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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:CLSTN3-C1S (FusionGDB2 ID:HG9746TG716)

Fusion Gene Summary for CLSTN3-C1S

check button Fusion gene summary
Fusion gene informationFusion gene name: CLSTN3-C1S
Fusion gene ID: hg9746tg716
HgeneTgene
Gene symbol

CLSTN3

C1S

Gene ID

9746

716

Gene namecalsyntenin 3complement C1s
SynonymsCDHR14|CSTN3|alcbetaEDSPD2
Cytomap('CLSTN3')('C1S')

12p13.31

12p13.31

Type of geneprotein-codingprotein-coding
Descriptioncalsyntenin-3alc-betaalcadein betacadherin-related family member 14complement C1s subcomponentC1 esterasebasic proline-rich peptide IB-1complement component 1 subcomponent scomplement component 1, s subcomponent
Modification date2020032020200313
UniProtAcc.

P09871

Ensembl transtripts involved in fusion geneENST00000266546, ENST00000537408, 
ENST00000331148, 
Fusion gene scores* DoF score7 X 5 X 5=17510 X 11 X 3=330
# samples 810
** MAII scorelog2(8/175*10)=-1.12928301694497
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/330*10)=-1.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLSTN3 [Title/Abstract] AND C1S [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLSTN3(7288987)-C1S(7169056), # samples:3
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


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
ChimerDB4LIHCTCGA-ZP-A9CZ-01ACLSTN3chr12

7288987

-C1Schr12

7169056

+
ChimerDB4LIHCTCGA-ZP-A9CZ-01ACLSTN3chr12

7288987

+C1Schr12

7169056

+
ChimerDB4LIHCTCGA-ZP-A9CZ-01ACLSTN3chr12

7288987

+C1Schr12

7169143

+


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Fusion Gene ORF analysis for CLSTN3-C1S

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-5UTRENST00000266546ENST00000328916CLSTN3chr12

7288987

+C1Schr12

7169056

+
5CDS-5UTRENST00000266546ENST00000328916CLSTN3chr12

7288987

+C1Schr12

7169143

+
5CDS-5UTRENST00000266546ENST00000360817CLSTN3chr12

7288987

+C1Schr12

7169143

+
5CDS-5UTRENST00000266546ENST00000402681CLSTN3chr12

7288987

+C1Schr12

7169056

+
5CDS-5UTRENST00000266546ENST00000402681CLSTN3chr12

7288987

+C1Schr12

7169143

+
5CDS-5UTRENST00000266546ENST00000406697CLSTN3chr12

7288987

+C1Schr12

7169143

+
5CDS-5UTRENST00000537408ENST00000328916CLSTN3chr12

7288987

+C1Schr12

7169056

+
5CDS-5UTRENST00000537408ENST00000328916CLSTN3chr12

7288987

+C1Schr12

7169143

+
5CDS-5UTRENST00000537408ENST00000360817CLSTN3chr12

7288987

+C1Schr12

7169143

+
5CDS-5UTRENST00000537408ENST00000402681CLSTN3chr12

7288987

+C1Schr12

7169056

+
5CDS-5UTRENST00000537408ENST00000402681CLSTN3chr12

7288987

+C1Schr12

7169143

+
5CDS-5UTRENST00000537408ENST00000406697CLSTN3chr12

7288987

+C1Schr12

7169143

+
5CDS-intronENST00000266546ENST00000360817CLSTN3chr12

7288987

+C1Schr12

7169056

+
5CDS-intronENST00000266546ENST00000406697CLSTN3chr12

7288987

+C1Schr12

7169056

+
5CDS-intronENST00000266546ENST00000495061CLSTN3chr12

7288987

+C1Schr12

7169056

+
5CDS-intronENST00000266546ENST00000495061CLSTN3chr12

7288987

+C1Schr12

7169143

+
5CDS-intronENST00000537408ENST00000360817CLSTN3chr12

7288987

+C1Schr12

7169056

+
5CDS-intronENST00000537408ENST00000406697CLSTN3chr12

7288987

+C1Schr12

7169056

+
5CDS-intronENST00000537408ENST00000495061CLSTN3chr12

7288987

+C1Schr12

7169056

+
5CDS-intronENST00000537408ENST00000495061CLSTN3chr12

7288987

+C1Schr12

7169143

+
intron-5UTRENST00000331148ENST00000328916CLSTN3chr12

7288987

+C1Schr12

7169056

+
intron-5UTRENST00000331148ENST00000328916CLSTN3chr12

7288987

+C1Schr12

7169143

+
intron-5UTRENST00000331148ENST00000360817CLSTN3chr12

7288987

+C1Schr12

7169143

+
intron-5UTRENST00000331148ENST00000402681CLSTN3chr12

7288987

+C1Schr12

7169056

+
intron-5UTRENST00000331148ENST00000402681CLSTN3chr12

7288987

+C1Schr12

7169143

+
intron-5UTRENST00000331148ENST00000406697CLSTN3chr12

7288987

+C1Schr12

7169143

+
intron-intronENST00000331148ENST00000360817CLSTN3chr12

7288987

+C1Schr12

7169056

+
intron-intronENST00000331148ENST00000406697CLSTN3chr12

7288987

+C1Schr12

7169056

+
intron-intronENST00000331148ENST00000495061CLSTN3chr12

7288987

+C1Schr12

7169056

+
intron-intronENST00000331148ENST00000495061CLSTN3chr12

7288987

+C1Schr12

7169143

+

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 CLSTN3-C1S


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)
CLSTN3chr127288987+C1Schr127169142+0.397359430.60264057
CLSTN3chr127288987+C1Schr127169055+0.0135310670.9864689
CLSTN3chr127288987+C1Schr127169142+0.397359430.60264057
CLSTN3chr127288987+C1Schr127169055+0.0135310670.9864689


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 CLSTN3-C1S


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/:7288987/:7169056)
- 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
.C1S

P09871

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: C1s B chain is a serine protease that combines with C1q and C1r to form C1, the first component of the classical pathway of the complement system. C1r activates C1s so that it can, in turn, activate C2 and C4.

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 CLSTN3-C1S


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 CLSTN3-C1S


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 CLSTN3-C1S


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneC1SP09871DB06404Human C1-esterase inhibitorInhibitorBiotechApproved
TgeneC1SP09871DB14548Zinc sulfate, unspecified formModulatorSmall moleculeApproved|Experimental
TgeneC1SP09871DB01593ZincSmall moleculeApproved|Investigational
TgeneC1SP09871DB09130CopperSmall moleculeApproved|Investigational
TgeneC1SP09871DB09228Conestat alfaInhibitorBiotechApproved|Investigational
TgeneC1SP09871DB14487Zinc acetateSmall moleculeApproved|Investigational
TgeneC1SP09871DB14533Zinc chlorideModulatorSmall moleculeApproved|Investigational

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Related Diseases for CLSTN3-C1S


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC4310681EHLERS-DANLOS SYNDROME, PERIODONTAL TYPE, 22CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0004364Autoimmune Diseases1CTD_human
TgeneC0024141Lupus Erythematosus, Systemic1GENOMICS_ENGLAND
TgeneC0241910Autoimmune Chronic Hepatitis1CTD_human
TgeneC0268347Ehlers-Danlos Syndrome, Type VIII1ORPHANET
TgeneC0272242Complement deficiency disease1GENOMICS_ENGLAND
TgeneC0677607Hashimoto Disease1CTD_human
TgeneC1862892Hereditary Angioedema Type II1CTD_human
TgeneC2717905Hereditary Angioedema Types I and II1CTD_human
TgeneC2717906Hereditary Angioedema Type I1CTD_human
TgeneC3151078Complement Component C1s Deficiency1CTD_human;GENOMICS_ENGLAND