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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:VPS13B-MYO9B (FusionGDB2 ID:97611)

Fusion Gene Summary for VPS13B-MYO9B

check button Fusion gene summary
Fusion gene informationFusion gene name: VPS13B-MYO9B
Fusion gene ID: 97611
HgeneTgene
Gene symbol

VPS13B

MYO9B

Gene ID

157680

4650

Gene namevacuolar protein sorting 13 homolog Bmyosin IXB
SynonymsCHS1|COH1CELIAC4|MYR5
Cytomap

8q22.2

19p13.11

Type of geneprotein-codingprotein-coding
Descriptionvacuolar protein sorting-associated protein 13Bunconventional myosin-IXbmyosin-IXbunconventional myosin-9b
Modification date2020031320200313
UniProtAcc.

Q13459

Ensembl transtripts involved in fusion geneENST00000395996, ENST00000358544, 
ENST00000357162, ENST00000355155, 
ENST00000441350, ENST00000521932, 
ENST00000595618, ENST00000594824, 
ENST00000397274, ENST00000593411, 
Fusion gene scores* DoF score43 X 36 X 17=2631615 X 18 X 8=2160
# samples 5018
** MAII scorelog2(50/26316*10)=-5.71786831273266
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(18/2160*10)=-3.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: VPS13B [Title/Abstract] AND MYO9B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointVPS13B(100205285)-MYO9B(17322456), # samples:3
Anticipated loss of major functional domain due to fusion event.VPS13B-MYO9B seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* 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
TgeneMYO9B

GO:0030048

actin filament-based movement

9490638

TgeneMYO9B

GO:0032011

ARF protein signal transduction

15644318

TgeneMYO9B

GO:0035385

Roundabout signaling pathway

26529257


check buttonFusion gene breakpoints across VPS13B (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 MYO9B (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
ChimerDB4BLCATCGA-DK-A1A6-01AVPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
ChimerDB4BLCATCGA-DK-A1A6-01AVPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
ChimerDB4BLCATCGA-DK-A1A6-01AVPS13Bchr8

100205285

-MYO9Bchr19

17322456

+


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Fusion Gene ORF analysis for VPS13B-MYO9B

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
Frame-shiftENST00000395996ENST00000595618VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
Frame-shiftENST00000395996ENST00000594824VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
Frame-shiftENST00000395996ENST00000397274VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
5CDS-intronENST00000395996ENST00000593411VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
Frame-shiftENST00000358544ENST00000595618VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
Frame-shiftENST00000358544ENST00000594824VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
Frame-shiftENST00000358544ENST00000397274VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
5CDS-intronENST00000358544ENST00000593411VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
Frame-shiftENST00000357162ENST00000595618VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
Frame-shiftENST00000357162ENST00000594824VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
Frame-shiftENST00000357162ENST00000397274VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
5CDS-intronENST00000357162ENST00000593411VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
Frame-shiftENST00000355155ENST00000595618VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
Frame-shiftENST00000355155ENST00000594824VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
Frame-shiftENST00000355155ENST00000397274VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
5CDS-intronENST00000355155ENST00000593411VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
intron-3CDSENST00000441350ENST00000595618VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
intron-3CDSENST00000441350ENST00000594824VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
intron-3CDSENST00000441350ENST00000397274VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
intron-intronENST00000441350ENST00000593411VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
3UTR-3CDSENST00000521932ENST00000595618VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
3UTR-3CDSENST00000521932ENST00000594824VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
3UTR-3CDSENST00000521932ENST00000397274VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+
3UTR-intronENST00000521932ENST00000593411VPS13Bchr8

100205285

+MYO9Bchr19

17322456

+

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 VPS13B-MYO9B


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)
VPS13Bchr8100205285+MYO9Bchr1917322459+8.67E-141
VPS13Bchr8100205285+MYO9Bchr1917322459+8.67E-141

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 VPS13B-MYO9B


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.MYO9B

Q13459

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Myosins are actin-based motor molecules with ATPase activity. Unconventional myosins serve in intracellular movements. Binds actin with high affinity both in the absence and presence of ATP and its mechanochemical activity is inhibited by calcium ions (PubMed:9490638). Also acts as a GTPase activator for RHOA (PubMed:9490638, PubMed:26529257). Plays a role in the regulation of cell migration via its role as RHOA GTPase activator. This is regulated by its interaction with the SLIT2 receptor ROBO1; interaction with ROBO1 impairs interaction with RHOA and subsequent activation of RHOA GTPase activity, and thereby leads to increased levels of active, GTP-bound RHOA (PubMed:26529257). {ECO:0000269|PubMed:26529257, ECO:0000269|PubMed:9490638}.

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 VPS13B-MYO9B


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 VPS13B-MYO9B


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 VPS13B-MYO9B


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 VPS13B-MYO9B


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneVPS13BC0265223Cohen syndrome10CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneVPS13BC1854061Cutis Verticis Gyrata, Retinitis Pigmentosa, and Sensorineural Deafness8CLINGEN
TgeneMYO9BC0036341Schizophrenia3PSYGENET
TgeneMYO9BC0007570Celiac Disease1CTD_human;GENOMICS_ENGLAND
TgeneMYO9BC2931456Prostate cancer, familial1CTD_human
TgeneMYO9BC4722327PROSTATE CANCER, HEREDITARY, 11CTD_human