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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:GNAS-CHMP2A (FusionGDB2 ID:33611)

Fusion Gene Summary for GNAS-CHMP2A

check button Fusion gene summary
Fusion gene informationFusion gene name: GNAS-CHMP2A
Fusion gene ID: 33611
HgeneTgene
Gene symbol

GNAS

CHMP2A

Gene ID

2778

27243

Gene nameGNAS complex locuscharged multivesicular body protein 2A
SynonymsAHO|C20orf45|GNAS1|GPSA|GSA|GSP|NESP|PITA3|POH|SCG6|SgVIBC-2|BC2|CHMP2|VPS2|VPS2A
Cytomap

20q13.32

19q13.43

Type of geneprotein-codingprotein-coding
Descriptionprotein ALEXprotein GNASprotein SCG6 (secretogranin VI)G protein subunit alpha Sadenylate cyclase-stimulating G alpha proteinalternative gene product encoded by XL-exonextra large alphas proteinguanine nucleotide binding protein (G protein), alpha charged multivesicular body protein 2aVPS2 homolog Achromatin modifying protein 2Aputative breast adenocarcinoma marker (32kD)putative breast adenocarcinoma marker BC-2vacuolar protein sorting-associated protein 2-1vps2-1
Modification date2020032920200313
UniProtAcc

P63092

O43633

Ensembl transtripts involved in fusion geneENST00000265620, ENST00000313949, 
ENST00000354359, ENST00000371075, 
ENST00000371085, ENST00000371095, 
ENST00000371100, ENST00000371102, 
ENST00000464624, ENST00000306090, 
ENST00000306120, ENST00000371081, 
ENST00000371098, ENST00000371099, 
ENST00000312547, ENST00000600118, 
ENST00000601220, 
Fusion gene scores* DoF score44 X 25 X 16=176005 X 4 X 3=60
# samples 515
** MAII scorelog2(51/17600*10)=-5.10893437155316
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GNAS [Title/Abstract] AND CHMP2A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGNAS(57486236)-CHMP2A(59066451), # 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
TgeneCHMP2A

GO:0039702

viral budding via host ESCRT complex

24878737


check buttonFusion gene breakpoints across GNAS (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 CHMP2A (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/ABU789739GNASchr20

57486236

+CHMP2Achr19

59066451

-


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Fusion Gene ORF analysis for GNAS-CHMP2A

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-5UTRENST00000265620ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-5UTRENST00000313949ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-5UTRENST00000354359ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-5UTRENST00000371075ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-5UTRENST00000371085ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-5UTRENST00000371095ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-5UTRENST00000371100ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-5UTRENST00000371102ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-5UTRENST00000464624ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000265620ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000265620ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000313949ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000313949ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000354359ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000354359ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000371075ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000371075ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000371085ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000371085ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000371095ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000371095ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000371100ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000371100ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000371102ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000371102ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000464624ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
3UTR-intronENST00000464624ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-
5CDS-5UTRENST00000306090ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
5CDS-intronENST00000306090ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
5CDS-intronENST00000306090ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-
intron-5UTRENST00000306120ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
intron-5UTRENST00000371081ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
intron-5UTRENST00000371098ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
intron-5UTRENST00000371099ENST00000312547GNASchr20

57486236

+CHMP2Achr19

59066451

-
intron-intronENST00000306120ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
intron-intronENST00000306120ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-
intron-intronENST00000371081ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
intron-intronENST00000371081ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-
intron-intronENST00000371098ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
intron-intronENST00000371098ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-
intron-intronENST00000371099ENST00000600118GNASchr20

57486236

+CHMP2Achr19

59066451

-
intron-intronENST00000371099ENST00000601220GNASchr20

57486236

+CHMP2Achr19

59066451

-

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 GNAS-CHMP2A


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 GNAS-CHMP2A


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/:57486236/:59066451)
- 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
GNAS

P63092

CHMP2A

O43633

FUNCTION: Guanine nucleotide-binding proteins (G proteins) function as transducers in numerous signaling pathways controlled by G protein-coupled receptors (GPCRs) (PubMed:17110384). Signaling involves the activation of adenylyl cyclases, resulting in increased levels of the signaling molecule cAMP (PubMed:26206488, PubMed:8702665). GNAS functions downstream of several GPCRs, including beta-adrenergic receptors (PubMed:21488135). Stimulates the Ras signaling pathway via RAPGEF2 (PubMed:12391161). {ECO:0000269|PubMed:12391161, ECO:0000269|PubMed:17110384, ECO:0000269|PubMed:21488135, ECO:0000269|PubMed:26206488, ECO:0000269|PubMed:8702665}.FUNCTION: Probable core component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis (PubMed:21310966). Together with SPAST, the ESCRT-III complex promotes nuclear envelope sealing and mitotic spindle disassembly during late anaphase (PubMed:26040712). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. {ECO:0000269|PubMed:21310966, ECO:0000269|PubMed:26040712, ECO:0000305}.; FUNCTION: (Microbial infection) The ESCRT machinery functions in topologically equivalent membrane fission events, such as the budding of enveloped viruses (HIV-1 and other lentiviruses). Involved in HIV-1 p6- and p9-dependent virus release. {ECO:0000269|PubMed:14505570, ECO:0000269|PubMed:14519844}.

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 GNAS-CHMP2A


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 GNAS-CHMP2A


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 GNAS-CHMP2A


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 GNAS-CHMP2A


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