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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:PDIA3-CHD1L (FusionGDB2 ID:63885)

Fusion Gene Summary for PDIA3-CHD1L

check button Fusion gene summary
Fusion gene informationFusion gene name: PDIA3-CHD1L
Fusion gene ID: 63885
HgeneTgene
Gene symbol

PDIA3

CHD1L

Gene ID

2923

9557

Gene nameprotein disulfide isomerase family A member 3chromodomain helicase DNA binding protein 1 like
SynonymsER60|ERp57|ERp60|ERp61|GRP57|GRP58|HEL-S-269|HEL-S-93n|HsT17083|P58|PI-PLCALC1|CHDL
Cytomap

15q15.3

1q21.1

Type of geneprotein-codingprotein-coding
Descriptionprotein disulfide-isomerase A358 kDa glucose-regulated protein58 kDa microsomal proteinER protein 57ER protein 60disulfide isomerase ER-60endoplasmic reticulum P58endoplasmic reticulum resident protein 57endoplasmic reticulum resident protein 60echromodomain-helicase-DNA-binding protein 1-likeamplified in liver cancer 1amplified in liver cancer protein 1
Modification date2020031320200313
UniProtAcc.

Q86WJ1

Ensembl transtripts involved in fusion geneENST00000300289, ENST00000538521, 
ENST00000469684, 		ENST00000361293, 
ENST00000369258, ENST00000369259, 
ENST00000431239, ENST00000467213, 
Fusion gene scores* DoF score13 X 14 X 5=91010 X 11 X 5=550
# samples 1614
** MAII scorelog2(16/910*10)=-2.5077946401987
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/550*10)=-1.97400479146706
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PDIA3 [Title/Abstract] AND CHD1L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPDIA3(44053731)-CHD1L(146649618), # samples:2
CHD1L(146651512)-PDIA3(44063348), # 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
TgeneCHD1L

GO:0006338

chromatin remodeling

19661379

TgeneCHD1L

GO:0006974

cellular response to DNA damage stimulus

19661379


check buttonFusion gene breakpoints across PDIA3 (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 CHD1L (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/ABF340027PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
ChiTaRS5.0N/ABP277691PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
ChiTaRS5.0N/ABP281530PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
ChiTaRS5.0N/ABP281695PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
ChiTaRS5.0N/ADA038832PDIA3chr15

44048964

+CHD1Lchr1

146649618

+


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Fusion Gene ORF analysis for PDIA3-CHD1L

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-intronENST00000300289ENST00000361293PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
5CDS-intronENST00000300289ENST00000361293PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000361293PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000361293PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000369258PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
5CDS-intronENST00000300289ENST00000369258PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000369258PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000369258PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000369259PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
5CDS-intronENST00000300289ENST00000369259PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000369259PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000369259PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000431239PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
5CDS-intronENST00000300289ENST00000431239PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000431239PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000431239PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000467213PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
5CDS-intronENST00000300289ENST00000467213PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000467213PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
5CDS-intronENST00000300289ENST00000467213PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000361293PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
5CDS-intronENST00000538521ENST00000361293PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000361293PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000361293PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000369258PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
5CDS-intronENST00000538521ENST00000369258PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000369258PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000369258PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000369259PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
5CDS-intronENST00000538521ENST00000369259PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000369259PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000369259PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000431239PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
5CDS-intronENST00000538521ENST00000431239PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000431239PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000431239PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000467213PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
5CDS-intronENST00000538521ENST00000467213PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000467213PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
5CDS-intronENST00000538521ENST00000467213PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000361293PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
intron-intronENST00000469684ENST00000361293PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000361293PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000361293PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000369258PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
intron-intronENST00000469684ENST00000369258PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000369258PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000369258PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000369259PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
intron-intronENST00000469684ENST00000369259PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000369259PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000369259PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000431239PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
intron-intronENST00000469684ENST00000431239PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000431239PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000431239PDIA3chr15

44048964

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000467213PDIA3chr15

44059109

+CHD1Lchr1

146650008

+
intron-intronENST00000469684ENST00000467213PDIA3chr15

44053731

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000467213PDIA3chr15

44053722

+CHD1Lchr1

146649618

+
intron-intronENST00000469684ENST00000467213PDIA3chr15

44048964

+CHD1Lchr1

146649618

+

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 PDIA3-CHD1L


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 PDIA3-CHD1L


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/:44053731/:146649618)
- 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
.CHD1L

Q86WJ1

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}.FUNCTION: DNA helicase which plays a role in chromatin-remodeling following DNA damage (PubMed:19661379, PubMed:29220653). Targeted to sites of DNA damage through interaction with poly(ADP-ribose) and functions to regulate chromatin during DNA repair (PubMed:19661379). Able to catalyze nucleosome sliding in an ATP-dependent manner (PubMed:19661379). Helicase activity is strongly stimulated upon poly(ADP-ribose)-binding (PubMed:19661379, PubMed:29220653). {ECO:0000269|PubMed:19661379, ECO:0000269|PubMed:29220653}.

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 PDIA3-CHD1L


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 PDIA3-CHD1L


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 PDIA3-CHD1L


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 PDIA3-CHD1L


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