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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:CDH13-IDH1 (FusionGDB2 ID:HG1012TG3417)

Fusion Gene Summary for CDH13-IDH1

check button Fusion gene summary
Fusion gene informationFusion gene name: CDH13-IDH1
Fusion gene ID: hg1012tg3417
HgeneTgene
Gene symbol

CDH13

IDH1

Gene ID

1012

3417

Gene namecadherin 13isocitrate dehydrogenase (NADP(+)) 1
SynonymsCDHH|P105HEL-216|HEL-S-26|IDCD|IDH|IDP|IDPC|PICD
Cytomap('CDH13')('IDH1')

16q23.3

2q34

Type of geneprotein-codingprotein-coding
Descriptioncadherin-13H-cadherin (heart)T-cadT-cadherincadherin 13, H-cadherin (heart)heart cadherinisocitrate dehydrogenase [NADP] cytoplasmicNADP(+)-specific ICDHNADP-dependent isocitrate dehydrogenase, cytosolicNADP-dependent isocitrate dehydrogenase, peroxisomalepididymis luminal protein 216epididymis secretory protein Li 26epididymis secretor
Modification date2020031520200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000268613, ENST00000428848, 
ENST00000431540, ENST00000446376, 
ENST00000565636, ENST00000566620, 
ENST00000567445, ENST00000569454, 
Fusion gene scores* DoF score15 X 15 X 4=9006 X 5 X 3=90
# samples 176
** MAII scorelog2(17/900*10)=-2.40439025507934
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/90*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CDH13 [Title/Abstract] AND IDH1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCDH13(83185581)-IDH1(209107512), # 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
HgeneCDH13

GO:0002040

sprouting angiogenesis

16873731

HgeneCDH13

GO:0007156

homophilic cell adhesion via plasma membrane adhesion molecules

10601632

HgeneCDH13

GO:0007162

negative regulation of cell adhesion

14729458

HgeneCDH13

GO:0008285

negative regulation of cell proliferation

10737605

HgeneCDH13

GO:0016339

calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules

10601632

HgeneCDH13

GO:0030032

lamellipodium assembly

15703273

HgeneCDH13

GO:0030335

positive regulation of cell migration

14729458

HgeneCDH13

GO:0043542

endothelial cell migration

14729458

HgeneCDH13

GO:0043616

keratinocyte proliferation

15816843

HgeneCDH13

GO:0050850

positive regulation of calcium-mediated signaling

16013438

HgeneCDH13

GO:0050927

positive regulation of positive chemotaxis

16013438

HgeneCDH13

GO:0055096

low-density lipoprotein particle mediated signaling

16013438

TgeneIDH1

GO:0006102

isocitrate metabolic process

10521434|19935646|20171178

TgeneIDH1

GO:0006103

2-oxoglutarate metabolic process

19935646



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/AAV689639CDH13chr16

83185581

+IDH1chr2

209107512

-


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Fusion Gene ORF analysis for CDH13-IDH1

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-intronENST00000268613ENST00000345146CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000268613ENST00000415913CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000268613ENST00000446179CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000428848ENST00000345146CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000428848ENST00000415913CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000428848ENST00000446179CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000431540ENST00000345146CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000431540ENST00000415913CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000431540ENST00000446179CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000446376ENST00000345146CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000446376ENST00000415913CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000446376ENST00000446179CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000565636ENST00000345146CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000565636ENST00000415913CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000565636ENST00000446179CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000566620ENST00000345146CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000566620ENST00000415913CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000566620ENST00000446179CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000567445ENST00000345146CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000567445ENST00000415913CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000567445ENST00000446179CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000569454ENST00000345146CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000569454ENST00000415913CDH13chr16

83185581

+IDH1chr2

209107512

-
intron-intronENST00000569454ENST00000446179CDH13chr16

83185581

+IDH1chr2

209107512

-

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 CDH13-IDH1


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 CDH13-IDH1


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/:83185581/:209107512)
- 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 CDH13-IDH1


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 CDH13-IDH1


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 CDH13-IDH1


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 CDH13-IDH1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCDH13C0001973Alcoholic Intoxication, Chronic3PSYGENET
HgeneCDH13C2239176Liver carcinoma3CTD_human
HgeneCDH13C0033578Prostatic Neoplasms2CTD_human
HgeneCDH13C0376358Malignant neoplasm of prostate2CTD_human
HgeneCDH13C0004763Barrett Esophagus1CTD_human
HgeneCDH13C0007131Non-Small Cell Lung Carcinoma1CTD_human
HgeneCDH13C0011570Mental Depression1PSYGENET
HgeneCDH13C0011581Depressive disorder1PSYGENET
HgeneCDH13C0013146Drug abuse1CTD_human
HgeneCDH13C0013170Drug habituation1CTD_human
HgeneCDH13C0013222Drug Use Disorders1CTD_human
HgeneCDH13C0014859Esophageal Neoplasms1CTD_human
HgeneCDH13C0024121Lung Neoplasms1CTD_human
HgeneCDH13C0029231Organic Mental Disorders, Substance-Induced1CTD_human
HgeneCDH13C0038580Substance Dependence1CTD_human
HgeneCDH13C0038586Substance Use Disorders1CTD_human
HgeneCDH13C0236733Amphetamine-Related Disorders1CTD_human
HgeneCDH13C0236804Amphetamine Addiction1CTD_human
HgeneCDH13C0236807Amphetamine Abuse1CTD_human
HgeneCDH13C0236969Substance-Related Disorders1CTD_human
HgeneCDH13C0242379Malignant neoplasm of lung1CTD_human
HgeneCDH13C0546837Malignant neoplasm of esophagus1CTD_human
HgeneCDH13C0740858Substance abuse problem1CTD_human
HgeneCDH13C1258085Barrett Epithelium1CTD_human
HgeneCDH13C1510472Drug Dependence1CTD_human
HgeneCDH13C4316881Prescription Drug Abuse1CTD_human
TgeneC0017638Glioma5CGI;CTD_human;UNIPROT
TgeneC0259783mixed gliomas5CTD_human
TgeneC0555198Malignant Glioma5CTD_human
TgeneC0013366Dyschondroplasias2ORPHANET
TgeneC0014084Enchondromatosis2CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC0023467Leukemia, Myelocytic, Acute2CGI;CTD_human
TgeneC0024454Maffucci Syndrome2CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC0026998Acute Myeloid Leukemia, M12CTD_human
TgeneC0936248Chondroma2CTD_human
TgeneC1704356Enchondroma2CTD_human
TgeneC1879321Acute Myeloid Leukemia (AML-M2)2CTD_human
TgeneC3553958METAPHYSEAL ENCHONDROMATOSIS WITH D-2-HYDROXYGLUTARIC ACIDURIA2GENOMICS_ENGLAND;ORPHANET
TgeneC0018916Hemangioma1CTD_human
TgeneC0023452Childhood Acute Lymphoblastic Leukemia1CTD_human
TgeneC0023453L2 Acute Lymphoblastic Leukemia1CTD_human
TgeneC0023487Acute Promyelocytic Leukemia1CTD_human
TgeneC0027643Neoplasm Recurrence, Local1CTD_human
TgeneC0028945oligodendroglioma1CTD_human
TgeneC0033578Prostatic Neoplasms1CTD_human
TgeneC0205788Histiocytoid hemangioma1CTD_human
TgeneC0205789Hemangioma, Intramuscular1CTD_human
TgeneC0206698Cholangiocarcinoma1CGI;CTD_human
TgeneC0206726gliosarcoma1ORPHANET
TgeneC0279070Adult Oligodendroglioma1CTD_human
TgeneC0280475Childhood Oligodendroglioma1CTD_human
TgeneC0280793Mixed Oligodendroglioma-Astrocytoma1CTD_human
TgeneC0334588Giant Cell Glioblastoma1ORPHANET
TgeneC0334590Anaplastic Oligodendroglioma1CTD_human
TgeneC0344461Oligodendroblastoma1CTD_human
TgeneC0345905Intrahepatic Cholangiocarcinoma1CTD_human
TgeneC0376358Malignant neoplasm of prostate1CTD_human
TgeneC0677608Chorioangioma1CTD_human
TgeneC0751395Mixed Oligodendroglioma-Ependymoma1CTD_human
TgeneC0751396Well Differentiated Oligodendroglioma1CTD_human
TgeneC1959588Angioma1CTD_human
TgeneC1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1CTD_human
TgeneC2239176Liver carcinoma1CTD_human
TgeneC3805278Extrahepatic Cholangiocarcinoma1CTD_human