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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:CNST-RAP1GAP (FusionGDB2 ID:HG163882TG5909)

Fusion Gene Summary for CNST-RAP1GAP

check button Fusion gene summary
Fusion gene informationFusion gene name: CNST-RAP1GAP
Fusion gene ID: hg163882tg5909
HgeneTgene
Gene symbol

CNST

RAP1GAP

Gene ID

163882

5909

Gene nameconsortin, connexin sorting proteinRAP1 GTPase activating protein
SynonymsC1orf71|PPP1R64RAP1GA1|RAP1GAP1|RAP1GAPII|RAPGAP
Cytomap('CNST')('RAP1GAP')

1q44

1p36.12

Type of geneprotein-codingprotein-coding
Descriptionconsortinprotein phosphatase 1, regulatory subunit 64rap1 GTPase-activating protein 1
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000483271, ENST00000366512, 
ENST00000366513, 
Fusion gene scores* DoF score8 X 6 X 8=3845 X 5 X 5=125
# samples 116
** MAII scorelog2(11/384*10)=-1.8036027871965
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/125*10)=-1.05889368905357
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CNST [Title/Abstract] AND RAP1GAP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCNST(246729965)-RAP1GAP(21952890), # 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
HgeneCNST

GO:0010923

negative regulation of phosphatase activity

19389623

TgeneRAP1GAP

GO:0043087

regulation of GTPase activity

18309292

TgeneRAP1GAP

GO:0043547

positive regulation of GTPase activity

15141215



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
ChimerDB4LGGTCGA-KT-A7W1-01ACNSTchr1

246729965

-RAP1GAPchr1

21952890

-
ChimerDB4LGGTCGA-KT-A7W1-01ACNSTchr1

246729965

+RAP1GAPchr1

21952890

-
ChimerDB4LGGTCGA-KT-A7W1CNSTchr1

246729965

+RAP1GAPchr1

21952890

-


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Fusion Gene ORF analysis for CNST-RAP1GAP

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-5UTRENST00000483271ENST00000374757CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
3UTR-5UTRENST00000483271ENST00000374765CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
3UTR-5UTRENST00000483271ENST00000542643CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
3UTR-intronENST00000483271ENST00000290101CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
3UTR-intronENST00000483271ENST00000374761CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
3UTR-intronENST00000483271ENST00000374763CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
5UTR-5UTRENST00000366512ENST00000374757CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
5UTR-5UTRENST00000366512ENST00000374765CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
5UTR-5UTRENST00000366512ENST00000542643CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
5UTR-5UTRENST00000366513ENST00000374757CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
5UTR-5UTRENST00000366513ENST00000374765CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
5UTR-5UTRENST00000366513ENST00000542643CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
5UTR-intronENST00000366512ENST00000290101CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
5UTR-intronENST00000366512ENST00000374761CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
5UTR-intronENST00000366512ENST00000374763CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
5UTR-intronENST00000366513ENST00000290101CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
5UTR-intronENST00000366513ENST00000374761CNSTchr1

246729965

+RAP1GAPchr1

21952890

-
5UTR-intronENST00000366513ENST00000374763CNSTchr1

246729965

+RAP1GAPchr1

21952890

-

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 CNST-RAP1GAP


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)


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Fusion Protein Features for CNST-RAP1GAP


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/:246729965/:21952890)
- 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
..
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}.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


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Fusion Gene Sequence for CNST-RAP1GAP


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 CNST-RAP1GAP


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 CNST-RAP1GAP


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 CNST-RAP1GAP


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCNSTC0040128Thyroid Diseases1CTD_human
TgeneC0025202melanoma2CTD_human
TgeneC0023487Acute Promyelocytic Leukemia1CTD_human
TgeneC0030297Pancreatic Neoplasm1CTD_human
TgeneC0040136Thyroid Neoplasm1CTD_human
TgeneC0151468Thyroid Gland Follicular Adenoma1CTD_human
TgeneC0235874Disease Exacerbation1CTD_human
TgeneC0346647Malignant neoplasm of pancreas1CTD_human
TgeneC0549473Thyroid carcinoma1CTD_human