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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:MSH2-EPCAM (FusionGDB2 ID:54941)

Fusion Gene Summary for MSH2-EPCAM

check button Fusion gene summary
Fusion gene informationFusion gene name: MSH2-EPCAM
Fusion gene ID: 54941
HgeneTgene
Gene symbol

MSH2

EPCAM

Gene ID

4436

4072

Gene namemutS homolog 2epithelial cell adhesion molecule
SynonymsCOCA1|FCC1|HNPCC|HNPCC1|LCFS2|hMSH2DIAR5|EGP-2|EGP314|EGP40|ESA|HNPCC8|KS1/4|KSA|M4S1|MIC18|MK-1|TACSTD1|TROP1
Cytomap

2p21-p16.3

2p21

Type of geneprotein-codingprotein-coding
DescriptionDNA mismatch repair protein Msh2DNA mismatch repair protein Msh2 transcriptmutS homolog 2, colon cancer, nonpolyposis type 1epithelial cell adhesion moleculeadenocarcinoma-associated antigencell surface glycoprotein Trop-1epithelial glycoprotein 314human epithelial glycoprotein-2major gastrointestinal tumor-associated protein GA733-2membrane component, chromosome 4, surf
Modification date2020032220200322
UniProtAcc.

P16422

Ensembl transtripts involved in fusion geneENST00000233146, ENST00000543555, 
ENST00000406134, ENST00000461394, 
ENST00000405271, ENST00000263735, 
Fusion gene scores* DoF score15 X 12 X 10=18006 X 10 X 5=300
# samples 2310
** MAII scorelog2(23/1800*10)=-2.96829114027266
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/300*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MSH2 [Title/Abstract] AND EPCAM [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMSH2(47630541)-EPCAM(47612305), # samples:3
MSH2(47643568)-EPCAM(47612305), # samples:3
Anticipated loss of major functional domain due to fusion event.MSH2-EPCAM seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
MSH2-EPCAM seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
MSH2-EPCAM 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
HgeneMSH2

GO:0006281

DNA repair

8942985

HgeneMSH2

GO:0006298

mismatch repair

7923193|11555625

HgeneMSH2

GO:0006301

postreplication repair

7923193

HgeneMSH2

GO:0045910

negative regulation of DNA recombination

17715146

HgeneMSH2

GO:0051096

positive regulation of helicase activity

17715146

TgeneEPCAM

GO:0008284

positive regulation of cell proliferation

15195135

TgeneEPCAM

GO:0045944

positive regulation of transcription by RNA polymerase II

15195135|15922867

TgeneEPCAM

GO:2000048

negative regulation of cell-cell adhesion mediated by cadherin

9382878


check buttonFusion gene breakpoints across MSH2 (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 EPCAM (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
ChimerDB4ESCATCGA-L5-A8NI-01AMSH2chr2

47630541

+EPCAMchr2

47612305

+
ChimerDB4ESCATCGA-LN-A5U7-01AMSH2chr2

47643568

+EPCAMchr2

47596067

+
ChimerDB4STADTCGA-CD-8533-01AMSH2chr2

47643568

+EPCAMchr2

47612305

+
ChimerDB4ESCATCGA-L5-A8NIMSH2chr2

47630541

+EPCAMchr2

47612304

+
ChimerDB4ESCATCGA-L5-A8NIMSH2chr2

47630541

+EPCAMchr2

47612304

+
ChimerDB4ESCATCGA-L5-A8NIMSH2chr2

47630541

+EPCAMchr2

47612305

+
ChimerDB4ESCATCGA-LN-A5U7MSH2chr2

47643568

+EPCAMchr2

47596067

+
ChimerDB4STADTCGA-CD-8533-01AMSH2chr2

47643568

+EPCAMchr2

47612305

+
ChimerDB4STADTCGA-CD-8533-01AMSH2chr2

47643568

-EPCAMchr2

47612305

+
ChimerDB4ESCATCGA-L5-A8NI-01AMSH2chr2

47630541

-EPCAMchr2

47612305

+


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Fusion Gene ORF analysis for MSH2-EPCAM

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
Frame-shiftENST00000233146ENST00000405271MSH2chr2

47630541

+EPCAMchr2

47612305

+
Frame-shiftENST00000233146ENST00000263735MSH2chr2

47630541

+EPCAMchr2

47612305

+
Frame-shiftENST00000543555ENST00000405271MSH2chr2

47630541

+EPCAMchr2

47612305

+
Frame-shiftENST00000543555ENST00000263735MSH2chr2

47630541

+EPCAMchr2

47612305

+
Frame-shiftENST00000406134ENST00000405271MSH2chr2

47630541

+EPCAMchr2

47612305

+
Frame-shiftENST00000406134ENST00000263735MSH2chr2

47630541

+EPCAMchr2

47612305

+
intron-3CDSENST00000461394ENST00000405271MSH2chr2

47630541

+EPCAMchr2

47612305

+
intron-3CDSENST00000461394ENST00000263735MSH2chr2

47630541

+EPCAMchr2

47612305

+
5CDS-5UTRENST00000233146ENST00000405271MSH2chr2

47643568

+EPCAMchr2

47596067

+
5CDS-intronENST00000233146ENST00000263735MSH2chr2

47643568

+EPCAMchr2

47596067

+
5CDS-5UTRENST00000543555ENST00000405271MSH2chr2

47643568

+EPCAMchr2

47596067

+
5CDS-intronENST00000543555ENST00000263735MSH2chr2

47643568

+EPCAMchr2

47596067

+
5CDS-5UTRENST00000406134ENST00000405271MSH2chr2

47643568

+EPCAMchr2

47596067

+
5CDS-intronENST00000406134ENST00000263735MSH2chr2

47643568

+EPCAMchr2

47596067

+
intron-5UTRENST00000461394ENST00000405271MSH2chr2

47643568

+EPCAMchr2

47596067

+
intron-intronENST00000461394ENST00000263735MSH2chr2

47643568

+EPCAMchr2

47596067

+
Frame-shiftENST00000233146ENST00000405271MSH2chr2

47643568

+EPCAMchr2

47612305

+
Frame-shiftENST00000233146ENST00000263735MSH2chr2

47643568

+EPCAMchr2

47612305

+
Frame-shiftENST00000543555ENST00000405271MSH2chr2

47643568

+EPCAMchr2

47612305

+
Frame-shiftENST00000543555ENST00000263735MSH2chr2

47643568

+EPCAMchr2

47612305

+
Frame-shiftENST00000406134ENST00000405271MSH2chr2

47643568

+EPCAMchr2

47612305

+
Frame-shiftENST00000406134ENST00000263735MSH2chr2

47643568

+EPCAMchr2

47612305

+
intron-3CDSENST00000461394ENST00000405271MSH2chr2

47643568

+EPCAMchr2

47612305

+
intron-3CDSENST00000461394ENST00000263735MSH2chr2

47643568

+EPCAMchr2

47612305

+
Frame-shiftENST00000233146ENST00000405271MSH2chr2

47630541

+EPCAMchr2

47612304

+
Frame-shiftENST00000233146ENST00000263735MSH2chr2

47630541

+EPCAMchr2

47612304

+
Frame-shiftENST00000543555ENST00000405271MSH2chr2

47630541

+EPCAMchr2

47612304

+
Frame-shiftENST00000543555ENST00000263735MSH2chr2

47630541

+EPCAMchr2

47612304

+
Frame-shiftENST00000406134ENST00000405271MSH2chr2

47630541

+EPCAMchr2

47612304

+
Frame-shiftENST00000406134ENST00000263735MSH2chr2

47630541

+EPCAMchr2

47612304

+
intron-3CDSENST00000461394ENST00000405271MSH2chr2

47630541

+EPCAMchr2

47612304

+
intron-3CDSENST00000461394ENST00000263735MSH2chr2

47630541

+EPCAMchr2

47612304

+

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 MSH2-EPCAM


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 MSH2-EPCAM


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.EPCAM

P16422

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: May act as a physical homophilic interaction molecule between intestinal epithelial cells (IECs) and intraepithelial lymphocytes (IELs) at the mucosal epithelium for providing immunological barrier as a first line of defense against mucosal infection. Plays a role in embryonic stem cells proliferation and differentiation. Up-regulates the expression of FABP5, MYC and cyclins A and E. {ECO:0000269|PubMed:15195135, ECO:0000269|PubMed:15922867, ECO:0000269|PubMed:19785009, ECO:0000269|PubMed:20064925}.

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 MSH2-EPCAM


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 MSH2-EPCAM


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 MSH2-EPCAM


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneEPCAMP16422DB11075HypromelloseSmall moleculeApproved
TgeneEPCAMP16422DB11075HypromelloseSmall moleculeApproved
TgeneEPCAMP16422DB11075HypromelloseSmall moleculeApproved
TgeneEPCAMP16422DB11075HypromelloseSmall moleculeApproved
TgeneEPCAMP16422DB11075HypromelloseSmall moleculeApproved
TgeneEPCAMP16422DB11075HypromelloseSmall moleculeApproved
TgeneEPCAMP16422DB11075HypromelloseSmall moleculeApproved
TgeneEPCAMP16422DB06607CatumaxomabLigandBiotechApproved|Investigational|Withdrawn
TgeneEPCAMP16422DB06607CatumaxomabLigandBiotechApproved|Investigational|Withdrawn
TgeneEPCAMP16422DB06607CatumaxomabLigandBiotechApproved|Investigational|Withdrawn
TgeneEPCAMP16422DB06607CatumaxomabLigandBiotechApproved|Investigational|Withdrawn
TgeneEPCAMP16422DB06607CatumaxomabLigandBiotechApproved|Investigational|Withdrawn
TgeneEPCAMP16422DB06607CatumaxomabLigandBiotechApproved|Investigational|Withdrawn
TgeneEPCAMP16422DB06607CatumaxomabLigandBiotechApproved|Investigational|Withdrawn
TgeneEPCAMP16422DB09336Technetium Tc-99m nofetumomab merpentanBinderSmall moleculeApproved|Withdrawn
TgeneEPCAMP16422DB09336Technetium Tc-99m nofetumomab merpentanBinderSmall moleculeApproved|Withdrawn
TgeneEPCAMP16422DB09336Technetium Tc-99m nofetumomab merpentanBinderSmall moleculeApproved|Withdrawn
TgeneEPCAMP16422DB09336Technetium Tc-99m nofetumomab merpentanBinderSmall moleculeApproved|Withdrawn
TgeneEPCAMP16422DB09336Technetium Tc-99m nofetumomab merpentanBinderSmall moleculeApproved|Withdrawn
TgeneEPCAMP16422DB09336Technetium Tc-99m nofetumomab merpentanBinderSmall moleculeApproved|Withdrawn
TgeneEPCAMP16422DB09336Technetium Tc-99m nofetumomab merpentanBinderSmall moleculeApproved|Withdrawn

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Related Diseases for MSH2-EPCAM


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMSH2C2936783Colorectal cancer, hereditary nonpolyposis, type 155GENOMICS_ENGLAND;UNIPROT
HgeneMSH2C0265325Turcot syndrome (disorder)14CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneMSH2C1333990Hereditary Nonpolyposis Colorectal Cancer11CLINGEN;CTD_human;ORPHANET
HgeneMSH2C4321324Constitutional Mismatch Repair Deficiency Syndrome10CLINGEN
HgeneMSH2C4552100Lynch Syndrome10CLINGEN;CTD_human;GENOMICS_ENGLAND
HgeneMSH2C0009405Hereditary Nonpolyposis Colorectal Neoplasms9CLINGEN;CTD_human
HgeneMSH2C1112155Hereditary non-polyposis colorectal cancer syndrome7CLINGEN;ORPHANET
HgeneMSH2C0009402Colorectal Carcinoma5CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneMSH2C1321489Torre-Muir syndrome4CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneMSH2C0346153Breast Cancer, Familial2CLINGEN
HgeneMSH2C0009404Colorectal Neoplasms1CTD_human
HgeneMSH2C0919267ovarian neoplasm1CGI;CTD_human
HgeneMSH2C1140680Malignant neoplasm of ovary1CGI;CTD_human;GENOMICS_ENGLAND
HgeneMSH2C2931459Lynch syndrome I (site-specific colonic cancer)1CTD_human
HgeneMSH2C4733333familial non-medullary thyroid cancer1GENOMICS_ENGLAND
TgeneEPCAMC2750471COLORECTAL CANCER, HEREDITARY NONPOLYPOSIS, TYPE 87CLINGEN;CTD_human;GENOMICS_ENGLAND
TgeneEPCAMC1333990Hereditary Nonpolyposis Colorectal Cancer3CTD_human;ORPHANET
TgeneEPCAMC2750737DIARRHEA 5, WITH TUFTING ENTEROPATHY, CONGENITAL3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneEPCAMC1112155Hereditary non-polyposis colorectal cancer syndrome2ORPHANET
TgeneEPCAMC0007097Carcinoma1CTD_human
TgeneEPCAMC0009405Hereditary Nonpolyposis Colorectal Neoplasms1CTD_human
TgeneEPCAMC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneEPCAMC0024667Animal Mammary Neoplasms1CTD_human
TgeneEPCAMC0024668Mammary Neoplasms, Experimental1CTD_human
TgeneEPCAMC0030297Pancreatic Neoplasm1CTD_human
TgeneEPCAMC0033578Prostatic Neoplasms1CTD_human
TgeneEPCAMC0205696Anaplastic carcinoma1CTD_human
TgeneEPCAMC0205697Carcinoma, Spindle-Cell1CTD_human
TgeneEPCAMC0205698Undifferentiated carcinoma1CTD_human
TgeneEPCAMC0205699Carcinomatosis1CTD_human
TgeneEPCAMC0346647Malignant neoplasm of pancreas1CTD_human
TgeneEPCAMC0376358Malignant neoplasm of prostate1CTD_human
TgeneEPCAMC0919267ovarian neoplasm1CTD_human
TgeneEPCAMC1140680Malignant neoplasm of ovary1CTD_human
TgeneEPCAMC1257925Mammary Carcinoma, Animal1CTD_human
TgeneEPCAMC2931459Lynch syndrome I (site-specific colonic cancer)1CTD_human
TgeneEPCAMC4552100Lynch Syndrome1CTD_human;GENOMICS_ENGLAND