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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:COL6A3-PLCB4 (FusionGDB2 ID:HG1293TG5332)

Fusion Gene Summary for COL6A3-PLCB4

check button Fusion gene summary
Fusion gene informationFusion gene name: COL6A3-PLCB4
Fusion gene ID: hg1293tg5332
HgeneTgene
Gene symbol

COL6A3

PLCB4

Gene ID

1293

5332

Gene namecollagen type VI alpha 3 chainphospholipase C beta 4
SynonymsBTHLM1|DYT27|UCMD1ARCND2|PI-PLC
Cytomap('COL6A3')('PLCB4')

2q37.3

20p12.3-p12.2

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-3(VI) chaincollagen VI, alpha-3 polypeptidecollagen, type VI, alpha 3epididymis secretory sperm binding protein1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-41-phosphatidyl-D-myo-inositol-4,5-bisphosphatePLC-beta-4dJ1119D9.2 (Phopholipase C, beta 4 (1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Beta 4))inositoltrisphosphohydrolase
Modification date2020032820200320
UniProtAcc

P12111

.
Ensembl transtripts involved in fusion geneENST00000295550, ENST00000346358, 
ENST00000347401, ENST00000353578, 
ENST00000392003, ENST00000392004, 
ENST00000409809, ENST00000472056, 
ENST00000473258, 
Fusion gene scores* DoF score13 X 12 X 6=93611 X 12 X 3=396
# samples 1312
** MAII scorelog2(13/936*10)=-2.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/396*10)=-1.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COL6A3 [Title/Abstract] AND PLCB4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOL6A3(238305370)-PLCB4(9416207), # samples:1
Anticipated loss of major functional domain due to fusion event.COL6A3-PLCB4 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
COL6A3-PLCB4 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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


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-BR-8365-01ACOL6A3chr2

238305370

-PLCB4chr20

9416207

+


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Fusion Gene ORF analysis for COL6A3-PLCB4

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-3UTRENST00000295550ENST00000378493COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000295550ENST00000378501COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000295550ENST00000492632COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000346358ENST00000378493COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000346358ENST00000378501COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000346358ENST00000492632COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000347401ENST00000378493COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000347401ENST00000378501COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000347401ENST00000492632COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000353578ENST00000378493COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000353578ENST00000378501COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000353578ENST00000492632COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000392003ENST00000378493COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000392003ENST00000378501COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000392003ENST00000492632COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000392004ENST00000378493COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000392004ENST00000378501COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000392004ENST00000492632COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000409809ENST00000378493COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000409809ENST00000378501COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000409809ENST00000492632COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000472056ENST00000378493COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000472056ENST00000378501COL6A3chr2

238305370

-PLCB4chr20

9416207

+
5CDS-3UTRENST00000472056ENST00000492632COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000295550ENST00000278655COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000295550ENST00000334005COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000295550ENST00000378473COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000295550ENST00000414679COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000346358ENST00000278655COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000346358ENST00000334005COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000346358ENST00000378473COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000346358ENST00000414679COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000347401ENST00000278655COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000347401ENST00000334005COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000347401ENST00000378473COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000347401ENST00000414679COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000353578ENST00000278655COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000353578ENST00000334005COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000353578ENST00000378473COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000353578ENST00000414679COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000392003ENST00000278655COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000392003ENST00000334005COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000392003ENST00000378473COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000392003ENST00000414679COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000392004ENST00000278655COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000392004ENST00000334005COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000392004ENST00000378473COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000392004ENST00000414679COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000409809ENST00000278655COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000409809ENST00000334005COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000409809ENST00000378473COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000409809ENST00000414679COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000472056ENST00000278655COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000472056ENST00000334005COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000472056ENST00000378473COL6A3chr2

238305370

-PLCB4chr20

9416207

+
Frame-shiftENST00000472056ENST00000414679COL6A3chr2

238305370

-PLCB4chr20

9416207

+
intron-3CDSENST00000473258ENST00000278655COL6A3chr2

238305370

-PLCB4chr20

9416207

+
intron-3CDSENST00000473258ENST00000334005COL6A3chr2

238305370

-PLCB4chr20

9416207

+
intron-3CDSENST00000473258ENST00000378473COL6A3chr2

238305370

-PLCB4chr20

9416207

+
intron-3CDSENST00000473258ENST00000414679COL6A3chr2

238305370

-PLCB4chr20

9416207

+
intron-3UTRENST00000473258ENST00000378493COL6A3chr2

238305370

-PLCB4chr20

9416207

+
intron-3UTRENST00000473258ENST00000378501COL6A3chr2

238305370

-PLCB4chr20

9416207

+
intron-3UTRENST00000473258ENST00000492632COL6A3chr2

238305370

-PLCB4chr20

9416207

+

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 COL6A3-PLCB4


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)
COL6A3chr2238305369-PLCB4chr209416206+0.0008332540.9991667
COL6A3chr2238305369-PLCB4chr209416206+0.0008332540.9991667


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 COL6A3-PLCB4


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/:238305370/:9416207)
- 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
COL6A3

P12111

.
FUNCTION: Collagen VI acts as a cell-binding protein.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 COL6A3-PLCB4


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 COL6A3-PLCB4


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 COL6A3-PLCB4


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 COL6A3-PLCB4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL6A3C1834674BETHLEM MYOPATHY 15CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCOL6A3C0410179Ullrich congenital muscular dystrophy 14CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL6A3C4225336DYSTONIA 272GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL6A3C0000786Spontaneous abortion1CTD_human
HgeneCOL6A3C0000822Abortion, Tubal1CTD_human
HgeneCOL6A3C0027708Nephroblastoma1CTD_human
HgeneCOL6A3C2930471Bilateral Wilms Tumor1CTD_human
HgeneCOL6A3C3830362Early Pregnancy Loss1CTD_human
HgeneCOL6A3C4552766Miscarriage1CTD_human
TgeneC0025202melanoma1CTD_human
TgeneC0152423Congenital small ears1GENOMICS_ENGLAND
TgeneC0220633Uveal melanoma1CTD_human
TgeneC1865295Auriculo-condylar syndrome1CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC3553404AURICULOCONDYLAR SYNDROME 21GENOMICS_ENGLAND;UNIPROT