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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:ARHGAP6-KDM6A (FusionGDB2 ID:6149)

Fusion Gene Summary for ARHGAP6-KDM6A

check button Fusion gene summary
Fusion gene informationFusion gene name: ARHGAP6-KDM6A
Fusion gene ID: 6149
HgeneTgene
Gene symbol

ARHGAP6

KDM6A

Gene ID

395

7403

Gene nameRho GTPase activating protein 6lysine demethylase 6A
SynonymsRHOGAP6|RHOGAPX-1KABUK2|UTX|bA386N14.2
Cytomap

Xp22.2

Xp11.3

Type of geneprotein-codingprotein-coding
Descriptionrho GTPase-activating protein 6Rho-type GTPase-activating protein RhoGAPX-1rho-type GTPase-activating protein 6lysine-specific demethylase 6AbA386N14.2 (ubiquitously transcribed X chromosome tetratricopeptide repeat protein (UTX))histone demethylase UTXlysine (K)-specific demethylase 6Aubiquitously transcribed tetratricopeptide repeat protein X-linkedubiquito
Modification date2020031320200313
UniProtAcc

O43182

O15550

Ensembl transtripts involved in fusion geneENST00000380736, ENST00000303025, 
ENST00000337414, ENST00000380718, 
ENST00000380732, ENST00000413512, 
ENST00000491514, ENST00000534860, 
ENST00000377967, ENST00000382899, 
ENST00000536777, ENST00000543216, 
ENST00000479423, 
Fusion gene scores* DoF score5 X 5 X 3=7513 X 15 X 6=1170
# samples 616
** MAII scorelog2(6/75*10)=-0.321928094887362
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1170*10)=-2.8703647195834
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARHGAP6 [Title/Abstract] AND KDM6A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKDM6A(44918711)-ARHGAP6(11272827), # samples:5
ARHGAP6(11445668)-KDM6A(44920569), # samples:2
ARHGAP6(11445668)-KDM6A(44922667), # 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

check buttonFusion gene breakpoints across ARHGAP6 (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 KDM6A (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
ChimerDB4PRADTCGA-EJ-8469-01AARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
ChimerDB4PRADTCGA-EJ-8469-01AARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
ChimerDB4PRADTCGA-EJ-8469ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
ChimerDB4PRADTCGA-EJ-8469ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+


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Fusion Gene ORF analysis for ARHGAP6-KDM6A

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
5UTR-3CDSENST00000380736ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
5UTR-3CDSENST00000380736ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
5UTR-3CDSENST00000380736ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
5UTR-3CDSENST00000380736ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
5UTR-3CDSENST00000380736ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
5UTR-3CDSENST00000380736ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
5UTR-3CDSENST00000380736ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
5UTR-3CDSENST00000380736ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
5UTR-intronENST00000380736ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
5UTR-intronENST00000380736ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000303025ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000303025ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000303025ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000303025ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000303025ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000303025ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000303025ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000303025ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000337414ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000337414ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000337414ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000337414ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000337414ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000337414ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000337414ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000337414ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000380718ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000380718ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000380718ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000380718ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000380718ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000380718ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000380718ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000380718ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000380732ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000380732ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000380732ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000380732ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000380732ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000380732ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000380732ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000380732ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000413512ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000413512ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000413512ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000413512ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000413512ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000413512ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000413512ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000413512ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000491514ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000491514ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000491514ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000491514ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000491514ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000491514ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000491514ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000491514ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000534860ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000534860ENST00000377967ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000534860ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000534860ENST00000382899ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000534860ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000534860ENST00000536777ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-3CDSENST00000534860ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-3CDSENST00000534860ENST00000543216ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-intronENST00000303025ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-intronENST00000303025ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-intronENST00000337414ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-intronENST00000337414ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-intronENST00000380718ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-intronENST00000380718ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-intronENST00000380732ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-intronENST00000380732ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-intronENST00000413512ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-intronENST00000413512ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-intronENST00000491514ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-intronENST00000491514ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+
intron-intronENST00000534860ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44920569

+
intron-intronENST00000534860ENST00000479423ARHGAP6chrX

11445668

-KDM6AchrX

44922667

+

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 ARHGAP6-KDM6A


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)
ARHGAP6chrX11445667-KDM6AchrX44922666+0.016656320.98334366
ARHGAP6chrX11445667-KDM6AchrX44922666+0.016656320.98334366
ARHGAP6chrX11445667-KDM6AchrX44920568+0.0002362480.9997638
ARHGAP6chrX11445667-KDM6AchrX44920568+0.0002362480.9997638
ARHGAP6chrX11445667-KDM6AchrX44922666+0.016656320.98334366
ARHGAP6chrX11445667-KDM6AchrX44922666+0.016656320.98334366
ARHGAP6chrX11445667-KDM6AchrX44920568+0.0002362480.9997638
ARHGAP6chrX11445667-KDM6AchrX44920568+0.0002362480.9997638

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.
genomic feature of top 1%

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Fusion Protein Features for ARHGAP6-KDM6A


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/:44918711/:11272827)
- 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
ARHGAP6

O43182

KDM6A

O15550

FUNCTION: GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. Could regulate the interactions of signaling molecules with the actin cytoskeleton. Promotes continuous elongation of cytoplasmic processes during cell motility and simultaneous retraction of the cell body changing the cell morphology. {ECO:0000269|PubMed:10699171}.FUNCTION: Histone demethylase that specifically demethylates 'Lys-27' of histone H3, thereby playing a central role in histone code (PubMed:17851529, PubMed:17713478, PubMed:17761849). Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-27' (PubMed:17851529, PubMed:17713478, PubMed:17761849). Plays a central role in regulation of posterior development, by regulating HOX gene expression (PubMed:17851529). Demethylation of 'Lys-27' of histone H3 is concomitant with methylation of 'Lys-4' of histone H3, and regulates the recruitment of the PRC1 complex and monoubiquitination of histone H2A (PubMed:17761849). Plays a demethylase-independent role in chromatin remodeling to regulate T-box family member-dependent gene expression (By similarity). {ECO:0000250|UniProtKB:O70546, ECO:0000269|PubMed:17713478, ECO:0000269|PubMed:17761849, ECO:0000269|PubMed:17851529, ECO:0000269|PubMed:18003914}.

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 ARHGAP6-KDM6A


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 ARHGAP6-KDM6A


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 ARHGAP6-KDM6A


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 ARHGAP6-KDM6A


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