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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:CLCN7-MLST8 (FusionGDB2 ID:17011)

Fusion Gene Summary for CLCN7-MLST8

check button Fusion gene summary
Fusion gene informationFusion gene name: CLCN7-MLST8
Fusion gene ID: 17011
HgeneTgene
Gene symbol

CLCN7

MLST8

Gene ID

1186

64223

Gene namechloride voltage-gated channel 7MTOR associated protein, LST8 homolog
SynonymsCLC-7|CLC7|HOD|OPTA2|OPTB4|PPP1R63GBL|GbetaL|LST8|POP3|WAT1
Cytomap

16p13.3

16p13.3

Type of geneprotein-codingprotein-coding
DescriptionH(+)/Cl(-) exchange transporter 7chloride channel 7 alpha subunitchloride channel protein 7chloride channel, voltage-sensitive 7protein phosphatase 1, regulatory subunit 63target of rapamycin complex subunit LST8TORC subunit LST8gablemammalian lethal with SEC13 protein 8protein GbetaL
Modification date2020031520200320
UniProtAcc.

Q9BVC4

Ensembl transtripts involved in fusion geneENST00000262318, ENST00000382745, 
ENST00000448525, ENST00000566812, 
ENST00000301724, ENST00000301725, 
ENST00000397124, ENST00000561651, 
ENST00000565250, ENST00000382450, 
ENST00000564088, ENST00000569417, 
Fusion gene scores* DoF score5 X 6 X 4=1202 X 2 X 2=8
# samples 52
** MAII scorelog2(5/120*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/8*10)=1.32192809488736
Context

PubMed: CLCN7 [Title/Abstract] AND MLST8 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLCN7(1510816)-MLST8(2256358), # samples:1
Anticipated loss of major functional domain due to fusion event.CLCN7-MLST8 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CLCN7-MLST8 seems lost the major protein functional domain in Tgene 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

check buttonFusion gene breakpoints across CLCN7 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across MLST8 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChimerDB4LGGTCGA-CS-4944CLCN7chr16

1510816

-MLST8chr16

2256358

+


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Fusion Gene ORF analysis for CLCN7-MLST8

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-3UTRENST00000262318ENST00000301724CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000262318ENST00000301725CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000262318ENST00000397124CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000262318ENST00000561651CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000262318ENST00000565250CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000382745ENST00000301724CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000382745ENST00000301725CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000382745ENST00000397124CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000382745ENST00000561651CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000382745ENST00000565250CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000448525ENST00000301724CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000448525ENST00000301725CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000448525ENST00000397124CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000448525ENST00000561651CLCN7chr16

1510816

-MLST8chr16

2256358

+
5CDS-3UTRENST00000448525ENST00000565250CLCN7chr16

1510816

-MLST8chr16

2256358

+
Frame-shiftENST00000262318ENST00000382450CLCN7chr16

1510816

-MLST8chr16

2256358

+
Frame-shiftENST00000262318ENST00000564088CLCN7chr16

1510816

-MLST8chr16

2256358

+
Frame-shiftENST00000262318ENST00000569417CLCN7chr16

1510816

-MLST8chr16

2256358

+
Frame-shiftENST00000382745ENST00000382450CLCN7chr16

1510816

-MLST8chr16

2256358

+
Frame-shiftENST00000382745ENST00000564088CLCN7chr16

1510816

-MLST8chr16

2256358

+
Frame-shiftENST00000382745ENST00000569417CLCN7chr16

1510816

-MLST8chr16

2256358

+
Frame-shiftENST00000448525ENST00000382450CLCN7chr16

1510816

-MLST8chr16

2256358

+
Frame-shiftENST00000448525ENST00000564088CLCN7chr16

1510816

-MLST8chr16

2256358

+
Frame-shiftENST00000448525ENST00000569417CLCN7chr16

1510816

-MLST8chr16

2256358

+
intron-3CDSENST00000566812ENST00000382450CLCN7chr16

1510816

-MLST8chr16

2256358

+
intron-3CDSENST00000566812ENST00000564088CLCN7chr16

1510816

-MLST8chr16

2256358

+
intron-3CDSENST00000566812ENST00000569417CLCN7chr16

1510816

-MLST8chr16

2256358

+
intron-3UTRENST00000566812ENST00000301724CLCN7chr16

1510816

-MLST8chr16

2256358

+
intron-3UTRENST00000566812ENST00000301725CLCN7chr16

1510816

-MLST8chr16

2256358

+
intron-3UTRENST00000566812ENST00000397124CLCN7chr16

1510816

-MLST8chr16

2256358

+
intron-3UTRENST00000566812ENST00000561651CLCN7chr16

1510816

-MLST8chr16

2256358

+
intron-3UTRENST00000566812ENST00000565250CLCN7chr16

1510816

-MLST8chr16

2256358

+

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 CLCN7-MLST8


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)
CLCN7chr161510816-MLST8chr162256361+0.0048786740.9951213
CLCN7chr161510816-MLST8chr162256361+0.0048786740.9951213

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.

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 CLCN7-MLST8


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/:1510816/:2256358)
- 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
.MLST8

Q9BVC4

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: Subunit of both mTORC1 and mTORC2, which regulates cell growth and survival in response to nutrient and hormonal signals. mTORC1 is activated in response to growth factors or amino acids. Growth factor-stimulated mTORC1 activation involves a AKT1-mediated phosphorylation of TSC1-TSC2, which leads to the activation of the RHEB GTPase that potently activates the protein kinase activity of mTORC1. Amino acid-signaling to mTORC1 requires its relocalization to the lysosomes mediated by the Ragulator complex and the Rag GTPases. Activated mTORC1 up-regulates protein synthesis by phosphorylating key regulators of mRNA translation and ribosome synthesis. mTORC1 phosphorylates EIF4EBP1 and releases it from inhibiting the elongation initiation factor 4E (eiF4E). mTORC1 phosphorylates and activates S6K1 at 'Thr-389', which then promotes protein synthesis by phosphorylating PDCD4 and targeting it for degradation. Within mTORC1, LST8 interacts directly with MTOR and enhances its kinase activity. In nutrient-poor conditions, stabilizes the MTOR-RPTOR interaction and favors RPTOR-mediated inhibition of MTOR activity. mTORC2 is also activated by growth factors, but seems to be nutrient-insensitive. mTORC2 seems to function upstream of Rho GTPases to regulate the actin cytoskeleton, probably by activating one or more Rho-type guanine nucleotide exchange factors. mTORC2 promotes the serum-induced formation of stress-fibers or F-actin. mTORC2 plays a critical role in AKT1 'Ser-473' phosphorylation, which may facilitate the phosphorylation of the activation loop of AKT1 on 'Thr-308' by PDK1 which is a prerequisite for full activation. mTORC2 regulates the phosphorylation of SGK1 at 'Ser-422'. mTORC2 also modulates the phosphorylation of PRKCA on 'Ser-657'. {ECO:0000250|UniProtKB:Q9DCJ1, ECO:0000269|PubMed:12718876, ECO:0000269|PubMed:15467718}.

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 CLCN7-MLST8


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 CLCN7-MLST8


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 CLCN7-MLST8


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 CLCN7-MLST8


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource