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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-LRRC23 (FusionGDB2 ID:17360)

Fusion Gene Summary for CLSTN3-LRRC23

check button Fusion gene summary
Fusion gene informationFusion gene name: CLSTN3-LRRC23
Fusion gene ID: 17360
HgeneTgene
Gene symbol

CLSTN3

LRRC23

Gene ID

9746

10233

Gene namecalsyntenin 3leucine rich repeat containing 23
SynonymsCDHR14|CSTN3|alcbetaLRPB7
Cytomap

12p13.31

12p13.31

Type of geneprotein-codingprotein-coding
Descriptioncalsyntenin-3alc-betaalcadein betacadherin-related family member 14leucine-rich repeat-containing protein 23leucine-rich protein B7
Modification date2020032020200313
UniProtAcc

Q9BQT9

Q53EV4

Ensembl transtripts involved in fusion geneENST00000266546, ENST00000537408, 
ENST00000331148, 		ENST00000007969, 
ENST00000323702, ENST00000429740, 
ENST00000436789, ENST00000443597, 
ENST00000433346, ENST00000449039, 
Fusion gene scores* DoF score7 X 5 X 5=1757 X 7 X 7=343
# samples 810
** MAII scorelog2(8/175*10)=-1.12928301694497
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/343*10)=-1.77820857639809
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLSTN3 [Title/Abstract] AND LRRC23 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLSTN3(7295907)-LRRC23(7023055), # 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 buttonFusion gene breakpoints across CLSTN3 (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 LRRC23 (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
ChimerDB4LIHCTCGA-DD-AADA-01ACLSTN3chr12

7295907

-LRRC23chr12

7023055

+
ChimerDB4LIHCTCGA-DD-AADA-01ACLSTN3chr12

7295907

+LRRC23chr12

7023055

+
ChimerDB4LIHCTCGA-DD-AADACLSTN3chr12

7295907

+LRRC23chr12

7023054

+
ChimerDB4LIHCTCGA-DD-AADACLSTN3chr12

7295907

+LRRC23chr12

7023055

+


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Fusion Gene ORF analysis for CLSTN3-LRRC23

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-3UTRENST00000266546ENST00000007969CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-3UTRENST00000266546ENST00000007969CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
5CDS-3UTRENST00000266546ENST00000323702CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-3UTRENST00000266546ENST00000323702CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
5CDS-3UTRENST00000266546ENST00000429740CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-3UTRENST00000266546ENST00000429740CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
5CDS-3UTRENST00000266546ENST00000436789CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-3UTRENST00000266546ENST00000436789CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
5CDS-3UTRENST00000266546ENST00000443597CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-3UTRENST00000266546ENST00000443597CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
5CDS-3UTRENST00000537408ENST00000007969CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-3UTRENST00000537408ENST00000007969CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
5CDS-3UTRENST00000537408ENST00000323702CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-3UTRENST00000537408ENST00000323702CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
5CDS-3UTRENST00000537408ENST00000429740CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-3UTRENST00000537408ENST00000429740CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
5CDS-3UTRENST00000537408ENST00000436789CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-3UTRENST00000537408ENST00000436789CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
5CDS-3UTRENST00000537408ENST00000443597CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-3UTRENST00000537408ENST00000443597CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
5CDS-intronENST00000266546ENST00000433346CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-intronENST00000266546ENST00000433346CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
5CDS-intronENST00000266546ENST00000449039CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-intronENST00000266546ENST00000449039CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
5CDS-intronENST00000537408ENST00000433346CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-intronENST00000537408ENST00000433346CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
5CDS-intronENST00000537408ENST00000449039CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
5CDS-intronENST00000537408ENST00000449039CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
intron-3UTRENST00000331148ENST00000007969CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
intron-3UTRENST00000331148ENST00000007969CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
intron-3UTRENST00000331148ENST00000323702CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
intron-3UTRENST00000331148ENST00000323702CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
intron-3UTRENST00000331148ENST00000429740CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
intron-3UTRENST00000331148ENST00000429740CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
intron-3UTRENST00000331148ENST00000436789CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
intron-3UTRENST00000331148ENST00000436789CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
intron-3UTRENST00000331148ENST00000443597CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
intron-3UTRENST00000331148ENST00000443597CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
intron-intronENST00000331148ENST00000433346CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
intron-intronENST00000331148ENST00000433346CLSTN3chr12

7295907

+LRRC23chr12

7023054

+
intron-intronENST00000331148ENST00000449039CLSTN3chr12

7295907

+LRRC23chr12

7023055

+
intron-intronENST00000331148ENST00000449039CLSTN3chr12

7295907

+LRRC23chr12

7023054

+

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-LRRC23


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)
CLSTN3chr127295907+LRRC23chr127023054+4.83E-050.9999517
CLSTN3chr127295907+LRRC23chr127023054+4.83E-050.9999517
CLSTN3chr127295907+LRRC23chr127023054+4.83E-050.9999517
CLSTN3chr127295907+LRRC23chr127023054+4.83E-050.9999517

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 CLSTN3-LRRC23


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/:7295907/:7023055)
- 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
CLSTN3

Q9BQT9

LRRC23

Q53EV4

FUNCTION: May modulate calcium-mediated postsynaptic signals. Complex formation with APBA2 and APP, stabilizes APP metabolism and enhances APBA2-mediated suppression of beta-APP40 secretion, due to the retardation of intracellular APP maturation. {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 CLSTN3-LRRC23


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-LRRC23


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-LRRC23


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 CLSTN3-LRRC23


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