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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:EWSR1-NCAPH2 (FusionGDB2 ID:27844)

Fusion Gene Summary for EWSR1-NCAPH2

check button Fusion gene summary
Fusion gene informationFusion gene name: EWSR1-NCAPH2
Fusion gene ID: 27844
HgeneTgene
Gene symbol

EWSR1

NCAPH2

Gene ID

2130

29781

Gene nameEWS RNA binding protein 1non-SMC condensin II complex subunit H2
SynonymsEWS|EWS-FLI1|bK984G1.4CAPH2
Cytomap

22q12.2

22q13.33

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein EWSEWS RNA-binding protein variant 6Ewing sarcoma breakpoint region 1Ewings sarcoma EWS-Fli1 (type 1) oncogenecondensin-2 complex subunit H2CAP-H2 subunit of the condensin II complexCTA-384D8.36chromosome-associated protein H2kleisin beta
Modification date2020032920200313
UniProtAcc

Q01844

Q6IBW4

Ensembl transtripts involved in fusion geneENST00000331029, ENST00000332050, 
ENST00000333395, ENST00000397938, 
ENST00000406548, ENST00000414183, 
ENST00000332035, 		ENST00000520297, 
ENST00000299821, ENST00000395698, 
ENST00000395701, ENST00000420993, 
Fusion gene scores* DoF score44 X 91 X 16=640645 X 5 X 3=75
# samples 985
** MAII scorelog2(98/64064*10)=-6.03058831983342
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
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: EWSR1 [Title/Abstract] AND NCAPH2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEWSR1(29678546)-NCAPH2(50954876), # samples:2
Anticipated loss of major functional domain due to fusion event.EWSR1-NCAPH2 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
EWSR1-NCAPH2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
EWSR1-NCAPH2 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

check buttonFusion gene breakpoints across EWSR1 (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 NCAPH2 (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
ChimerDB4LGGTCGA-HT-7686-01AEWSR1chr22

29678546

+NCAPH2chr22

50954876

+
ChimerDB4LGGTCGA-HT-7686EWSR1chr22

29678546

+NCAPH2chr22

50954876

+


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Fusion Gene ORF analysis for EWSR1-NCAPH2

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
5CDS-intronENST00000331029ENST00000520297EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
5CDS-intronENST00000332050ENST00000520297EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
5CDS-intronENST00000333395ENST00000520297EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
5CDS-intronENST00000397938ENST00000520297EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
5CDS-intronENST00000406548ENST00000520297EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
5CDS-intronENST00000414183ENST00000520297EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000331029ENST00000299821EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000331029ENST00000395698EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000331029ENST00000395701EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000331029ENST00000420993EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000332050ENST00000299821EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000332050ENST00000395698EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000332050ENST00000395701EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000332050ENST00000420993EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000333395ENST00000299821EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000333395ENST00000395698EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000333395ENST00000395701EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000333395ENST00000420993EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000397938ENST00000299821EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000397938ENST00000395698EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000397938ENST00000395701EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000397938ENST00000420993EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000406548ENST00000299821EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000406548ENST00000395698EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000406548ENST00000395701EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000406548ENST00000420993EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000414183ENST00000299821EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000414183ENST00000395698EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000414183ENST00000395701EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
Frame-shiftENST00000414183ENST00000420993EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
intron-3CDSENST00000332035ENST00000299821EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
intron-3CDSENST00000332035ENST00000395698EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
intron-3CDSENST00000332035ENST00000395701EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
intron-3CDSENST00000332035ENST00000420993EWSR1chr22

29678546

+NCAPH2chr22

50954876

+
intron-intronENST00000332035ENST00000520297EWSR1chr22

29678546

+NCAPH2chr22

50954876

+

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 EWSR1-NCAPH2


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)
EWSR1chr2229678546+NCAPH2chr2250954875+4.86E-070.9999995
EWSR1chr2229678546+NCAPH2chr2250954875+4.86E-070.9999995
EWSR1chr2229678546+NCAPH2chr2250954875+4.86E-070.9999995
EWSR1chr2229678546+NCAPH2chr2250954875+4.86E-070.9999995

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 EWSR1-NCAPH2


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/:29678546/:50954876)
- 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
EWSR1

Q01844

NCAPH2

Q6IBW4

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: Regulatory subunit of the condensin-2 complex, a complex that seems to provide chromosomes with an additional level of organization and rigidity and in establishing mitotic chromosome architecture (PubMed:14532007). May promote the resolution of double-strand DNA catenanes (intertwines) between sister chromatids. Condensin-mediated compaction likely increases tension in catenated sister chromatids, providing directionality for type II topoisomerase-mediated strand exchanges toward chromatid decatenation. Required for decatenation of chromatin bridges at anaphase. Early in neurogenesis, may play an essential role to ensure accurate mitotic chromosome condensation in neuron stem cells, ultimately affecting neuron pool and cortex size (By similarity). Seems to have lineage-specific role in T-cell development (PubMed:14532007). {ECO:0000250|UniProtKB:Q8BSP2, ECO:0000269|PubMed:14532007}.

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 EWSR1-NCAPH2


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 EWSR1-NCAPH2


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 EWSR1-NCAPH2


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 EWSR1-NCAPH2


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