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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:LCP1-BCL6 (FusionGDB2 ID:HG3936TG604)

Fusion Gene Summary for LCP1-BCL6

check button Fusion gene summary
Fusion gene informationFusion gene name: LCP1-BCL6
Fusion gene ID: hg3936tg604
HgeneTgene
Gene symbol

LCP1

BCL6

Gene ID

3936

604

Gene namelymphocyte cytosolic protein 1BCL6 transcription repressor
SynonymsCP64|HEL-S-37|L-PLASTIN|LC64P|LPL|PLS2BCL5|BCL6A|LAZ3|ZBTB27|ZNF51
Cytomap('LCP1')('BCL6')

13q14.13

3q27.3

Type of geneprotein-codingprotein-coding
Descriptionplastin-2L-plastin (Lymphocyte cytosolic protein 1) (LCP-1) (LC64P)LCP-1Lymphocyte cytosolic protein-1 (plasmin)bA139H14.1 (lymphocyte cytosolic protein 1 (L-plastin))epididymis secretory protein Li 37B-cell lymphoma 6 proteinB cell CLL/lymphoma 6B-cell lymphoma 5 proteinB-cell lymphoma 6 protein transcriptBCL-5BCL-6cys-his2 zinc finger transcription factorlymphoma-associated zinc finger gene on chromosome 3protein LAZ-3zinc finger and BTB dom
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000323076, ENST00000398576, 
ENST00000460190, ENST00000435666, 
ENST00000323076, ENST00000398576, 
ENST00000460190, ENST00000435666, 
Fusion gene scores* DoF score10 X 10 X 4=40015 X 9 X 4=540
# samples 1010
** MAII scorelog2(10/400*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/540*10)=-2.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LCP1 [Title/Abstract] AND BCL6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint
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
HgeneLCP1

GO:0002286

T cell activation involved in immune response

17294403

HgeneLCP1

GO:0033157

regulation of intracellular protein transport

17294403

TgeneBCL6

GO:0000122

negative regulation of transcription by RNA polymerase II

11929873|15577913

TgeneBCL6

GO:0006974

cellular response to DNA damage stimulus

15577913

TgeneBCL6

GO:0030308

negative regulation of cell growth

10490843

TgeneBCL6

GO:0043065

positive regulation of apoptotic process

10490843



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
ChimerKB3..LCP1chr13

46756245

+BCL6chr3

187449718

-
ChimerKB3..LCP1chr13

46756245

-BCL6chr3

187452695

-
ChimerKB4..LCP1chr13

46756245

+BCL6chr3

187449718

-


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Fusion Gene ORF analysis for LCP1-BCL6

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-3CDSENST00000323076ENST00000232014LCP1chr13

46756245

+BCL6chr3

187449718

-
5UTR-3CDSENST00000323076ENST00000406870LCP1chr13

46756245

+BCL6chr3

187449718

-
5UTR-3CDSENST00000323076ENST00000450123LCP1chr13

46756245

+BCL6chr3

187449718

-
5UTR-3CDSENST00000398576ENST00000232014LCP1chr13

46756245

+BCL6chr3

187449718

-
5UTR-3CDSENST00000398576ENST00000406870LCP1chr13

46756245

+BCL6chr3

187449718

-
5UTR-3CDSENST00000398576ENST00000450123LCP1chr13

46756245

+BCL6chr3

187449718

-
5UTR-3CDSENST00000460190ENST00000232014LCP1chr13

46756245

+BCL6chr3

187449718

-
5UTR-3CDSENST00000460190ENST00000406870LCP1chr13

46756245

+BCL6chr3

187449718

-
5UTR-3CDSENST00000460190ENST00000450123LCP1chr13

46756245

+BCL6chr3

187449718

-
5UTR-5UTRENST00000323076ENST00000232014LCP1chr13

46756245

-BCL6chr3

187452695

-
5UTR-5UTRENST00000323076ENST00000406870LCP1chr13

46756245

-BCL6chr3

187452695

-
5UTR-5UTRENST00000398576ENST00000232014LCP1chr13

46756245

-BCL6chr3

187452695

-
5UTR-5UTRENST00000398576ENST00000406870LCP1chr13

46756245

-BCL6chr3

187452695

-
5UTR-5UTRENST00000460190ENST00000232014LCP1chr13

46756245

-BCL6chr3

187452695

-
5UTR-5UTRENST00000460190ENST00000406870LCP1chr13

46756245

-BCL6chr3

187452695

-
5UTR-intronENST00000323076ENST00000450123LCP1chr13

46756245

-BCL6chr3

187452695

-
5UTR-intronENST00000323076ENST00000496823LCP1chr13

46756245

+BCL6chr3

187449718

-
5UTR-intronENST00000323076ENST00000496823LCP1chr13

46756245

-BCL6chr3

187452695

-
5UTR-intronENST00000398576ENST00000450123LCP1chr13

46756245

-BCL6chr3

187452695

-
5UTR-intronENST00000398576ENST00000496823LCP1chr13

46756245

+BCL6chr3

187449718

-
5UTR-intronENST00000398576ENST00000496823LCP1chr13

46756245

-BCL6chr3

187452695

-
5UTR-intronENST00000460190ENST00000450123LCP1chr13

46756245

-BCL6chr3

187452695

-
5UTR-intronENST00000460190ENST00000496823LCP1chr13

46756245

+BCL6chr3

187449718

-
5UTR-intronENST00000460190ENST00000496823LCP1chr13

46756245

-BCL6chr3

187452695

-
intron-3CDSENST00000435666ENST00000232014LCP1chr13

46756245

+BCL6chr3

187449718

-
intron-3CDSENST00000435666ENST00000406870LCP1chr13

46756245

+BCL6chr3

187449718

-
intron-3CDSENST00000435666ENST00000450123LCP1chr13

46756245

+BCL6chr3

187449718

-
intron-5UTRENST00000435666ENST00000232014LCP1chr13

46756245

-BCL6chr3

187452695

-
intron-5UTRENST00000435666ENST00000406870LCP1chr13

46756245

-BCL6chr3

187452695

-
intron-intronENST00000435666ENST00000450123LCP1chr13

46756245

-BCL6chr3

187452695

-
intron-intronENST00000435666ENST00000496823LCP1chr13

46756245

+BCL6chr3

187449718

-
intron-intronENST00000435666ENST00000496823LCP1chr13

46756245

-BCL6chr3

187452695

-

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 LCP1-BCL6


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 LCP1-BCL6


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/:/:)
- 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 LCP1-BCL6


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 LCP1-BCL6


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 LCP1-BCL6


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 LCP1-BCL6


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLCP1C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneLCP1C0028043Nicotine Dependence1CTD_human
HgeneLCP1C0040332Tobacco Dependence1CTD_human
HgeneLCP1C0376384Nicotine Use Disorder1CTD_human
TgeneC0024301Lymphoma, Follicular1ORPHANET
TgeneC0024302Reticulosarcoma1CTD_human
TgeneC0024304Lymphoma, Mixed-Cell1CTD_human
TgeneC0024305Lymphoma, Non-Hodgkin1CGI;CTD_human
TgeneC0024306Lymphoma, Undifferentiated1CTD_human
TgeneC0079740High Grade Lymphoma (neoplasm)1CTD_human
TgeneC0079741Lymphoma, Intermediate-Grade1CTD_human
TgeneC0079747Low Grade Lymphoma (neoplasm)1CTD_human
TgeneC0079757Diffuse Mixed-Cell Lymphoma1CTD_human
TgeneC0079770Lymphoma, Small Noncleaved-Cell1CTD_human
TgeneC0079772T-Cell Lymphoma1CTD_human
TgeneC1292754Mediastinal (Thymic) Large B-Cell Lymphoma1ORPHANET
TgeneC3714542Lymphoma, Diffuse1CTD_human
TgeneC4721532Lymphoma, Non-Hodgkin, Familial1CTD_human