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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:CHD7-CLVS1 (FusionGDB2 ID:16374)

Fusion Gene Summary for CHD7-CLVS1

check button Fusion gene summary
Fusion gene informationFusion gene name: CHD7-CLVS1
Fusion gene ID: 16374
HgeneTgene
Gene symbol

CHD7

CLVS1

Gene ID

55636

157807

Gene namechromodomain helicase DNA binding protein 7clavesin 1
SynonymsCRG|HH5|IS3|KAL5C6orf212L|CRALBPL|RLBP1L1
Cytomap

8q12.2

8q12.2-q12.3

Type of geneprotein-codingprotein-coding
Descriptionchromodomain-helicase-DNA-binding protein 7ATP-dependent helicase CHD7CHARGE associationchromodomain helicase DNA binding protein 7 isoform CRA_eclavesin-1clathrin vesicle-associated Sec14 protein 1retinaldehyde-binding protein 1-like 1
Modification date2020032820200313
UniProtAcc

Q9P2D1

Q8IUQ0

Ensembl transtripts involved in fusion geneENST00000423902, ENST00000525508, 
ENST00000524602, ENST00000529472, 
ENST00000325897, ENST00000518592, 
ENST00000518858, ENST00000519846, 
Fusion gene scores* DoF score12 X 8 X 8=76815 X 16 X 12=2880
# samples 1720
** MAII scorelog2(17/768*10)=-2.17557156458345
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(20/2880*10)=-3.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CHD7 [Title/Abstract] AND CLVS1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCHD7(61591641)-CLVS1(62289163), # samples:1
CHD7(61714152)-CLVS1(62044329), # samples:1
CHD7(61591641)-CLVS1(62289164), # samples:1
CHD7(61591641)-CLVS1(62366700), # samples:1
CHD7(61592350)-CLVS1(62289164), # 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

check buttonFusion gene breakpoints across CHD7 (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 CLVS1 (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
ChimerDB4HNSCTCGA-P3-A6T3CHD7chr8

61714152

+CLVS1chr8

62044329

+
ChimerDB4OVTCGA-57-1994-01ACHD7chr8

61591641

+CLVS1chr8

62289164

+
ChimerDB4OVTCGA-57-1994-01ACHD7chr8

61591641

+CLVS1chr8

62366700

+
ChimerDB4OVTCGA-57-1994-01ACHD7chr8

61592350

+CLVS1chr8

62289164

+
ChimerDB4OVTCGA-57-1994CHD7chr8

61591641

+CLVS1chr8

62289163

+


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Fusion Gene ORF analysis for CHD7-CLVS1

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-intronENST00000423902ENST00000325897CHD7chr8

61714152

+CLVS1chr8

62044329

+
5CDS-intronENST00000423902ENST00000518592CHD7chr8

61714152

+CLVS1chr8

62044329

+
5CDS-intronENST00000423902ENST00000518858CHD7chr8

61714152

+CLVS1chr8

62044329

+
5CDS-intronENST00000423902ENST00000519846CHD7chr8

61714152

+CLVS1chr8

62044329

+
5CDS-intronENST00000525508ENST00000325897CHD7chr8

61714152

+CLVS1chr8

62044329

+
5CDS-intronENST00000525508ENST00000518592CHD7chr8

61714152

+CLVS1chr8

62044329

+
5CDS-intronENST00000525508ENST00000518858CHD7chr8

61714152

+CLVS1chr8

62044329

+
5CDS-intronENST00000525508ENST00000519846CHD7chr8

61714152

+CLVS1chr8

62044329

+
5UTR-3CDSENST00000423902ENST00000519846CHD7chr8

61591641

+CLVS1chr8

62289164

+
5UTR-3CDSENST00000423902ENST00000519846CHD7chr8

61591641

+CLVS1chr8

62366700

+
5UTR-3CDSENST00000423902ENST00000519846CHD7chr8

61591641

+CLVS1chr8

62289163

+
5UTR-5UTRENST00000423902ENST00000325897CHD7chr8

61591641

+CLVS1chr8

62289164

+
5UTR-5UTRENST00000423902ENST00000325897CHD7chr8

61591641

+CLVS1chr8

62366700

+
5UTR-5UTRENST00000423902ENST00000325897CHD7chr8

61591641

+CLVS1chr8

62289163

+
5UTR-5UTRENST00000423902ENST00000518592CHD7chr8

61591641

+CLVS1chr8

62289164

+
5UTR-5UTRENST00000423902ENST00000518592CHD7chr8

61591641

+CLVS1chr8

62366700

+
5UTR-5UTRENST00000423902ENST00000518592CHD7chr8

61591641

+CLVS1chr8

62289163

+
5UTR-intronENST00000423902ENST00000518858CHD7chr8

61591641

+CLVS1chr8

62289164

+
5UTR-intronENST00000423902ENST00000518858CHD7chr8

61591641

+CLVS1chr8

62366700

+
5UTR-intronENST00000423902ENST00000518858CHD7chr8

61591641

+CLVS1chr8

62289163

+
intron-3CDSENST00000423902ENST00000519846CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-3CDSENST00000524602ENST00000519846CHD7chr8

61591641

+CLVS1chr8

62289164

+
intron-3CDSENST00000524602ENST00000519846CHD7chr8

61591641

+CLVS1chr8

62366700

+
intron-3CDSENST00000524602ENST00000519846CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-3CDSENST00000524602ENST00000519846CHD7chr8

61591641

+CLVS1chr8

62289163

+
intron-3CDSENST00000525508ENST00000519846CHD7chr8

61591641

+CLVS1chr8

62289164

+
intron-3CDSENST00000525508ENST00000519846CHD7chr8

61591641

+CLVS1chr8

62366700

+
intron-3CDSENST00000525508ENST00000519846CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-3CDSENST00000525508ENST00000519846CHD7chr8

61591641

+CLVS1chr8

62289163

+
intron-3CDSENST00000529472ENST00000519846CHD7chr8

61591641

+CLVS1chr8

62289164

+
intron-3CDSENST00000529472ENST00000519846CHD7chr8

61591641

+CLVS1chr8

62366700

+
intron-3CDSENST00000529472ENST00000519846CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-3CDSENST00000529472ENST00000519846CHD7chr8

61591641

+CLVS1chr8

62289163

+
intron-5UTRENST00000423902ENST00000325897CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-5UTRENST00000423902ENST00000518592CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-5UTRENST00000524602ENST00000325897CHD7chr8

61591641

+CLVS1chr8

62289164

+
intron-5UTRENST00000524602ENST00000325897CHD7chr8

61591641

+CLVS1chr8

62366700

+
intron-5UTRENST00000524602ENST00000325897CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-5UTRENST00000524602ENST00000325897CHD7chr8

61591641

+CLVS1chr8

62289163

+
intron-5UTRENST00000524602ENST00000518592CHD7chr8

61591641

+CLVS1chr8

62289164

+
intron-5UTRENST00000524602ENST00000518592CHD7chr8

61591641

+CLVS1chr8

62366700

+
intron-5UTRENST00000524602ENST00000518592CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-5UTRENST00000524602ENST00000518592CHD7chr8

61591641

+CLVS1chr8

62289163

+
intron-5UTRENST00000525508ENST00000325897CHD7chr8

61591641

+CLVS1chr8

62289164

+
intron-5UTRENST00000525508ENST00000325897CHD7chr8

61591641

+CLVS1chr8

62366700

+
intron-5UTRENST00000525508ENST00000325897CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-5UTRENST00000525508ENST00000325897CHD7chr8

61591641

+CLVS1chr8

62289163

+
intron-5UTRENST00000525508ENST00000518592CHD7chr8

61591641

+CLVS1chr8

62289164

+
intron-5UTRENST00000525508ENST00000518592CHD7chr8

61591641

+CLVS1chr8

62366700

+
intron-5UTRENST00000525508ENST00000518592CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-5UTRENST00000525508ENST00000518592CHD7chr8

61591641

+CLVS1chr8

62289163

+
intron-5UTRENST00000529472ENST00000325897CHD7chr8

61591641

+CLVS1chr8

62289164

+
intron-5UTRENST00000529472ENST00000325897CHD7chr8

61591641

+CLVS1chr8

62366700

+
intron-5UTRENST00000529472ENST00000325897CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-5UTRENST00000529472ENST00000325897CHD7chr8

61591641

+CLVS1chr8

62289163

+
intron-5UTRENST00000529472ENST00000518592CHD7chr8

61591641

+CLVS1chr8

62289164

+
intron-5UTRENST00000529472ENST00000518592CHD7chr8

61591641

+CLVS1chr8

62366700

+
intron-5UTRENST00000529472ENST00000518592CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-5UTRENST00000529472ENST00000518592CHD7chr8

61591641

+CLVS1chr8

62289163

+
intron-intronENST00000423902ENST00000518858CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-intronENST00000524602ENST00000325897CHD7chr8

61714152

+CLVS1chr8

62044329

+
intron-intronENST00000524602ENST00000518592CHD7chr8

61714152

+CLVS1chr8

62044329

+
intron-intronENST00000524602ENST00000518858CHD7chr8

61714152

+CLVS1chr8

62044329

+
intron-intronENST00000524602ENST00000518858CHD7chr8

61591641

+CLVS1chr8

62289164

+
intron-intronENST00000524602ENST00000518858CHD7chr8

61591641

+CLVS1chr8

62366700

+
intron-intronENST00000524602ENST00000518858CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-intronENST00000524602ENST00000518858CHD7chr8

61591641

+CLVS1chr8

62289163

+
intron-intronENST00000524602ENST00000519846CHD7chr8

61714152

+CLVS1chr8

62044329

+
intron-intronENST00000525508ENST00000518858CHD7chr8

61591641

+CLVS1chr8

62289164

+
intron-intronENST00000525508ENST00000518858CHD7chr8

61591641

+CLVS1chr8

62366700

+
intron-intronENST00000525508ENST00000518858CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-intronENST00000525508ENST00000518858CHD7chr8

61591641

+CLVS1chr8

62289163

+
intron-intronENST00000529472ENST00000325897CHD7chr8

61714152

+CLVS1chr8

62044329

+
intron-intronENST00000529472ENST00000518592CHD7chr8

61714152

+CLVS1chr8

62044329

+
intron-intronENST00000529472ENST00000518858CHD7chr8

61714152

+CLVS1chr8

62044329

+
intron-intronENST00000529472ENST00000518858CHD7chr8

61591641

+CLVS1chr8

62289164

+
intron-intronENST00000529472ENST00000518858CHD7chr8

61591641

+CLVS1chr8

62366700

+
intron-intronENST00000529472ENST00000518858CHD7chr8

61592350

+CLVS1chr8

62289164

+
intron-intronENST00000529472ENST00000518858CHD7chr8

61591641

+CLVS1chr8

62289163

+
intron-intronENST00000529472ENST00000519846CHD7chr8

61714152

+CLVS1chr8

62044329

+

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 CHD7-CLVS1


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)
CHD7chr861591641+CLVS1chr862366699+0.0083274510.9916726
CHD7chr861591641+CLVS1chr862289163+0.0022117060.9977883
CHD7chr861591641+CLVS1chr862289163+0.0022117060.9977883
CHD7chr861591641+CLVS1chr862366699+0.0083274510.9916726
CHD7chr861591641+CLVS1chr862289163+0.0022117060.9977883
CHD7chr861591641+CLVS1chr862289163+0.0022117060.9977883

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 CHD7-CLVS1


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/:61591641/:62289163)
- 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
CHD7

Q9P2D1

CLVS1

Q8IUQ0

FUNCTION: Probable transcription regulator. Maybe involved in the in 45S precursor rRNA production. {ECO:0000269|PubMed:22646239}.FUNCTION: Required for normal morphology of late endosomes and/or lysosomes in neurons (By similarity). Binds phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2). {ECO:0000250, ECO:0000269|PubMed:19651769}.

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 CHD7-CLVS1


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 CHD7-CLVS1


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 CHD7-CLVS1


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 CHD7-CLVS1


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