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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:CLCN5-PAGE1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CLCN5-PAGE1
FusionPDB ID: 17002
FusionGDB2.0 ID: 17002
HgeneTgene
Gene symbol

CLCN5

PAGE1

Gene ID

1184

8712

Gene namechloride voltage-gated channel 5PAGE family member 1
SynonymsCLC5|CLCK2|ClC-5|DENTS|NPHL1|NPHL2|XLRH|XRN|hCIC-K2AL5|CT16.3|GAGE-9|GAGEB1|PAGE-1
Cytomap

Xp11.23

Xp11.23

Type of geneprotein-codingprotein-coding
DescriptionH(+)/Cl(-) exchange transporter 5chloride channel, voltage-sensitive 5chloride transporter ClC-5voltage-gated chloride ion channel CLCN5P antigen family member 1G antigen 9G antigen family B member 1G antigen, family B, 1 (prostate associated)P antigen family, member 1 (prostate associated)prostate associated gene 1prostate-associated gene 1 protein
Modification date2020031320200313
UniProtAcc

P51795

.
Ensembl transtripts involved in fusion geneENST idsENST00000376088, ENST00000376091, 
ENST00000482218, ENST00000307367, 
ENST00000376108, 		ENST00000376150, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score6 X 4 X 4=963 X 3 X 3=27
# samples 63
** MAII scorelog2(6/96*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: CLCN5 [Title/Abstract] AND PAGE1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CLCN5(49689924)-PAGE1(49455977), # samples:3
Anticipated loss of major functional domain due to fusion event.CLCN5-PAGE1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
CLCN5-PAGE1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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 CLCN5 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across PAGE1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4STADTCGA-VQ-AA6J-01ACLCN5chrX

49689924

-PAGE1chrX

49455977

-
ChimerDB4STADTCGA-VQ-AA6J-01ACLCN5chrX

49689924

+PAGE1chrX

49455977

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000376088CLCN5chrX49689924+ENST00000376150PAGE1chrX49455977-1023657593931112
ENST00000376091CLCN5chrX49689924+ENST00000376150PAGE1chrX49455977-714348284622112
ENST00000482218CLCN5chrX49689924+ENST00000376150PAGE1chrX49455977-589223159497112

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
ENST00000376088ENST00000376150CLCN5chrX49689924+PAGE1chrX49455977-0.0956694260.90433055
ENST00000376091ENST00000376150CLCN5chrX49689924+PAGE1chrX49455977-0.066975390.93302464
ENST00000482218ENST00000376150CLCN5chrX49689924+PAGE1chrX49455977-0.054903780.94509625

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>17002_17002_1_CLCN5-PAGE1_CLCN5_chrX_49689924_ENST00000376088_PAGE1_chrX_49455977_ENST00000376150_length(amino acids)=112AA_BP=63
MGNSACDPSVGEDRIKMAMWQGQEPEADSQELVQPKTGCELGDGPDTKRVCLRNEEQMKLPAEGPEPEADSQEQVHPKTGCERGDGPDVQ

--------------------------------------------------------------

>17002_17002_2_CLCN5-PAGE1_CLCN5_chrX_49689924_ENST00000376091_PAGE1_chrX_49455977_ENST00000376150_length(amino acids)=112AA_BP=63
MGNSACDPSVGEDRIKMAMWQGQEPEADSQELVQPKTGCELGDGPDTKRVCLRNEEQMKLPAEGPEPEADSQEQVHPKTGCERGDGPDVQ

--------------------------------------------------------------

>17002_17002_3_CLCN5-PAGE1_CLCN5_chrX_49689924_ENST00000482218_PAGE1_chrX_49455977_ENST00000376150_length(amino acids)=112AA_BP=63
MGNSACDPSVGEDRIKMAMWQGQEPEADSQELVQPKTGCELGDGPDTKRVCLRNEEQMKLPAEGPEPEADSQEQVHPKTGCERGDGPDVQ

--------------------------------------------------------------

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Fusion Protein Functional Features


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/chrX:49689924/chrX:49455977)
- 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
CLCN5

P51795

.
FUNCTION: Proton-coupled chloride transporter. Functions as antiport system and exchanges chloride ions against protons. Important for normal acidification of the endosome lumen. May play an important role in renal tubular function.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112656_7200747.0DomainCBS 1
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112752_8120747.0DomainCBS 2
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315656_7205.333333333333333817.0DomainCBS 1
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315752_8125.333333333333333817.0DomainCBS 2
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315656_7205.333333333333333817.0DomainCBS 1
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315752_8125.333333333333333817.0DomainCBS 2
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112656_7200747.0DomainCBS 1
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112752_8120747.0DomainCBS 2
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112240_2470747.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112312_3240747.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112328_3360747.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112570_5840747.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112585_5870747.0IntramembraneNote%3DLoop between two helices
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112588_5990747.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112600_6040747.0IntramembraneNote%3DLoop between two helices
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315240_2475.333333333333333817.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315312_3245.333333333333333817.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315328_3365.333333333333333817.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315570_5845.333333333333333817.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315585_5875.333333333333333817.0IntramembraneNote%3DLoop between two helices
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315588_5995.333333333333333817.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315600_6045.333333333333333817.0IntramembraneNote%3DLoop between two helices
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315240_2475.333333333333333817.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315312_3245.333333333333333817.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315328_3365.333333333333333817.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315570_5845.333333333333333817.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315585_5875.333333333333333817.0IntramembraneNote%3DLoop between two helices
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315588_5995.333333333333333817.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315600_6045.333333333333333817.0IntramembraneNote%3DLoop between two helices
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112240_2470747.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112312_3240747.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112328_3360747.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112570_5840747.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112585_5870747.0IntramembraneNote%3DLoop between two helices
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112588_5990747.0IntramembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112600_6040747.0IntramembraneNote%3DLoop between two helices
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112237_2410747.0MotifSelectivity filter part_1
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112279_2830747.0MotifSelectivity filter part_2
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112523_5270747.0MotifSelectivity filter part_3
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315237_2415.333333333333333817.0MotifSelectivity filter part_1
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315279_2835.333333333333333817.0MotifSelectivity filter part_2
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315523_5275.333333333333333817.0MotifSelectivity filter part_3
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315237_2415.333333333333333817.0MotifSelectivity filter part_1
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315279_2835.333333333333333817.0MotifSelectivity filter part_2
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315523_5275.333333333333333817.0MotifSelectivity filter part_3
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112237_2410747.0MotifSelectivity filter part_1
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112279_2830747.0MotifSelectivity filter part_2
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112523_5270747.0MotifSelectivity filter part_3
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112687_6890747.0Nucleotide bindingATP
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112794_7970747.0Nucleotide bindingATP
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315687_6895.333333333333333817.0Nucleotide bindingATP
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315794_7975.333333333333333817.0Nucleotide bindingATP
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315687_6895.333333333333333817.0Nucleotide bindingATP
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315794_7975.333333333333333817.0Nucleotide bindingATP
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112687_6890747.0Nucleotide bindingATP
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112794_7970747.0Nucleotide bindingATP
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+1121_1240747.0Topological domainCytoplasmic
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112623_8160747.0Topological domainCytoplasmic
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+3151_1245.333333333333333817.0Topological domainCytoplasmic
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315623_8165.333333333333333817.0Topological domainCytoplasmic
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+3151_1245.333333333333333817.0Topological domainCytoplasmic
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315623_8165.333333333333333817.0Topological domainCytoplasmic
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+1121_1240747.0Topological domainCytoplasmic
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112623_8160747.0Topological domainCytoplasmic
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112125_1620747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112208_2310747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112256_2750747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112281_3000747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112348_3660747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112389_4150747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112422_4420747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112498_5180747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112523_5420747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000307367+112605_6220747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315125_1625.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315208_2315.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315256_2755.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315281_3005.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315348_3665.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315389_4155.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315422_4425.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315498_5185.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315523_5425.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376088+315605_6225.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315125_1625.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315208_2315.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315256_2755.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315281_3005.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315348_3665.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315389_4155.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315422_4425.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315498_5185.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315523_5425.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376091+315605_6225.333333333333333817.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112125_1620747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112208_2310747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112256_2750747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112281_3000747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112348_3660747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112389_4150747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112422_4420747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112498_5180747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112523_5420747.0TransmembraneHelical
HgeneCLCN5chrX:49689924chrX:49455977ENST00000376108+112605_6220747.0TransmembraneHelical


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
CLCN5
PAGE1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to CLCN5-PAGE1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to CLCN5-PAGE1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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