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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:CAPN1-LDLRAD4 (FusionGDB2 ID:12864)

Fusion Gene Summary for CAPN1-LDLRAD4

check button Fusion gene summary
Fusion gene informationFusion gene name: CAPN1-LDLRAD4
Fusion gene ID: 12864
HgeneTgene
Gene symbol

CAPN1

LDLRAD4

Gene ID

823

753

Gene namecalpain 1low density lipoprotein receptor class A domain containing 4
SynonymsCANP|CANP1|CANPL1|SPG76|muCANP|muCLC18orf1
Cytomap

11q13.1

18p11.21

Type of geneprotein-codingprotein-coding
Descriptioncalpain-1 catalytic subunitCANP 1calcium-activated neutral proteinase 1calpain 1, (mu/I) large subunitcalpain mu-typecalpain, large polypeptide L1calpain-1 large subunitcell proliferation-inducing gene 30 proteincell proliferation-inducing proteinlow-density lipoprotein receptor class A domain-containing protein 4clone 22
Modification date2020032220200320
UniProtAcc

P07384

O15165

Ensembl transtripts involved in fusion geneENST00000279247, ENST00000524773, 
ENST00000533820, ENST00000527323, 
ENST00000527469, ENST00000533129, 
ENST00000359446, ENST00000361205, 
ENST00000399848, ENST00000585931, 
ENST00000586765, ENST00000587757, 
ENST00000590308, ENST00000592991, 
Fusion gene scores* DoF score13 X 11 X 8=114422 X 20 X 7=3080
# samples 1324
** MAII scorelog2(13/1144*10)=-3.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(24/3080*10)=-3.68182403997374
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CAPN1 [Title/Abstract] AND LDLRAD4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCAPN1(64979477)-LDLRAD4(13464738), # 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
HgeneCAPN1

GO:0006508

proteolysis

2400579|2407243|16411745|21531719

HgeneCAPN1

GO:0050790

regulation of catalytic activity

8954105|9271093

HgeneCAPN1

GO:0097264

self proteolysis

8769305|8954105

TgeneLDLRAD4

GO:0010991

negative regulation of SMAD protein complex assembly

24627487


check buttonFusion gene breakpoints across CAPN1 (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 LDLRAD4 (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
ChiTaRS5.0N/ANM_001198868CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
ChiTaRS5.0N/ANM_001198869CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
ChiTaRS5.0N/ANM_005186CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-


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Fusion Gene ORF analysis for CAPN1-LDLRAD4

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-intronENST00000279247ENST00000359446CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000279247ENST00000361205CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000279247ENST00000399848CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000279247ENST00000585931CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000279247ENST00000586765CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000279247ENST00000587757CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000279247ENST00000590308CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000279247ENST00000592991CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000524773ENST00000359446CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000524773ENST00000361205CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000524773ENST00000399848CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000524773ENST00000585931CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000524773ENST00000586765CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000524773ENST00000587757CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000524773ENST00000590308CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000524773ENST00000592991CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000533820ENST00000359446CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000533820ENST00000361205CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000533820ENST00000399848CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000533820ENST00000585931CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000533820ENST00000586765CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000533820ENST00000587757CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000533820ENST00000590308CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
5CDS-intronENST00000533820ENST00000592991CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527323ENST00000359446CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527323ENST00000361205CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527323ENST00000399848CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527323ENST00000585931CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527323ENST00000586765CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527323ENST00000587757CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527323ENST00000590308CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527323ENST00000592991CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527469ENST00000359446CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527469ENST00000361205CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527469ENST00000399848CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527469ENST00000585931CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527469ENST00000586765CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527469ENST00000587757CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527469ENST00000590308CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000527469ENST00000592991CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000533129ENST00000359446CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000533129ENST00000361205CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000533129ENST00000399848CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000533129ENST00000585931CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000533129ENST00000586765CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000533129ENST00000587757CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000533129ENST00000590308CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-
intron-intronENST00000533129ENST00000592991CAPN1chr11

64979477

+LDLRAD4chr18

13464738

-

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 CAPN1-LDLRAD4


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)

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.

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Fusion Protein Features for CAPN1-LDLRAD4


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/:64979477/:13464738)
- 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
CAPN1

P07384

LDLRAD4

O15165

FUNCTION: Calcium-regulated non-lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction (PubMed:21531719, PubMed:2400579). Proteolytically cleaves CTBP1 at 'Asn-375', 'Gly-387' and 'His-409' (PubMed:23707407). {ECO:0000269|PubMed:21531719, ECO:0000269|PubMed:23707407, ECO:0000269|PubMed:2400579}.FUNCTION: Functions as a negative regulator of TGF-beta signaling and thereby probably plays a role in cell proliferation, differentiation, apoptosis, motility, extracellular matrix production and immunosuppression. In the canonical TGF-beta pathway, ZFYVE9/SARA recruits the intracellular signal transducer and transcriptional modulators SMAD2 and SMAD3 to the TGF-beta receptor. Phosphorylated by the receptor, SMAD2 and SMAD3 then form a heteromeric complex with SMAD4 that translocates to the nucleus to regulate transcription. Through interaction with SMAD2 and SMAD3, LDLRAD4 may compete with ZFYVE9 and SMAD4 and prevent propagation of the intracellular signal. {ECO:0000269|PubMed:24627487}.

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 CAPN1-LDLRAD4


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 CAPN1-LDLRAD4


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 CAPN1-LDLRAD4


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 CAPN1-LDLRAD4


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