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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:BCAR3-PIBF1 (FusionGDB2 ID:HG8412TG10464)

Fusion Gene Summary for BCAR3-PIBF1

check button Fusion gene summary
Fusion gene informationFusion gene name: BCAR3-PIBF1
Fusion gene ID: hg8412tg10464
HgeneTgene
Gene symbol

BCAR3

PIBF1

Gene ID

8412

10464

Gene nameBCAR3 adaptor protein, NSP family memberprogesterone immunomodulatory binding factor 1
SynonymsAND-34|NSP2|SH2D3BC13orf24|CEP90|JBTS33|PIBF
Cytomap('BCAR3')('PIBF1')

1p22.1

13q21.33-q22.1

Type of geneprotein-codingprotein-coding
Descriptionbreast cancer anti-estrogen resistance protein 3BCAR3, NSP family adaptor proteinSH2 domain-containing protein 3Bbreast cancer anti-estrogen resistance 3breast cancer antiestrogen resistance 3 proteindJ1033H22.2 (breast cancer anti-estrogen resistancprogesterone-induced-blocking factor 1centrosomal protein of 90 kDa
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000260502, ENST00000370243, 
ENST00000370244, ENST00000370247, 
ENST00000466632, ENST00000539242, 
Fusion gene scores* DoF score11 X 12 X 9=118816 X 13 X 13=2704
# samples 1223
** MAII scorelog2(12/1188*10)=-3.30742852519225
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(23/2704*10)=-3.55538938533781
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BCAR3 [Title/Abstract] AND PIBF1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBCAR3(94107859)-PIBF1(73572959), # samples:1
Anticipated loss of major functional domain due to fusion event.BCAR3-PIBF1 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.
BCAR3-PIBF1 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.
BCAR3-PIBF1 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
TgenePIBF1

GO:0031393

negative regulation of prostaglandin biosynthetic process

3863495

TgenePIBF1

GO:0032695

negative regulation of interleukin-12 production

14634107

TgenePIBF1

GO:0032733

positive regulation of interleukin-10 production

14634107

TgenePIBF1

GO:0032815

negative regulation of natural killer cell activation

12516630

TgenePIBF1

GO:0042531

positive regulation of tyrosine phosphorylation of STAT protein

16393965

TgenePIBF1

GO:0042532

negative regulation of tyrosine phosphorylation of STAT protein

16393965

TgenePIBF1

GO:0042976

activation of Janus kinase activity

16393965


check buttonFusion gene breakpoints across BCAR3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across PIBF1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4STADTCGA-D7-6518BCAR3chr1

94107859

-PIBF1chr13

73572959

+


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Fusion Gene ORF analysis for BCAR3-PIBF1

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-3UTRENST00000260502ENST00000489922BCAR3chr1

94107859

-PIBF1chr13

73572959

+
5CDS-3UTRENST00000370243ENST00000489922BCAR3chr1

94107859

-PIBF1chr13

73572959

+
5CDS-3UTRENST00000370244ENST00000489922BCAR3chr1

94107859

-PIBF1chr13

73572959

+
Frame-shiftENST00000260502ENST00000326291BCAR3chr1

94107859

-PIBF1chr13

73572959

+
Frame-shiftENST00000370244ENST00000326291BCAR3chr1

94107859

-PIBF1chr13

73572959

+
In-frameENST00000370243ENST00000326291BCAR3chr1

94107859

-PIBF1chr13

73572959

+
intron-3CDSENST00000370247ENST00000326291BCAR3chr1

94107859

-PIBF1chr13

73572959

+
intron-3CDSENST00000466632ENST00000326291BCAR3chr1

94107859

-PIBF1chr13

73572959

+
intron-3CDSENST00000539242ENST00000326291BCAR3chr1

94107859

-PIBF1chr13

73572959

+
intron-3UTRENST00000370247ENST00000489922BCAR3chr1

94107859

-PIBF1chr13

73572959

+
intron-3UTRENST00000466632ENST00000489922BCAR3chr1

94107859

-PIBF1chr13

73572959

+
intron-3UTRENST00000539242ENST00000489922BCAR3chr1

94107859

-PIBF1chr13

73572959

+

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)
ENST00000370243BCAR3chr194107859-ENST00000326291PIBF1chr1373572959+139163268856262

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
ENST00000370243ENST00000326291BCAR3chr194107859-PIBF1chr1373572959+0.004275670.9957243

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Fusion Genomic Features for BCAR3-PIBF1


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)
BCAR3chr194107859-PIBF1chr1373572959+3.86E-050.9999615
BCAR3chr194107859-PIBF1chr1373572959+3.86E-050.9999615

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.
genomic feature

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 BCAR3-PIBF1


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/chr1:94107859/chr13:73572959)
- 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
HgeneBCAR3chr1:94107859chr13:73572959ENST00000260502-312479_482119826.0Compositional biasNote=Poly-Asp
HgeneBCAR3chr1:94107859chr13:73572959ENST00000370243-312479_482119826.0Compositional biasNote=Poly-Asp
HgeneBCAR3chr1:94107859chr13:73572959ENST00000370244-514479_482119826.0Compositional biasNote=Poly-Asp
HgeneBCAR3chr1:94107859chr13:73572959ENST00000370247-110479_4820735.0Compositional biasNote=Poly-Asp
HgeneBCAR3chr1:94107859chr13:73572959ENST00000539242-18479_4820502.0Compositional biasNote=Poly-Asp
HgeneBCAR3chr1:94107859chr13:73572959ENST00000260502-312154_253119826.0DomainSH2
HgeneBCAR3chr1:94107859chr13:73572959ENST00000260502-312548_818119826.0DomainRas-GEF
HgeneBCAR3chr1:94107859chr13:73572959ENST00000370243-312154_253119826.0DomainSH2
HgeneBCAR3chr1:94107859chr13:73572959ENST00000370243-312548_818119826.0DomainRas-GEF
HgeneBCAR3chr1:94107859chr13:73572959ENST00000370244-514154_253119826.0DomainSH2
HgeneBCAR3chr1:94107859chr13:73572959ENST00000370244-514548_818119826.0DomainRas-GEF
HgeneBCAR3chr1:94107859chr13:73572959ENST00000370247-110154_2530735.0DomainSH2
HgeneBCAR3chr1:94107859chr13:73572959ENST00000370247-110548_8180735.0DomainRas-GEF
HgeneBCAR3chr1:94107859chr13:73572959ENST00000539242-18154_2530502.0DomainSH2
HgeneBCAR3chr1:94107859chr13:73572959ENST00000539242-18548_8180502.0DomainRas-GEF
TgenePIBF1chr1:94107859chr13:73572959ENST0000032629115181_184683758.0RegionSufficient for NK inhibitory function
TgenePIBF1chr1:94107859chr13:73572959ENST0000032629115181_419683758.0RegionMediates modulation of Th2 dominant cytokine production


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Fusion Gene Sequence for BCAR3-PIBF1


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.
>9169_9169_1_BCAR3-PIBF1_BCAR3_chr1_94107859_ENST00000370243_PIBF1_chr13_73572959_ENST00000326291_length(transcript)=1391nt_BP=632nt
GAGCGCGCTGGGACTCCCCGAGACGTGGCCCACGGCGGGGAGCGCTCAGCGATTGGCGGCCAGGCATCTTGCTCGGTGGCACTCGAGCGG
CATCTTCCCGGGCGCTGGCCTCGCCCGACCCCCTGCCCGTCGGAGCTGCTCTGCCGGCCACCCCGCCCTGTCCCGCCCGTCCCCTCTTCG
CAGAAGCCGGCCGGGGTCGGGCAGATGCGAGGGCCCAGAGCGCTCTGGTGGAAGCCCAAGGCTCCGAGGAGGCGAGTTTCTCCGAGTTGA
GAATTATGGCTGCAGGAAAATTTGCAAGCCTTCCCAGAAACATGCCGGTGAATCACCAGTTCCCCCTGGCCTCATCCATGGACCTTCTGA
GCAGCAGGTCCCCTCTCGCTGAGCATCGCCCAGATGCCTATCAAGATGTGTCTATACATGGCACCCTTCCACGGAAGAAAAAAGGTCCTC
CTCCCATAAGGTCCTGTGATGACTTCAGTCACATGGGCACCCTCCCCCACTCCAAATCCCCACGGCAGAACTCGCCTGTGACCCAGGATG
GCATCCAGGAGAGCCCATGGCAGGACCGGCACGGCGAAACCTTCACCTTCAGGGATCCACATCTTCTGGACCCAACTGTGGAATATGTGA
AGGAATTGGCAGCAATGAAACAGATTCTCGTTAAGATGCATAGTAAACATTCTGAGAACAGCTTACTTCTCACTAAAACAGAACCAAAAC
ATGTGACAGAAAATCAGAAATCAAAGACTTTGAATGTGCCTAAAGAGCATGAAGACAATATATTTACACCTAAACCAACACTCTTTACTA
AAAAAGAAGCACCTGAGTGGTCTAAGAAACAAAAGATGAAGACCTAGTGTTTTGGATGGGAAGCACCTGTAGACCATTATATACTCCTGA
AGTTCTTTTTCTGATGGAAAACAAAATTCAGCTTAATCGTGTACTCAGCATTTTTTAAATAACAATGTTTATTTGAACTAATATTAAATT
AACAAATTCAGTGTAATCAAAATGTGTAAAGAACAATCAATATACTTTATTTTTTTTTCTATTTTATAAAATAAATATATATGCTATGCT
TTAAATTTTGGAGCTTTCATAAATGTTCAATGCATTTTAAGTGTGTGGCTTATAAATATTTTGGTATTTTTCTATACTACGTAAATTCTG
AGTTTAAATGTCATACACAAATACTAAGACACTTTGCATTTTTAAAAATTAAGAATCATTTGTGAAGTCCACTACGAGGTACTTCAAAAG
CCCAGTAATGGTGGTCAGATACCATGTAGATGGATACAGATTGTTGACTCTTTTGAAGTTGTTTTTTTCTTATATTTTATATTACCATTA

>9169_9169_1_BCAR3-PIBF1_BCAR3_chr1_94107859_ENST00000370243_PIBF1_chr13_73572959_ENST00000326291_length(amino acids)=262AA_BP=188
MLGGTRAASSRALASPDPLPVGAALPATPPCPARPLFAEAGRGRADARAQSALVEAQGSEEASFSELRIMAAGKFASLPRNMPVNHQFPL
ASSMDLLSSRSPLAEHRPDAYQDVSIHGTLPRKKKGPPPIRSCDDFSHMGTLPHSKSPRQNSPVTQDGIQESPWQDRHGETFTFRDPHLL

--------------------------------------------------------------

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Fusion Gene PPI Analysis for BCAR3-PIBF1


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 BCAR3-PIBF1


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 BCAR3-PIBF1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBCAR3C0006142Malignant neoplasm of breast1CTD_human
HgeneBCAR3C0013146Drug abuse1CTD_human
HgeneBCAR3C0013170Drug habituation1CTD_human
HgeneBCAR3C0013222Drug Use Disorders1CTD_human
HgeneBCAR3C0029231Organic Mental Disorders, Substance-Induced1CTD_human
HgeneBCAR3C0038580Substance Dependence1CTD_human
HgeneBCAR3C0038586Substance Use Disorders1CTD_human
HgeneBCAR3C0236969Substance-Related Disorders1CTD_human
HgeneBCAR3C0678222Breast Carcinoma1CTD_human
HgeneBCAR3C0740858Substance abuse problem1CTD_human
HgeneBCAR3C1257931Mammary Neoplasms, Human1CTD_human
HgeneBCAR3C1458155Mammary Neoplasms1CTD_human
HgeneBCAR3C1510472Drug Dependence1CTD_human
HgeneBCAR3C4316881Prescription Drug Abuse1CTD_human
HgeneBCAR3C4704874Mammary Carcinoma, Human1CTD_human
TgeneC4540389JOUBERT SYNDROME 332GENOMICS_ENGLAND;UNIPROT
TgeneC0000821Threatened abortion1CTD_human
TgeneC0004134Ataxia1GENOMICS_ENGLAND
TgeneC0424605Developmental delay (disorder)1GENOMICS_ENGLAND
TgeneC0431399Familial aplasia of the vermis1GENOMICS_ENGLAND;ORPHANET
TgeneC0557874Global developmental delay1GENOMICS_ENGLAND
TgeneC4313693Vermis hypoplasia1GENOMICS_ENGLAND
TgeneC4551568Joubert syndrome 11ORPHANET