# samples 6112
** MAII scorelog2(61/31535*10)=-5.69200088030826
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/336*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BCAS3 [Title/Abstract] AND RNFT1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBCAS3(59161925)-RNFT1(58040645), # samples:4
Anticipated loss of major functional domain due to fusion event.BCAS3-RNFT1 seems lost the major protein functional domain in Hgene 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
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

TgeneRNFT1

GO:0051865

protein autoubiquitination

27485036



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-A7-A4SF-01ABCAS3chr17

58767122

+RNFT1chr17

58040645

-
ChimerDB4LGGTCGA-DB-A4XF-01ABCAS3chr17

59161925

-RNFT1chr17

58040645

-
ChimerDB4LGGTCGA-DB-A4XF-01ABCAS3chr17

59161925

+RNFT1chr17

58040645

-
ChimerDB4LGGTCGA-DB-A4XFBCAS3chr17

59161925

+RNFT1chr17

58040645

-


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Fusion Gene ORF analysis for BCAS3-RNFT1

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-5UTRENST00000390652ENST00000442346BCAS3chr17

58767122

+RNFT1chr17

58040645

-
5CDS-5UTRENST00000390652ENST00000442346BCAS3chr17

59161925

+RNFT1chr17

58040645

-
5CDS-5UTRENST00000407086ENST00000442346BCAS3chr17

58767122

+RNFT1chr17

58040645

-
5CDS-5UTRENST00000407086ENST00000442346BCAS3chr17

59161925

+RNFT1chr17

58040645

-
5CDS-5UTRENST00000408905ENST00000442346BCAS3chr17

58767122

+RNFT1chr17

58040645

-
5CDS-5UTRENST00000408905ENST00000442346BCAS3chr17

59161925

+RNFT1chr17

58040645

-
5CDS-5UTRENST00000585744ENST00000442346BCAS3chr17

59161925

+RNFT1chr17

58040645

-
5CDS-5UTRENST00000588462ENST00000442346BCAS3chr17

58767122

+RNFT1chr17

58040645

-
5CDS-5UTRENST00000588462ENST00000442346BCAS3chr17

59161925

+RNFT1chr17

58040645

-
5CDS-5UTRENST00000588874ENST00000442346BCAS3chr17

59161925

+RNFT1chr17

58040645

-
5CDS-5UTRENST00000589222ENST00000442346BCAS3chr17

58767122

+RNFT1chr17

58040645

-
5CDS-5UTRENST00000589222ENST00000442346BCAS3chr17

59161925

+RNFT1chr17

58040645

-
Frame-shiftENST00000390652ENST00000305783BCAS3chr17

58767122

+RNFT1chr17

58040645

-
Frame-shiftENST00000390652ENST00000305783BCAS3chr17

59161925

+RNFT1chr17

58040645

-
Frame-shiftENST00000407086ENST00000305783BCAS3chr17

58767122

+RNFT1chr17

58040645

-
Frame-shiftENST00000407086ENST00000305783BCAS3chr17

59161925

+RNFT1chr17

58040645

-
Frame-shiftENST00000408905ENST00000305783BCAS3chr17

58767122

+RNFT1chr17

58040645

-
Frame-shiftENST00000408905ENST00000305783BCAS3chr17

59161925

+RNFT1chr17

58040645

-
Frame-shiftENST00000585744ENST00000305783BCAS3chr17

59161925

+RNFT1chr17

58040645

-
Frame-shiftENST00000588462ENST00000305783BCAS3chr17

58767122

+RNFT1chr17

58040645

-
Frame-shiftENST00000588462ENST00000305783BCAS3chr17

59161925

+RNFT1chr17

58040645

-
Frame-shiftENST00000588874ENST00000305783BCAS3chr17

59161925

+RNFT1chr17

58040645

-
Frame-shiftENST00000589222ENST00000305783BCAS3chr17

58767122

+RNFT1chr17

58040645

-
Frame-shiftENST00000589222ENST00000305783BCAS3chr17

59161925

+RNFT1chr17

58040645

-
intron-3CDSENST00000585744ENST00000305783BCAS3chr17

58767122

+RNFT1chr17

58040645

-
intron-3CDSENST00000585812ENST00000305783BCAS3chr17

58767122

+RNFT1chr17

58040645

-
intron-3CDSENST00000585812ENST00000305783BCAS3chr17

59161925

+RNFT1chr17

58040645

-
intron-3CDSENST00000588874ENST00000305783BCAS3chr17

58767122

+RNFT1chr17

58040645

-
intron-5UTRENST00000585744ENST00000442346BCAS3chr17

58767122

+RNFT1chr17

58040645

-
intron-5UTRENST00000585812ENST00000442346BCAS3chr17

58767122

+RNFT1chr17

58040645

-
intron-5UTRENST00000585812ENST00000442346BCAS3chr17

59161925

+RNFT1chr17

58040645

-
intron-5UTRENST00000588874ENST00000442346BCAS3chr17

58767122

+RNFT1chr17

58040645

-

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-RNFT1


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)


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Fusion Protein Features for BCAS3-RNFT1


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/:59161925/:58040645)
- 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
BCAS3

Q9H6U6

.
FUNCTION: Plays a role in angiogenesis. Participates in the regulation of cell polarity and directional endothelial cell migration by mediating both the activation and recruitment of CDC42 and the reorganization of the actin cytoskeleton at the cell leading edge. Promotes filipodia formation (By similarity). Functions synergistically with PELP1 as a transcriptional coactivator of estrogen receptor-responsive genes. Stimulates histone acetyltransferase activity. Binds to chromatin. {ECO:0000250|UniProtKB:Q8CCN5, ECO:0000269|PubMed:17505058}.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 BCAS3-RNFT1


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-RNFT1


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-RNFT1


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-RNFT1


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