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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:EPCAM-KLHDC4 (FusionGDB2 ID:HG4072TG54758)

Fusion Gene Summary for EPCAM-KLHDC4

check button Fusion gene summary
Fusion gene informationFusion gene name: EPCAM-KLHDC4
Fusion gene ID: hg4072tg54758
HgeneTgene
Gene symbol

EPCAM

KLHDC4

Gene ID

4072

54758

Gene nameepithelial cell adhesion moleculekelch domain containing 4
SynonymsDIAR5|EGP-2|EGP314|EGP40|ESA|HNPCC8|KS1/4|KSA|M4S1|MIC18|MK-1|TACSTD1|TROP1-
Cytomap('EPCAM')('KLHDC4')

2p21

16q24.2

Type of geneprotein-codingprotein-coding
Descriptionepithelial cell adhesion moleculeadenocarcinoma-associated antigencell surface glycoprotein Trop-1epithelial glycoprotein 314human epithelial glycoprotein-2major gastrointestinal tumor-associated protein GA733-2membrane component, chromosome 4, surfkelch domain-containing protein 4
Modification date2020032220200320
UniProtAcc.

Q8TBB5

Ensembl transtripts involved in fusion geneENST00000263735, ENST00000405271, 
Fusion gene scores* DoF score11 X 12 X 4=5287 X 6 X 4=168
# samples 117
** MAII scorelog2(11/528*10)=-2.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/168*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: EPCAM [Title/Abstract] AND KLHDC4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEPCAM(47601086)-KLHDC4(87732190), # 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
HgeneEPCAM

GO:0008284

positive regulation of cell proliferation

15195135

HgeneEPCAM

GO:0045944

positive regulation of transcription by RNA polymerase II

15195135|15922867

HgeneEPCAM

GO:2000048

negative regulation of cell-cell adhesion mediated by cadherin

9382878



check button Fusion gene information
* 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


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Fusion Gene ORF analysis for EPCAM-KLHDC4

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

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 EPCAM-KLHDC4


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)


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Fusion Protein Features for EPCAM-KLHDC4


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/:47601086/:87732190)
- 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
.KLHDC4

Q8TBB5

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}.

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 EPCAM-KLHDC4


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 EPCAM-KLHDC4


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 EPCAM-KLHDC4


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 EPCAM-KLHDC4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneEPCAMC2750471COLORECTAL CANCER, HEREDITARY NONPOLYPOSIS, TYPE 87CLINGEN;CTD_human;GENOMICS_ENGLAND
HgeneEPCAMC1333990Hereditary Nonpolyposis Colorectal Cancer3CTD_human;ORPHANET
HgeneEPCAMC2750737DIARRHEA 5, WITH TUFTING ENTEROPATHY, CONGENITAL3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneEPCAMC1112155Hereditary non-polyposis colorectal cancer syndrome2ORPHANET
HgeneEPCAMC0007097Carcinoma1CTD_human
HgeneEPCAMC0009405Hereditary Nonpolyposis Colorectal Neoplasms1CTD_human
HgeneEPCAMC0023893Liver Cirrhosis, Experimental1CTD_human
HgeneEPCAMC0024667Animal Mammary Neoplasms1CTD_human
HgeneEPCAMC0024668Mammary Neoplasms, Experimental1CTD_human
HgeneEPCAMC0030297Pancreatic Neoplasm1CTD_human
HgeneEPCAMC0033578Prostatic Neoplasms1CTD_human
HgeneEPCAMC0205696Anaplastic carcinoma1CTD_human
HgeneEPCAMC0205697Carcinoma, Spindle-Cell1CTD_human
HgeneEPCAMC0205698Undifferentiated carcinoma1CTD_human
HgeneEPCAMC0205699Carcinomatosis1CTD_human
HgeneEPCAMC0346647Malignant neoplasm of pancreas1CTD_human
HgeneEPCAMC0376358Malignant neoplasm of prostate1CTD_human
HgeneEPCAMC0919267ovarian neoplasm1CTD_human
HgeneEPCAMC1140680Malignant neoplasm of ovary1CTD_human
HgeneEPCAMC1257925Mammary Carcinoma, Animal1CTD_human
HgeneEPCAMC2931459Lynch syndrome I (site-specific colonic cancer)1CTD_human
HgeneEPCAMC4552100Lynch Syndrome1CTD_human;GENOMICS_ENGLAND