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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:CLPTM1L-PDCD6 (FusionGDB2 ID:17313)

Fusion Gene Summary for CLPTM1L-PDCD6

check button Fusion gene summary
Fusion gene informationFusion gene name: CLPTM1L-PDCD6
Fusion gene ID: 17313
HgeneTgene
Gene symbol

CLPTM1L

PDCD6

Gene ID

81037

10016

Gene nameCLPTM1 likeprogrammed cell death 6
SynonymsCRR9ALG-2|ALG2|PEF1B
Cytomap

5p15.33

5p15.33

Type of geneprotein-codingprotein-coding
Descriptioncleft lip and palate transmembrane protein 1-like proteinCLPTM1-like proteincisplatin resistance related protein CRR9pcisplatin resistance-related protein 9programmed cell death protein 6apoptosis-linked gene 2 proteinapoptosis-linked gene 2 protein homologprobable calcium-binding protein ALG-2
Modification date2020031320200313
UniProtAcc

Q96KA5

O75340

Ensembl transtripts involved in fusion geneENST00000320895, ENST00000320927, 
ENST00000507807, ENST00000506641, 
ENST00000507528, ENST00000509581, 
ENST00000511482, ENST00000264933, 
ENST00000505221, 
Fusion gene scores* DoF score11 X 10 X 8=8806 X 4 X 5=120
# samples 117
** MAII scorelog2(11/880*10)=-3
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: CLPTM1L [Title/Abstract] AND PDCD6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLPTM1L(1320731)-PDCD6(304292), # 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
TgenePDCD6

GO:0001938

positive regulation of endothelial cell proliferation

21893193

TgenePDCD6

GO:0006886

intracellular protein transport

21122810

TgenePDCD6

GO:0010595

positive regulation of endothelial cell migration

21893193

TgenePDCD6

GO:0030948

negative regulation of vascular endothelial growth factor receptor signaling pathway

21893193

TgenePDCD6

GO:0032007

negative regulation of TOR signaling

21893193

TgenePDCD6

GO:0034605

cellular response to heat

21122810

TgenePDCD6

GO:0036324

vascular endothelial growth factor receptor-2 signaling pathway

21893193

TgenePDCD6

GO:0043280

positive regulation of cysteine-type endopeptidase activity involved in apoptotic process

16132846

TgenePDCD6

GO:0045766

positive regulation of angiogenesis

21893193

TgenePDCD6

GO:0051898

negative regulation of protein kinase B signaling

21893193


check buttonFusion gene breakpoints across CLPTM1L (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 PDCD6 (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
ChimerDB4KIRCTCGA-BP-4991-01ACLPTM1Lchr5

1320731

-PDCD6chr5

304292

+


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Fusion Gene ORF analysis for CLPTM1L-PDCD6

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-intronENST00000320895ENST00000507528CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
5CDS-intronENST00000320895ENST00000509581CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
5CDS-intronENST00000320895ENST00000511482CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
5CDS-intronENST00000320927ENST00000507528CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
5CDS-intronENST00000320927ENST00000509581CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
5CDS-intronENST00000320927ENST00000511482CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
5CDS-intronENST00000507807ENST00000507528CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
5CDS-intronENST00000507807ENST00000509581CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
5CDS-intronENST00000507807ENST00000511482CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
5UTR-3CDSENST00000506641ENST00000264933CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
5UTR-3CDSENST00000506641ENST00000505221CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
5UTR-intronENST00000506641ENST00000507528CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
5UTR-intronENST00000506641ENST00000509581CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
5UTR-intronENST00000506641ENST00000511482CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
Frame-shiftENST00000320895ENST00000264933CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
Frame-shiftENST00000320895ENST00000505221CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
Frame-shiftENST00000320927ENST00000264933CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
Frame-shiftENST00000320927ENST00000505221CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
Frame-shiftENST00000507807ENST00000264933CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+
Frame-shiftENST00000507807ENST00000505221CLPTM1Lchr5

1320731

-PDCD6chr5

304292

+

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 CLPTM1L-PDCD6


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)
CLPTM1Lchr51320730-PDCD6chr5304291+2.51E-050.99997485
CLPTM1Lchr51320730-PDCD6chr5304291+2.51E-050.99997485

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 CLPTM1L-PDCD6


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/:1320731/:304292)
- 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
CLPTM1L

Q96KA5

PDCD6

O75340

FUNCTION: Enhances cisplatin-mediated apoptosis, when overexpressed. {ECO:0000269|PubMed:11162647}.FUNCTION: Calcium sensor that plays a key role in processes such as endoplasmic reticulum (ER)-Golgi vesicular transport, endosomal biogenesis or membrane repair. Acts as an adapter that bridges unrelated proteins or stabilizes weak protein-protein complexes in response to calcium: calcium-binding triggers exposure of apolar surface, promoting interaction with different sets of proteins thanks to 3 different hydrophobic pockets, leading to translocation to membranes (PubMed:20691033, PubMed:25667979). Involved in ER-Golgi transport by promoting the association between PDCD6IP and TSG101, thereby bridging together the ESCRT-III and ESCRT-I complexes (PubMed:19520058). Together with PEF1, acts as calcium-dependent adapter for the BCR(KLHL12) complex, a complex involved in ER-Golgi transport by regulating the size of COPII coats (PubMed:27716508). In response to cytosolic calcium increase, the heterodimer formed with PEF1 interacts with, and bridges together the BCR(KLHL12) complex and SEC31 (SEC31A or SEC31B), promoting monoubiquitination of SEC31 and subsequent collagen export, which is required for neural crest specification (PubMed:27716508). Involved in the regulation of the distribution and function of MCOLN1 in the endosomal pathway (PubMed:19864416). Promotes localization and polymerization of TFG at endoplasmic reticulum exit site (PubMed:27813252). Required for T-cell receptor-, Fas-, and glucocorticoid-induced apoptosis (By similarity). May mediate Ca(2+)-regulated signals along the death pathway: interaction with DAPK1 can accelerate apoptotic cell death by increasing caspase-3 activity (PubMed:16132846). Its role in apoptosis may however be indirect, as suggested by knockout experiments (By similarity). May inhibit KDR/VEGFR2-dependent angiogenesis; the function involves inhibition of VEGF-induced phosphorylation of the Akt signaling pathway (PubMed:21893193). In case of infection by HIV-1 virus, indirectly inhibits HIV-1 production by affecting viral Gag expression and distribution (PubMed:27784779). {ECO:0000250|UniProtKB:P12815, ECO:0000269|PubMed:16132846, ECO:0000269|PubMed:19520058, ECO:0000269|PubMed:19864416, ECO:0000269|PubMed:20691033, ECO:0000269|PubMed:21893193, ECO:0000269|PubMed:25667979, ECO:0000269|PubMed:27716508, ECO:0000269|PubMed:27784779, ECO:0000269|PubMed:27813252}.; FUNCTION: [Isoform 2]: Has a lower Ca(2+) affinity than isoform 1 (By similarity). {ECO:0000250|UniProtKB:P12815}.

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 CLPTM1L-PDCD6


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 CLPTM1L-PDCD6


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 CLPTM1L-PDCD6


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 CLPTM1L-PDCD6


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