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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:ATF6-VCL (FusionGDB2 ID:HG22926TG7414)

Fusion Gene Summary for ATF6-VCL

check button Fusion gene summary
Fusion gene informationFusion gene name: ATF6-VCL
Fusion gene ID: hg22926tg7414
HgeneTgene
Gene symbol

ATF6

VCL

Gene ID

22926

7414

Gene nameactivating transcription factor 6vinculin
SynonymsACHM7|ATF6ACMD1W|CMH15|HEL114|MV|MVCL
Cytomap('ATF6')('VCL')

1q23.3

10q22.2

Type of geneprotein-codingprotein-coding
Descriptioncyclic AMP-dependent transcription factor ATF-6 alphacAMP-dependent transcription factor ATF-6 alphavinculinepididymis luminal protein 114epididymis secretory sperm binding proteinmeta-vinculinmetavinculin
Modification date2020031320200329
UniProtAcc

P18850

P18206

Ensembl transtripts involved in fusion geneENST00000367942, ENST00000476437, 
ENST00000476437, ENST00000367942, 
Fusion gene scores* DoF score12 X 10 X 8=96010 X 13 X 5=650
# samples 1212
** MAII scorelog2(12/960*10)=-3
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/650*10)=-2.4374053123073
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ATF6 [Title/Abstract] AND VCL [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATF6(161736232)-VCL(75854029), # samples:3
Anticipated loss of major functional domain due to fusion event.ATF6-VCL seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
VCL-ATF6 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
HgeneATF6

GO:0043065

positive regulation of apoptotic process

14752510

HgeneATF6

GO:0045944

positive regulation of transcription by RNA polymerase II

14973138

HgeneATF6

GO:1903893

positive regulation of ATF6-mediated unfolded protein response

9837962

HgeneATF6

GO:1990440

positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress

11163209|11256944|16469704

TgeneVCL

GO:1903140

regulation of establishment of endothelial barrier

26923917



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
ChimerDB4PRADTCGA-ZG-A9LY-01AATF6chr1

161736232

-VCLchr10

75854029

+
ChimerDB4PRADTCGA-ZG-A9LY-01AATF6chr1

161736232

+VCLchr10

75854029

+
ChimerDB4PRADTCGA-ZG-A9LYATF6chr1

161736232

+VCLchr10

75854028

+
ChimerDB4PRADTCGA-ZG-A9LYATF6chr1

161736232

+VCLchr10

75854029

+


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Fusion Gene ORF analysis for ATF6-VCL

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-intronENST00000367942ENST00000417648ATF6chr1

161736232

+VCLchr10

75854029

+
5CDS-intronENST00000367942ENST00000417648ATF6chr1

161736232

+VCLchr10

75854028

+
5CDS-intronENST00000367942ENST00000478896ATF6chr1

161736232

+VCLchr10

75854029

+
5CDS-intronENST00000367942ENST00000478896ATF6chr1

161736232

+VCLchr10

75854028

+
Frame-shiftENST00000367942ENST00000211998ATF6chr1

161736232

+VCLchr10

75854029

+
Frame-shiftENST00000367942ENST00000211998ATF6chr1

161736232

+VCLchr10

75854028

+
Frame-shiftENST00000367942ENST00000372755ATF6chr1

161736232

+VCLchr10

75854029

+
Frame-shiftENST00000367942ENST00000372755ATF6chr1

161736232

+VCLchr10

75854028

+
intron-3CDSENST00000476437ENST00000211998ATF6chr1

161736232

+VCLchr10

75854029

+
intron-3CDSENST00000476437ENST00000211998ATF6chr1

161736232

+VCLchr10

75854028

+
intron-3CDSENST00000476437ENST00000372755ATF6chr1

161736232

+VCLchr10

75854029

+
intron-3CDSENST00000476437ENST00000372755ATF6chr1

161736232

+VCLchr10

75854028

+
intron-intronENST00000476437ENST00000417648ATF6chr1

161736232

+VCLchr10

75854029

+
intron-intronENST00000476437ENST00000417648ATF6chr1

161736232

+VCLchr10

75854028

+
intron-intronENST00000476437ENST00000478896ATF6chr1

161736232

+VCLchr10

75854029

+
intron-intronENST00000476437ENST00000478896ATF6chr1

161736232

+VCLchr10

75854028

+

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 ATF6-VCL


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)
ATF6chr1161736232+VCLchr1075854028+2.32E-101
ATF6chr1161736232+VCLchr1075854028+2.32E-101
ATF6chr1161736232+VCLchr1075854028+2.32E-101
ATF6chr1161736232+VCLchr1075854028+2.32E-101


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 ATF6-VCL


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/:161736232/:75854029)
- 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
ATF6

P18850

VCL

P18206

FUNCTION: [Cyclic AMP-dependent transcription factor ATF-6 alpha]: Precursor of the transcription factor form (Processed cyclic AMP-dependent transcription factor ATF-6 alpha), which is embedded in the endoplasmic reticulum membrane (PubMed:10564271, PubMed:11158310, PubMed:11779464). Endoplasmic reticulum stress promotes processing of this form, releasing the transcription factor form that translocates into the nucleus, where it activates transcription of genes involved in the unfolded protein response (UPR) (PubMed:10564271, PubMed:11158310, PubMed:11779464). {ECO:0000269|PubMed:10564271, ECO:0000269|PubMed:11158310, ECO:0000269|PubMed:11779464}.; FUNCTION: [Processed cyclic AMP-dependent transcription factor ATF-6 alpha]: Transcription factor that initiates the unfolded protein response (UPR) during endoplasmic reticulum stress by activating transcription of genes involved in the UPR (PubMed:10564271, PubMed:11163209, PubMed:11158310, PubMed:11779464). Binds DNA on the 5'-CCAC[GA]-3'half of the ER stress response element (ERSE) (5'-CCAAT-N(9)-CCAC[GA]-3') and of ERSE II (5'-ATTGG-N-CCACG-3') (PubMed:10564271, PubMed:11158310, PubMed:11779464). Binding to ERSE requires binding of NF-Y to ERSE. Could also be involved in activation of transcription by the serum response factor (PubMed:10564271, PubMed:11158310, PubMed:11779464). May play a role in foveal development and cone function in the retina (PubMed:26029869). {ECO:0000269|PubMed:10564271, ECO:0000269|PubMed:11158310, ECO:0000269|PubMed:11163209, ECO:0000269|PubMed:11779464, ECO:0000269|PubMed:26029869}.FUNCTION: Actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion. {ECO:0000269|PubMed:20484056}.

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 ATF6-VCL


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 ATF6-VCL


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 ATF6-VCL


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 ATF6-VCL


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneATF6C0152200Achromatopsia2CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneATF6C4225297ACHROMATOPSIA 72CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneATF6C0003949Asbestosis1CTD_human
HgeneATF6C0009398Color vision defect1CTD_human
HgeneATF6C0022336Creutzfeldt-Jakob disease1CTD_human
HgeneATF6C0035334Retinitis Pigmentosa1CTD_human
HgeneATF6C0036457Scrapie1CTD_human
HgeneATF6C0085636Photophobia1CTD_human
HgeneATF6C0155015Color Blindness, Red1CTD_human
HgeneATF6C0155016Color Blindness, Red-Green1CTD_human
HgeneATF6C0155017Color Blindness, Blue1CTD_human
HgeneATF6C0155018Color Blindness, Acquired1CTD_human
HgeneATF6C0239777Color Blindness, Green1CTD_human
HgeneATF6C0242225Color blindness1CTD_human
HgeneATF6C0376329New Variant Creutzfeldt-Jakob Disease1CTD_human
HgeneATF6C0700501Congenital nystagmus1CTD_human
HgeneATF6C0751042Color Blindness, Inherited1CTD_human
HgeneATF6C0751043Monochromatopsia1CTD_human
HgeneATF6C0751254Creutzfeldt-Jakob Disease, Familial1CTD_human
HgeneATF6C2930617Pulmonary Fibrosis - from Asbestos Exposure1CTD_human
HgeneATF6C3489532Cone-Rod Dystrophy 21ORPHANET
TgeneC1969639Cardiomyopathy, Dilated, 1w5CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC2750459CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 154CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0007194Hypertrophic Cardiomyopathy3CLINGEN
TgeneC0001787Osteoporosis, Age-Related1CTD_human
TgeneC0029456Osteoporosis1CTD_human
TgeneC0029459Osteoporosis, Senile1CTD_human
TgeneC0340427Familial dilated cardiomyopathy1ORPHANET
TgeneC0751406Post-Traumatic Osteoporosis1CTD_human
TgeneC0948089Acute Coronary Syndrome1CTD_human