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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:CALM3-CCDC9 (FusionGDB2 ID:12568)

Fusion Gene Summary for CALM3-CCDC9

check button Fusion gene summary
Fusion gene informationFusion gene name: CALM3-CCDC9
Fusion gene ID: 12568
HgeneTgene
Gene symbol

CALM3

CCDC9

Gene ID

808

26093

Gene namecalmodulin 3coiled-coil domain containing 9
SynonymsCALM|CAM1|CAM2|CAMB|CPVT6|CaM|CaMIII|HEL-S-72|LQT16|PHKD|PHKD3-
Cytomap

19q13.32

19q13.32

Type of geneprotein-codingprotein-coding
Descriptioncalmodulin-3Calmodulin-1Calmodulin-2epididymis secretory protein Li 72phosphorylase kinase subunit deltaprepro-calmodulin 3coiled-coil domain-containing protein 9
Modification date2020031320200313
UniProtAcc

P0DP25

Q96F63

Ensembl transtripts involved in fusion geneENST00000477244, ENST00000291295, 
ENST00000597743, ENST00000594523, 
ENST00000598871, ENST00000391918, 
ENST00000596362, ENST00000599839, 
ENST00000221922, ENST00000601154, 
Fusion gene scores* DoF score11 X 9 X 7=6935 X 6 X 4=120
# samples 137
** MAII scorelog2(13/693*10)=-2.41434372910876
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/120*10)=-0.777607578663552
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CALM3 [Title/Abstract] AND CCDC9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCALM3(47104694)-CCDC9(47761587), # samples:2
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
HgeneCALM3

GO:0010880

regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum

20226167

HgeneCALM3

GO:0032516

positive regulation of phosphoprotein phosphatase activity

8631777

HgeneCALM3

GO:0035307

positive regulation of protein dephosphorylation

8631777

HgeneCALM3

GO:0051343

positive regulation of cyclic-nucleotide phosphodiesterase activity

8631777

HgeneCALM3

GO:0051592

response to calcium ion

7607248

HgeneCALM3

GO:0060316

positive regulation of ryanodine-sensitive calcium-release channel activity

20226167


check buttonFusion gene breakpoints across CALM3 (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 CCDC9 (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-DU-8166-01ACALM3chr19

47104694

+CCDC9chr19

47761587

+
ChimerDB4LGGTCGA-DU-8166CALM3chr19

47104694

+CCDC9chr19

47761586

+
ChimerDB4LGGTCGA-DU-8166CALM3chr19

47104694

+CCDC9chr19

47761587

+


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Fusion Gene ORF analysis for CALM3-CCDC9

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
3UTR-5UTRENST00000477244ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761587

+
3UTR-5UTRENST00000477244ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761586

+
3UTR-intronENST00000477244ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761587

+
3UTR-intronENST00000477244ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761586

+
5CDS-5UTRENST00000291295ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761587

+
5CDS-5UTRENST00000291295ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761586

+
5CDS-5UTRENST00000597743ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761587

+
5CDS-5UTRENST00000597743ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761586

+
5CDS-intronENST00000291295ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761587

+
5CDS-intronENST00000291295ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761586

+
5CDS-intronENST00000597743ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761587

+
5CDS-intronENST00000597743ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761586

+
5UTR-5UTRENST00000594523ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761587

+
5UTR-5UTRENST00000594523ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761586

+
5UTR-5UTRENST00000598871ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761587

+
5UTR-5UTRENST00000598871ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761586

+
5UTR-intronENST00000594523ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761587

+
5UTR-intronENST00000594523ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761586

+
5UTR-intronENST00000598871ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761587

+
5UTR-intronENST00000598871ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761586

+
intron-5UTRENST00000391918ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761587

+
intron-5UTRENST00000391918ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761586

+
intron-5UTRENST00000596362ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761587

+
intron-5UTRENST00000596362ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761586

+
intron-5UTRENST00000599839ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761587

+
intron-5UTRENST00000599839ENST00000221922CALM3chr19

47104694

+CCDC9chr19

47761586

+
intron-intronENST00000391918ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761587

+
intron-intronENST00000391918ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761586

+
intron-intronENST00000596362ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761587

+
intron-intronENST00000596362ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761586

+
intron-intronENST00000599839ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761587

+
intron-intronENST00000599839ENST00000601154CALM3chr19

47104694

+CCDC9chr19

47761586

+

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 CALM3-CCDC9


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)
CALM3chr1947104694+CCDC9chr1947761586+2.24E-050.9999776
CALM3chr1947104694+CCDC9chr1947761586+2.24E-050.9999776
CALM3chr1947104694+CCDC9chr1947761586+2.24E-050.9999776
CALM3chr1947104694+CCDC9chr1947761586+2.24E-050.9999776

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 CALM3-CCDC9


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/:47104694/:47761587)
- 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
CALM3

P0DP25

CCDC9

Q96F63

FUNCTION: Calmodulin mediates the control of a large number of enzymes, ion channels, aquaporins and other proteins through calcium-binding. Is a regulator of voltage-dependent L-type calcium channels (PubMed:31454269). Among the enzymes to be stimulated by the calmodulin-calcium complex are a number of protein kinases and phosphatases. Together with CCP110 and centrin, is involved in a genetic pathway that regulates the centrosome cycle and progression through cytokinesis. {ECO:0000250|UniProtKB:P0DP23, ECO:0000269|PubMed:16760425, ECO:0000269|PubMed:31454269}.

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 CALM3-CCDC9


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 CALM3-CCDC9


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 CALM3-CCDC9


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 CALM3-CCDC9


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