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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:CAMSAP3-PML (FusionGDB2 ID:12749)

Fusion Gene Summary for CAMSAP3-PML

check button Fusion gene summary
Fusion gene informationFusion gene name: CAMSAP3-PML
Fusion gene ID: 12749
HgeneTgene
Gene symbol

CAMSAP3

PML

Gene ID

57662

5371

Gene namecalmodulin regulated spectrin associated protein family member 3promyelocytic leukemia
SynonymsKIAA1543|NEZHA|PPP1R80MYL|PP8675|RNF71|TRIM19
Cytomap

19p13.2

15q24.1

Type of geneprotein-codingprotein-coding
Descriptioncalmodulin-regulated spectrin-associated protein 3protein phosphatase 1, regulatory subunit 80protein PMLPML/RARA fusionRING finger protein 71probable transcription factor PMLpromyelocytic leukemia proteinpromyelocytic leukemia, inducer oftripartite motif protein TRIM19tripartite motif-containing protein 19
Modification date2020031320200313
UniProtAcc

Q9P1Y5

PRAM1

Ensembl transtripts involved in fusion geneENST00000160298, ENST00000446248, 
ENST00000435786, ENST00000436891, 
ENST00000563500, ENST00000268058, 
ENST00000268059, ENST00000354026, 
ENST00000359928, ENST00000395132, 
ENST00000395135, ENST00000564428, 
ENST00000565898, ENST00000567543, 
ENST00000569161, ENST00000569477, 
ENST00000569965, 
Fusion gene scores* DoF score2 X 2 X 1=49 X 24 X 6=1296
# samples 228
** MAII scorelog2(2/4*10)=2.32192809488736log2(28/1296*10)=-2.21056698593966
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CAMSAP3 [Title/Abstract] AND PML [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCAMSAP3(7681311)-PML(74327589), # samples:1
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
HgeneCAMSAP3

GO:0000226

microtubule cytoskeleton organization

24486153|27693509

HgeneCAMSAP3

GO:0010923

negative regulation of phosphatase activity

19389623

HgeneCAMSAP3

GO:0030334

regulation of cell migration

27693509

HgeneCAMSAP3

GO:0030951

establishment or maintenance of microtubule cytoskeleton polarity

26715742|27802168

HgeneCAMSAP3

GO:0031113

regulation of microtubule polymerization

24486153

HgeneCAMSAP3

GO:0045198

establishment of epithelial cell apical/basal polarity

26715742|27802168

HgeneCAMSAP3

GO:0051893

regulation of focal adhesion assembly

27693509

HgeneCAMSAP3

GO:1903358

regulation of Golgi organization

28089391

TgenePML

GO:0001666

response to hypoxia

16915281

TgenePML

GO:0030308

negative regulation of cell growth

9448006

TgenePML

GO:0034097

response to cytokine

9412458

TgenePML

GO:0043161

proteasome-mediated ubiquitin-dependent protein catabolic process

22406621

TgenePML

GO:0045087

innate immune response

18248090

TgenePML

GO:0045892

negative regulation of transcription, DNA-templated

9448006

TgenePML

GO:0051457

maintenance of protein location in nucleus

17332504

TgenePML

GO:0065003

protein-containing complex assembly

12915590

TgenePML

GO:0090398

cellular senescence

22002537|22117195|23431171

TgenePML

GO:1902187

negative regulation of viral release from host cell

18248090


check buttonFusion gene breakpoints across CAMSAP3 (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 PML (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/ABI000919CAMSAP3chr19

7681311

+PMLchr15

74327589

-


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Fusion Gene ORF analysis for CAMSAP3-PML

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
intron-3UTRENST00000160298ENST00000435786CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-3UTRENST00000160298ENST00000436891CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-3UTRENST00000160298ENST00000563500CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-3UTRENST00000446248ENST00000435786CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-3UTRENST00000446248ENST00000436891CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-3UTRENST00000446248ENST00000563500CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000160298ENST00000268058CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000160298ENST00000268059CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000160298ENST00000354026CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000160298ENST00000359928CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000160298ENST00000395132CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000160298ENST00000395135CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000160298ENST00000564428CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000160298ENST00000565898CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000160298ENST00000567543CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000160298ENST00000569161CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000160298ENST00000569477CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000160298ENST00000569965CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000446248ENST00000268058CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000446248ENST00000268059CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000446248ENST00000354026CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000446248ENST00000359928CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000446248ENST00000395132CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000446248ENST00000395135CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000446248ENST00000564428CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000446248ENST00000565898CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000446248ENST00000567543CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000446248ENST00000569161CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000446248ENST00000569477CAMSAP3chr19

7681311

+PMLchr15

74327589

-
intron-intronENST00000446248ENST00000569965CAMSAP3chr19

7681311

+PMLchr15

74327589

-

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 CAMSAP3-PML


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 CAMSAP3-PML


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/:7681311/:74327589)
- 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
CAMSAP3

Q9P1Y5

PML

PRAM1

FUNCTION: Key microtubule-organizing protein that specifically binds the minus-end of non-centrosomal microtubules and regulates their dynamics and organization (PubMed:19041755, PubMed:23169647). Specifically recognizes growing microtubule minus-ends and autonomously decorates and stabilizes microtubule lattice formed by microtubule minus-end polymerization (PubMed:24486153). Acts on free microtubule minus-ends that are not capped by microtubule-nucleating proteins or other factors and protects microtubule minus-ends from depolymerization (PubMed:24486153). In addition, it also reduces the velocity of microtubule polymerization (PubMed:24486153). Required for the biogenesis and the maintenance of zonula adherens by anchoring the minus-end of microtubules to zonula adherens and by recruiting the kinesin KIFC3 to those junctional sites (PubMed:19041755). Required for orienting the apical-to-basal polarity of microtubules in epithelial cells: acts by tethering non-centrosomal microtubules to the apical cortex, leading to their longitudinal orientation (PubMed:27802168, PubMed:26715742). Plays a key role in early embryos, which lack centrosomes: accumulates at the microtubule bridges that connect pairs of cells and enables the formation of a non-centrosomal microtubule-organizing center that directs intracellular transport in the early embryo (By similarity). Couples non-centrosomal microtubules with actin: interaction with MACF1 at the minus ends of non-centrosomal microtubules, tethers the microtubules to actin filaments, regulating focal adhesion size and cell migration (PubMed:27693509). Plays a key role in the generation of non-centrosomal microtubules by accumulating in the pericentrosomal region and cooperating with KATNA1 to release non-centrosomal microtubules from the centrosome (PubMed:28386021). Through the microtubule cytoskeleton, also regulates the organization of cellular organelles including the Golgi and the early endosomes (PubMed:28089391). Through interaction with AKAP9, involved in translocation of Golgi vesicles in epithelial cells, where microtubules are mainly non-centrosomal (PubMed:28089391). Plays an important role in motile cilia function by facilitatating proper orientation of basal bodies and formation of central microtubule pairs in motile cilia (By similarity). {ECO:0000250|UniProtKB:Q80VC9, ECO:0000269|PubMed:19041755, ECO:0000269|PubMed:23169647, ECO:0000269|PubMed:24486153, ECO:0000269|PubMed:26715742, ECO:0000269|PubMed:27693509, ECO:0000269|PubMed:27802168, ECO:0000269|PubMed:28089391, ECO:0000269|PubMed:28386021}.670

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 CAMSAP3-PML


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 CAMSAP3-PML


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 CAMSAP3-PML


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 CAMSAP3-PML


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