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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:BCL6-RAF1 (FusionGDB2 ID:HG604TG5894)

Fusion Gene Summary for BCL6-RAF1

check button Fusion gene summary
Fusion gene informationFusion gene name: BCL6-RAF1
Fusion gene ID: hg604tg5894
HgeneTgene
Gene symbol

BCL6

RAF1

Gene ID

604

5894

Gene nameBCL6 transcription repressorRaf-1 proto-oncogene, serine/threonine kinase
SynonymsBCL5|BCL6A|LAZ3|ZBTB27|ZNF51CMD1NN|CRAF|NS5|Raf-1|c-Raf
Cytomap('BCL6')('RAF1')

3q27.3

3p25.2

Type of geneprotein-codingprotein-coding
DescriptionB-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 domRAF proto-oncogene serine/threonine-protein kinaseC-Raf proto-oncogene, serine/threonine kinaseOncogene RAF1proto-oncogene c-RAFraf proto-oncogene serine/threonine protein kinasev-raf-1 murine leukemia viral oncogene homolog 1v-raf-1 murine leukemia
Modification date2020031320200327
UniProtAcc.

P04049

Ensembl transtripts involved in fusion geneENST00000232014, ENST00000406870, 
ENST00000450123, ENST00000496823, 
Fusion gene scores* DoF score15 X 9 X 4=54019 X 16 X 7=2128
# samples 1618
** MAII scorelog2(16/540*10)=-1.75488750216347
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(18/2128*10)=-3.56342933917152
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BCL6 [Title/Abstract] AND RAF1 [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
HgeneBCL6

GO:0000122

negative regulation of transcription by RNA polymerase II

11929873|15577913

HgeneBCL6

GO:0006974

cellular response to DNA damage stimulus

15577913

HgeneBCL6

GO:0030308

negative regulation of cell growth

10490843

HgeneBCL6

GO:0043065

positive regulation of apoptotic process

10490843

TgeneRAF1

GO:0000186

activation of MAPKK activity

10644344

TgeneRAF1

GO:0007190

activation of adenylate cyclase activity

15385642

TgeneRAF1

GO:0008285

negative regulation of cell proliferation

9765203

TgeneRAF1

GO:0031333

negative regulation of protein complex assembly

19667065

TgeneRAF1

GO:0033138

positive regulation of peptidyl-serine phosphorylation

19667065

TgeneRAF1

GO:0043066

negative regulation of apoptotic process

19667065



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
ChimerKB4..BCL6chr3

187444686

-RAF1chr3

187444686

-


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Fusion Gene ORF analysis for BCL6-RAF1

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
intron-intronENST00000232014ENST00000251849BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000232014ENST00000442415BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000232014ENST00000534997BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000232014ENST00000542177BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000406870ENST00000251849BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000406870ENST00000442415BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000406870ENST00000534997BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000406870ENST00000542177BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000450123ENST00000251849BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000450123ENST00000442415BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000450123ENST00000534997BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000450123ENST00000542177BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000496823ENST00000251849BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000496823ENST00000442415BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000496823ENST00000534997BCL6chr3

187444686

-RAF1chr3

187444686

-
intron-intronENST00000496823ENST00000542177BCL6chr3

187444686

-RAF1chr3

187444686

-

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 BCL6-RAF1


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 BCL6-RAF1


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
.RAF1

P04049

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: Serine/threonine-protein kinase that acts as a regulatory link between the membrane-associated Ras GTPases and the MAPK/ERK cascade, and this critical regulatory link functions as a switch determining cell fate decisions including proliferation, differentiation, apoptosis, survival and oncogenic transformation. RAF1 activation initiates a mitogen-activated protein kinase (MAPK) cascade that comprises a sequential phosphorylation of the dual-specific MAPK kinases (MAP2K1/MEK1 and MAP2K2/MEK2) and the extracellular signal-regulated kinases (MAPK3/ERK1 and MAPK1/ERK2). The phosphorylated form of RAF1 (on residues Ser-338 and Ser-339, by PAK1) phosphorylates BAD/Bcl2-antagonist of cell death at 'Ser-75'. Phosphorylates adenylyl cyclases: ADCY2, ADCY5 and ADCY6, resulting in their activation. Phosphorylates PPP1R12A resulting in inhibition of the phosphatase activity. Phosphorylates TNNT2/cardiac muscle troponin T. Can promote NF-kB activation and inhibit signal transducers involved in motility (ROCK2), apoptosis (MAP3K5/ASK1 and STK3/MST2), proliferation and angiogenesis (RB1). Can protect cells from apoptosis also by translocating to the mitochondria where it binds BCL2 and displaces BAD/Bcl2-antagonist of cell death. Regulates Rho signaling and migration, and is required for normal wound healing. Plays a role in the oncogenic transformation of epithelial cells via repression of the TJ protein, occludin (OCLN) by inducing the up-regulation of a transcriptional repressor SNAI2/SLUG, which induces down-regulation of OCLN. Restricts caspase activation in response to selected stimuli, notably Fas stimulation, pathogen-mediated macrophage apoptosis, and erythroid differentiation. {ECO:0000269|PubMed:11427728, ECO:0000269|PubMed:11719507, ECO:0000269|PubMed:15385642, ECO:0000269|PubMed:15618521, ECO:0000269|PubMed:15849194, ECO:0000269|PubMed:16892053, ECO:0000269|PubMed:16924233, ECO:0000269|PubMed:9360956}.

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 BCL6-RAF1


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 BCL6-RAF1


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 BCL6-RAF1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneRAF1P04049DB08896RegorafenibInhibitorSmall moleculeApproved
TgeneRAF1P04049DB08896RegorafenibInhibitorSmall moleculeApproved
TgeneRAF1P04049DB00398SorafenibInhibitorSmall moleculeApproved|Investigational
TgeneRAF1P04049DB00398SorafenibInhibitorSmall moleculeApproved|Investigational
TgeneRAF1P04049DB08862CholecystokininAgonistSmall moleculeApproved|Investigational
TgeneRAF1P04049DB08862CholecystokininAgonistSmall moleculeApproved|Investigational
TgeneRAF1P04049DB08912DabrafenibAntagonist|InhibitorSmall moleculeApproved|Investigational
TgeneRAF1P04049DB08912DabrafenibAntagonist|InhibitorSmall moleculeApproved|Investigational
TgeneRAF1P04049DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgeneRAF1P04049DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational

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Related Diseases for BCL6-RAF1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBCL6C0024301Lymphoma, Follicular1ORPHANET
HgeneBCL6C0024302Reticulosarcoma1CTD_human
HgeneBCL6C0024304Lymphoma, Mixed-Cell1CTD_human
HgeneBCL6C0024305Lymphoma, Non-Hodgkin1CGI;CTD_human
HgeneBCL6C0024306Lymphoma, Undifferentiated1CTD_human
HgeneBCL6C0079740High Grade Lymphoma (neoplasm)1CTD_human
HgeneBCL6C0079741Lymphoma, Intermediate-Grade1CTD_human
HgeneBCL6C0079747Low Grade Lymphoma (neoplasm)1CTD_human
HgeneBCL6C0079757Diffuse Mixed-Cell Lymphoma1CTD_human
HgeneBCL6C0079770Lymphoma, Small Noncleaved-Cell1CTD_human
HgeneBCL6C0079772T-Cell Lymphoma1CTD_human
HgeneBCL6C1292754Mediastinal (Thymic) Large B-Cell Lymphoma1ORPHANET
HgeneBCL6C3714542Lymphoma, Diffuse1CTD_human
HgeneBCL6C4721532Lymphoma, Non-Hodgkin, Familial1CTD_human
TgeneC0028326Noonan Syndrome10CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC0175704LEOPARD Syndrome7CLINGEN;CTD_human;GENOMICS_ENGLAND
TgeneC1969057Noonan Syndrome 54CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC1969056LEOPARD SYNDROME 23CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0007194Hypertrophic Cardiomyopathy2CTD_human
TgeneC0041409Turner Syndrome, Male2CTD_human
TgeneC1519086Pilomyxoid astrocytoma2ORPHANET
TgeneC1527404Female Pseudo-Turner Syndrome2CTD_human
TgeneC4551472Hypertrophic obstructive cardiomyopathy2CTD_human
TgeneC4551602Noonan Syndrome 12CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneC0007193Cardiomyopathy, Dilated1CTD_human
TgeneC0017638Glioma1CTD_human
TgeneC0020429Hyperalgesia1CTD_human
TgeneC0022665Kidney Neoplasm1CTD_human
TgeneC0023903Liver neoplasms1CTD_human
TgeneC0024121Lung Neoplasms1CTD_human
TgeneC0242379Malignant neoplasm of lung1CTD_human
TgeneC0259783mixed gliomas1CTD_human
TgeneC0340427Familial dilated cardiomyopathy1ORPHANET
TgeneC0345904Malignant neoplasm of liver1CTD_human
TgeneC0345967Malignant mesothelioma1CTD_human
TgeneC0458247Allodynia1CTD_human
TgeneC0555198Malignant Glioma1CTD_human
TgeneC0587248Costello syndrome (disorder)1CLINGEN
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC0740457Malignant neoplasm of kidney1CTD_human
TgeneC0751211Hyperalgesia, Primary1CTD_human
TgeneC0751212Hyperalgesia, Secondary1CTD_human
TgeneC0751213Tactile Allodynia1CTD_human
TgeneC0751214Hyperalgesia, Thermal1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1275081Cardio-facio-cutaneous syndrome1CLINGEN
TgeneC1449563Cardiomyopathy, Familial Idiopathic1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC2936719Mechanical Allodynia1CTD_human
TgeneC4014656CARDIOMYOPATHY, DILATED, 1NN1CTD_human;UNIPROT
TgeneC4551484Leopard Syndrome 11CTD_human;GENOMICS_ENGLAND
TgeneC4704874Mammary Carcinoma, Human1CTD_human
TgeneC4721610Carcinoma, Ovarian Epithelial1CTD_human