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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:CCDC88A-VPS52 (FusionGDB2 ID:13958)

Fusion Gene Summary for CCDC88A-VPS52

check button Fusion gene summary
Fusion gene informationFusion gene name: CCDC88A-VPS52
Fusion gene ID: 13958
HgeneTgene
Gene symbol

CCDC88A

VPS52

Gene ID

55704

6293

Gene namecoiled-coil domain containing 88AVPS52 subunit of GARP complex
SynonymsAPE|GIRDIN|GIV|GRDN|HkRP1|KIAA1212|PEHO|PEHOLARE1|SAC2|SACM2L|dJ1033B10.5
Cytomap

2p16.1

6p21.32

Type of geneprotein-codingprotein-coding
DescriptiongirdinAKT-phosphorylation enhancerHook-related protein 1g alpha-interacting vesicle-associated proteingirders of actin filamentsvacuolar protein sorting-associated protein 52 homologSAC2 suppressor of actin mutations 2-like proteinVPS52, GARP complex subunitvacuolar protein sorting 52 homolog
Modification date2020032920200327
UniProtAcc

Q3V6T2

.
Ensembl transtripts involved in fusion geneENST00000263630, ENST00000336838, 
ENST00000413716, ENST00000422883, 
ENST00000436346, ENST00000471947, 
ENST00000383210, ENST00000421357, 
ENST00000428608, ENST00000436044, 
ENST00000441058, ENST00000443860, 
ENST00000445902, ENST00000448042, 
ENST00000471761, ENST00000478934, 
ENST00000482399, ENST00000483351, 
ENST00000484649, ENST00000485418, 
ENST00000488583, ENST00000489236, 
Fusion gene scores* DoF score4 X 5 X 1=205 X 5 X 3=75
# samples 55
** MAII scorelog2(5/20*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CCDC88A [Title/Abstract] AND VPS52 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCCDC88A(55535168)-VPS52(33226390), # 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
HgeneCCDC88A

GO:0007264

small GTPase mediated signal transduction

19211784|23509302|27621449|27864364

HgeneCCDC88A

GO:0032147

activation of protein kinase activity

21954290

HgeneCCDC88A

GO:0045742

positive regulation of epidermal growth factor receptor signaling pathway

20462955

HgeneCCDC88A

GO:0061024

membrane organization

15882442

HgeneCCDC88A

GO:0072660

maintenance of protein location in plasma membrane

20462955

TgeneVPS52

GO:0007041

lysosomal transport

25799061


check buttonFusion gene breakpoints across CCDC88A (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 VPS52 (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/AAI869070CCDC88Achr2

55535168

+VPS52chr6

33226390

-
ChiTaRS5.0N/ABF589526CCDC88Achr2

55535168

+VPS52chr6

33226390

-


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Fusion Gene ORF analysis for CCDC88A-VPS52

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-intronENST00000263630ENST00000383210CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000421357CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000428608CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000436044CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000441058CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000443860CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000445902CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000448042CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000471761CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000478934CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000482399CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000483351CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000484649CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000485418CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000488583CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000263630ENST00000489236CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000383210CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000421357CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000428608CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000436044CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000441058CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000443860CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000445902CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000448042CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000471761CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000478934CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000482399CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000483351CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000484649CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000485418CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000488583CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000336838ENST00000489236CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000383210CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000421357CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000428608CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000436044CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000441058CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000443860CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000445902CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000448042CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000471761CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000478934CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000482399CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000483351CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000484649CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000485418CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000488583CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000413716ENST00000489236CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000383210CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000421357CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000428608CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000436044CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000441058CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000443860CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000445902CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000448042CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000471761CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000478934CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000482399CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000483351CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000484649CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000485418CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000488583CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000422883ENST00000489236CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000383210CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000421357CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000428608CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000436044CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000441058CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000443860CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000445902CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000448042CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000471761CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000478934CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000482399CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000483351CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000484649CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000485418CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000488583CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000436346ENST00000489236CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000383210CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000421357CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000428608CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000436044CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000441058CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000443860CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000445902CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000448042CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000471761CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000478934CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000482399CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000483351CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000484649CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000485418CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000488583CCDC88Achr2

55535168

+VPS52chr6

33226390

-
intron-intronENST00000471947ENST00000489236CCDC88Achr2

55535168

+VPS52chr6

33226390

-

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 CCDC88A-VPS52


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 CCDC88A-VPS52


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/:55535168/:33226390)
- 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
CCDC88A

Q3V6T2

.
FUNCTION: Bifunctional modulator of guanine nucleotide-binding proteins (G proteins) (PubMed:19211784, PubMed:27621449). Acts as a non-receptor guanine nucleotide exchange factor which binds to and activates guanine nucleotide-binding protein G(i) alpha subunits (PubMed:19211784, PubMed:21954290, PubMed:23509302, PubMed:25187647). Also acts as a guanine nucleotide dissociation inhibitor for guanine nucleotide-binding protein G(s) subunit alpha GNAS (PubMed:27621449). Essential for cell migration (PubMed:20462955, PubMed:16139227, PubMed:19211784, PubMed:21954290). Interacts in complex with G(i) alpha subunits with the EGFR receptor, retaining EGFR at the cell membrane following ligand stimulation and promoting EGFR signaling which triggers cell migration (PubMed:20462955). Binding to Gi-alpha subunits displaces the beta and gamma subunits from the heterotrimeric G-protein complex which enhances phosphoinositide 3-kinase (PI3K)-dependent phosphorylation and kinase activity of AKT1/PKB (PubMed:19211784). Phosphorylation of AKT1/PKB induces the phosphorylation of downstream effectors GSK3 and FOXO1/FKHR, and regulates DNA replication and cell proliferation (By similarity). Binds in its tyrosine-phosphorylated form to the phosphatidylinositol 3-kinase (PI3K) regulatory subunit PIK3R1 which enables recruitment of PIK3R1 to the EGFR receptor, enhancing PI3K activity and cell migration (PubMed:21954290). Plays a role as a key modulator of the AKT-mTOR signaling pathway, controlling the tempo of the process of newborn neuron integration during adult neurogenesis, including correct neuron positioning, dendritic development and synapse formation (By similarity). Inhibition of G(s) subunit alpha GNAS leads to reduced cellular levels of cAMP and suppression of cell proliferation (PubMed:27621449). Essential for the integrity of the actin cytoskeleton (PubMed:16139227, PubMed:19211784). Required for formation of actin stress fibers and lamellipodia (PubMed:15882442). May be involved in membrane sorting in the early endosome (PubMed:15882442). Plays a role in ciliogenesis and cilium morphology and positioning and this may partly be through regulation of the localization of scaffolding protein CROCC/Rootletin (PubMed:27623382). {ECO:0000250|UniProtKB:Q5SNZ0, ECO:0000269|PubMed:15882442, ECO:0000269|PubMed:16139227, ECO:0000269|PubMed:19211784, ECO:0000269|PubMed:20462955, ECO:0000269|PubMed:21954290, ECO:0000269|PubMed:23509302, ECO:0000269|PubMed:25187647, ECO:0000269|PubMed:27621449, ECO:0000269|PubMed:27623382}.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 CCDC88A-VPS52


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 CCDC88A-VPS52


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 CCDC88A-VPS52


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 CCDC88A-VPS52


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