Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:CLPTM1-APOC2 (FusionGDB2 ID:HG1209TG344)

Fusion Gene Summary for CLPTM1-APOC2

check button Fusion gene summary
Fusion gene informationFusion gene name: CLPTM1-APOC2
Fusion gene ID: hg1209tg344
HgeneTgene
Gene symbol

CLPTM1

APOC2

Gene ID

1209

344

Gene nameCLPTM1 regulator of GABA type A receptor forward traffickingapolipoprotein C2
Synonyms-APO-CII|APOC-II
Cytomap('CLPTM1')('APOC2')

19q13.32

19q13.32

Type of geneprotein-codingprotein-coding
Descriptioncleft lip and palate transmembrane protein 1CLPTM1, transmembrane proteincleft lip and palate associated transmembrane protein 1apolipoprotein C-II
Modification date2020031320200313
UniProtAcc

O96005

.
Ensembl transtripts involved in fusion geneENST00000337392, ENST00000541297, 
ENST00000546079, ENST00000589158, 
Fusion gene scores* DoF score16 X 12 X 8=15362 X 1 X 2=4
# samples 202
** MAII scorelog2(20/1536*10)=-2.94110631094643
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/4*10)=2.32192809488736
Context

PubMed: CLPTM1 [Title/Abstract] AND APOC2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLPTM1(45465332)-APOC2(45451723), # 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
TgeneAPOC2

GO:0010518

positive regulation of phospholipase activity

10727238

TgeneAPOC2

GO:0010898

positive regulation of triglyceride catabolic process

10727238

TgeneAPOC2

GO:0010916

negative regulation of very-low-density lipoprotein particle clearance

1917954

TgeneAPOC2

GO:0033344

cholesterol efflux

11162594

TgeneAPOC2

GO:0033700

phospholipid efflux

11162594

TgeneAPOC2

GO:0034382

chylomicron remnant clearance

4020294

TgeneAPOC2

GO:0045723

positive regulation of fatty acid biosynthetic process

10727238

TgeneAPOC2

GO:0045833

negative regulation of lipid metabolic process

182536

TgeneAPOC2

GO:0048261

negative regulation of receptor-mediated endocytosis

1917954

TgeneAPOC2

GO:0051006

positive regulation of lipoprotein lipase activity

10727238|15878877

TgeneAPOC2

GO:0060697

positive regulation of phospholipid catabolic process

10727238



check button Fusion gene information
* 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
ChimerDB4BRCATCGA-AO-A129-01ACLPTM1chr19

45465332

+APOC2chr19

45451723

+


Top

Fusion Gene ORF analysis for CLPTM1-APOC2

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-5UTRENST00000337392ENST00000252490CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5CDS-5UTRENST00000337392ENST00000585786CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5CDS-5UTRENST00000337392ENST00000590360CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5CDS-5UTRENST00000337392ENST00000591597CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5CDS-5UTRENST00000337392ENST00000592257CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5CDS-5UTRENST00000541297ENST00000252490CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5CDS-5UTRENST00000541297ENST00000585786CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5CDS-5UTRENST00000541297ENST00000590360CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5CDS-5UTRENST00000541297ENST00000591597CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5CDS-5UTRENST00000541297ENST00000592257CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5UTR-5UTRENST00000546079ENST00000252490CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5UTR-5UTRENST00000546079ENST00000585786CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5UTR-5UTRENST00000546079ENST00000590360CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5UTR-5UTRENST00000546079ENST00000591597CLPTM1chr19

45465332

+APOC2chr19

45451723

+
5UTR-5UTRENST00000546079ENST00000592257CLPTM1chr19

45465332

+APOC2chr19

45451723

+
intron-5UTRENST00000589158ENST00000252490CLPTM1chr19

45465332

+APOC2chr19

45451723

+
intron-5UTRENST00000589158ENST00000585786CLPTM1chr19

45465332

+APOC2chr19

45451723

+
intron-5UTRENST00000589158ENST00000590360CLPTM1chr19

45465332

+APOC2chr19

45451723

+
intron-5UTRENST00000589158ENST00000591597CLPTM1chr19

45465332

+APOC2chr19

45451723

+
intron-5UTRENST00000589158ENST00000592257CLPTM1chr19

45465332

+APOC2chr19

45451723

+

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

Top

Fusion Genomic Features for CLPTM1-APOC2


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)
CLPTM1chr1945465332+APOC2chr1945451722+8.06E-070.99999917
CLPTM1chr1945465332+APOC2chr1945451722+8.06E-070.99999917


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%

Top

Fusion Protein Features for CLPTM1-APOC2


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/:45465332/:45451723)
- 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
CLPTM1

O96005

.
FUNCTION: May play a role in T-cell development. {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {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


Top

Fusion Gene Sequence for CLPTM1-APOC2


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.

Top

Fusion Gene PPI Analysis for CLPTM1-APOC2


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


Top

Related Drugs for CLPTM1-APOC2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for CLPTM1-APOC2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCLPTM1C0030297Pancreatic Neoplasm1CTD_human
HgeneCLPTM1C0346647Malignant neoplasm of pancreas1CTD_human
TgeneC1720779Apolipoprotein C-II Deficiency (disorder)4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0002726Amyloidosis1GENOMICS_ENGLAND
TgeneC0011609Drug Eruptions1CTD_human
TgeneC0019207Hepatoma, Morris1CTD_human
TgeneC0019208Hepatoma, Novikoff1CTD_human
TgeneC0023904Liver Neoplasms, Experimental1CTD_human
TgeneC0086404Experimental Hepatoma1CTD_human
TgeneC0268199Familial apolipoprotein C-II deficiency1ORPHANET
TgeneC0406537Morbilliform Drug Reaction1CTD_human