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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:IMMT-CDH1 (FusionGDB2 ID:HG10989TG999)

Fusion Gene Summary for IMMT-CDH1

check button Fusion gene summary
Fusion gene informationFusion gene name: IMMT-CDH1
Fusion gene ID: hg10989tg999
HgeneTgene
Gene symbol

IMMT

CDH1

Gene ID

10989

999

Gene nameinner membrane mitochondrial proteincadherin 1
SynonymsHMP|MICOS60|MINOS2|Mic60|P87|P87/89|P89|PIG4|PIG52Arc-1|BCDS1|CD324|CDHE|ECAD|LCAM|UVO
Cytomap('IMMT')('CDH1')

2p11.2|2

16q22.1

Type of geneprotein-codingprotein-coding
DescriptionMICOS complex subunit MIC60cell proliferation-inducing gene 4/52 proteincell proliferation-inducing protein 52heart muscle proteinmitochondrial contact site and cristae organizing system subunit 60mitochondrial inner membrane organizing system 2mitocadherin-1CAM 120/80E-cadherin 1cadherin 1, E-cadherin (epithelial)cadherin 1, type 1, E-cadherin (epithelial)calcium-dependent adhesion protein, epithelialcell-CAM 120/80epididymis secretory sperm binding proteinepithelial cadherinuvomorulin
Modification date2020032720200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000254636, ENST00000409051, 
ENST00000410111, ENST00000442664, 
ENST00000449247, ENST00000490238, 
Fusion gene scores* DoF score4 X 6 X 2=4819 X 20 X 5=1900
# samples 623
** MAII scorelog2(6/48*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(23/1900*10)=-3.04629365227394
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: IMMT [Title/Abstract] AND CDH1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointIMMT(86371797)-CDH1(68868897), # 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
TgeneCDH1

GO:0042307

positive regulation of protein import into nucleus

16338932

TgeneCDH1

GO:0045893

positive regulation of transcription, DNA-templated

16338932

TgeneCDH1

GO:0071285

cellular response to lithium ion

12937339

TgeneCDH1

GO:0071681

cellular response to indole-3-methanol

10868478

TgeneCDH1

GO:0072659

protein localization to plasma membrane

17620337

TgeneCDH1

GO:0098609

cell-cell adhesion

16338932|18593713



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/ABE075539IMMTchr2

86371797

-CDH1chr16

68868897

+


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Fusion Gene ORF analysis for IMMT-CDH1

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
intron-3UTRENST00000254636ENST00000261769IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-3UTRENST00000409051ENST00000261769IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-3UTRENST00000410111ENST00000261769IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-3UTRENST00000442664ENST00000261769IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-3UTRENST00000449247ENST00000261769IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-3UTRENST00000490238ENST00000261769IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-intronENST00000254636ENST00000422392IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-intronENST00000254636ENST00000562836IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-intronENST00000409051ENST00000422392IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-intronENST00000409051ENST00000562836IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-intronENST00000410111ENST00000422392IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-intronENST00000410111ENST00000562836IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-intronENST00000442664ENST00000422392IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-intronENST00000442664ENST00000562836IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-intronENST00000449247ENST00000422392IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-intronENST00000449247ENST00000562836IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-intronENST00000490238ENST00000422392IMMTchr2

86371797

-CDH1chr16

68868897

+
intron-intronENST00000490238ENST00000562836IMMTchr2

86371797

-CDH1chr16

68868897

+

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 IMMT-CDH1


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 IMMT-CDH1


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/:86371797/:68868897)
- 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
..
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: 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 IMMT-CDH1


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 IMMT-CDH1


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 IMMT-CDH1


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 IMMT-CDH1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneIMMTC0019193Hepatitis, Toxic1CTD_human
HgeneIMMTC0029408Degenerative polyarthritis1CTD_human
HgeneIMMTC0086743Osteoarthrosis Deformans1CTD_human
HgeneIMMTC0860207Drug-Induced Liver Disease1CTD_human
HgeneIMMTC1262760Hepatitis, Drug-Induced1CTD_human
HgeneIMMTC3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneIMMTC4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneIMMTC4279912Chemically-Induced Liver Toxicity1CTD_human
TgeneC1708349Hereditary Diffuse Gastric Cancer15CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0346153Breast Cancer, Familial12CLINGEN
TgeneC0009405Hereditary Nonpolyposis Colorectal Neoplasms6CLINGEN
TgeneC0024623Malignant neoplasm of stomach6CGI;CTD_human;UNIPROT
TgeneC0038356Stomach Neoplasms6CGI;CTD_human
TgeneC1112155Hereditary non-polyposis colorectal cancer syndrome6CLINGEN
TgeneC1333990Hereditary Nonpolyposis Colorectal Cancer6CLINGEN
TgeneC1333991Hereditary Non-Polyposis Colon Cancer Type 26CLINGEN
TgeneC2936783Colorectal cancer, hereditary nonpolyposis, type 16CLINGEN
TgeneC0006142Malignant neoplasm of breast4CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0033578Prostatic Neoplasms4CTD_human
TgeneC0376358Malignant neoplasm of prostate4CTD_human;GENOMICS_ENGLAND
TgeneC0678222Breast Carcinoma4CTD_human
TgeneC1257931Mammary Neoplasms, Human4CTD_human
TgeneC1458155Mammary Neoplasms4CTD_human
TgeneC4704874Mammary Carcinoma, Human4CTD_human
TgeneC0007097Carcinoma3CTD_human
TgeneC0205696Anaplastic carcinoma3CTD_human
TgeneC0205697Carcinoma, Spindle-Cell3CTD_human
TgeneC0205698Undifferentiated carcinoma3CTD_human
TgeneC0205699Carcinomatosis3CTD_human
TgeneC0005684Malignant neoplasm of urinary bladder2CTD_human
TgeneC0005695Bladder Neoplasm2CTD_human
TgeneC0009402Colorectal Carcinoma2CTD_human
TgeneC0009404Colorectal Neoplasms2CTD_human
TgeneC0019207Hepatoma, Morris2CTD_human
TgeneC0019208Hepatoma, Novikoff2CTD_human
TgeneC0021367Mammary Ductal Carcinoma2CTD_human
TgeneC0023904Liver Neoplasms, Experimental2CTD_human
TgeneC0027626Neoplasm Invasiveness2CTD_human
TgeneC0027627Neoplasm Metastasis2CTD_human
TgeneC0086404Experimental Hepatoma2CTD_human
TgeneC0206692Carcinoma, Lobular2CGI;CTD_human;UNIPROT
TgeneC1134719Invasive Ductal Breast Carcinoma2CTD_human
TgeneC2931456Prostate cancer, familial2CTD_human
TgeneC4551988BLEPHAROCHEILODONTIC SYNDROME 12GENOMICS_ENGLAND;UNIPROT
TgeneC4722327PROSTATE CANCER, HEREDITARY, 12CTD_human
TgeneC0007137Squamous cell carcinoma1CTD_human
TgeneC0007621Neoplastic Cell Transformation1CTD_human
TgeneC0009324Ulcerative Colitis1CTD_human
TgeneC0010606Adenoid Cystic Carcinoma1CTD_human
TgeneC0014170Endometrial Neoplasms1CTD_human
TgeneC0014476Eperythrozoonosis1CTD_human
TgeneC0024667Animal Mammary Neoplasms1CTD_human
TgeneC0024668Mammary Neoplasms, Experimental1CTD_human
TgeneC0025500Mesothelioma1CTD_human
TgeneC0026936Mycoplasma Infections1CTD_human
TgeneC0027645Neoplasm Seeding1CTD_human
TgeneC0027659Neoplasms, Experimental1CTD_human
TgeneC0027746Nerve Degeneration1CTD_human
TgeneC0030297Pancreatic Neoplasm1CTD_human
TgeneC0032927Precancerous Conditions1CTD_human
TgeneC0036095Salivary Gland Neoplasms1CTD_human
TgeneC0079487Helicobacter Infections1CTD_human
TgeneC0158646Cleft palate with cleft lip1ORPHANET
TgeneC0220636Malignant neoplasm of salivary gland1CTD_human
TgeneC0235874Disease Exacerbation1CTD_human
TgeneC0282313Condition, Preneoplastic1CTD_human
TgeneC0282612Prostatic Intraepithelial Neoplasias1CTD_human
TgeneC0346647Malignant neoplasm of pancreas1CTD_human
TgeneC0476089Endometrial Carcinoma1CTD_human;GENOMICS_ENGLAND
TgeneC0919267ovarian neoplasm1CTD_human
TgeneC1140680Malignant neoplasm of ovary1CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC1176475Ductal Carcinoma1CTD_human
TgeneC1257925Mammary Carcinoma, Animal1CTD_human
TgeneC1861536Blepharo-cheilo-dontic syndrome1ORPHANET