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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:CDH23-ABCC1 (FusionGDB2 ID:HG64072TG4363)

Fusion Gene Summary for CDH23-ABCC1

check button Fusion gene summary
Fusion gene informationFusion gene name: CDH23-ABCC1
Fusion gene ID: hg64072tg4363
HgeneTgene
Gene symbol

CDH23

ABCC1

Gene ID

64072

4363

Gene namecadherin related 23ATP binding cassette subfamily C member 1
SynonymsCDHR23|PITA5|USH1DABC29|ABCC|GS-X|MRP|MRP1
Cytomap('CDH23')('ABCC1')

10q22.1

16p13.11

Type of geneprotein-codingprotein-coding
Descriptioncadherin-23cadherin-like 23cadherin-related family member 23otocadherinmultidrug resistance-associated protein 1ATP-binding cassette transporter variant ABCC1delta-ex13ATP-binding cassette transporter variant ABCC1delta-ex13&14ATP-binding cassette transporter variant ABCC1delta-ex25ATP-binding cassette transporter varian
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000224721, ENST00000299366, 
ENST00000398788, ENST00000398809, 
ENST00000398842, ENST00000461841, 
ENST00000475158, 
Fusion gene scores* DoF score7 X 7 X 2=9816 X 13 X 5=1040
# samples 716
** MAII scorelog2(7/98*10)=-0.485426827170242
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(16/1040*10)=-2.70043971814109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CDH23 [Title/Abstract] AND ABCC1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCDH23(73348253)-ABCC1(16236894), # 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


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 CDH23-ABCC1

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 CDH23-ABCC1


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 CDH23-ABCC1


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/:73348253/:16236894)
- 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 CDH23-ABCC1


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 CDH23-ABCC1


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 CDH23-ABCC1


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 CDH23-ABCC1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCDH23C1832394Deafness, Autosomal Recessive 1210CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCDH23C1832845USHER SYNDROME, TYPE ID7GENOMICS_ENGLAND;UNIPROT
HgeneCDH23C0154860Hereditary retinal dystrophy6CLINGEN
HgeneCDH23C1568247Usher Syndrome, Type I6CLINGEN;GENOMICS_ENGLAND
HgeneCDH23C1848638USHER SYNDROME, TYPE IB (disorder)6CLINGEN
HgeneCDH23C1848639USHER SYNDROME, TYPE IA, FORMERLY6CLINGEN
HgeneCDH23C1848640USHER SYNDROME, TYPE I, FRENCH VARIETY, FORMERLY6CLINGEN
HgeneCDH23C3711374Nonsyndromic Deafness6CLINGEN
HgeneCDH23C0004681Bagassosis1CTD_human
HgeneCDH23C0010481Cushing Syndrome1ORPHANET
HgeneCDH23C0032273Pneumoconiosis1CTD_human
HgeneCDH23C0033375Prolactinoma1ORPHANET
HgeneCDH23C0221406Pituitary-dependent Cushing's disease1ORPHANET
HgeneCDH23C0346303Thyrotroph adenoma1ORPHANET
HgeneCDH23C1384666hearing impairment1GENOMICS_ENGLAND
HgeneCDH23C1863340PITUITARY ADENOMA PREDISPOSITION (disorder)1ORPHANET
HgeneCDH23C2931205Usher syndrome, type 1A1GENOMICS_ENGLAND
HgeneCDH23C4539685PITUITARY ADENOMA 5, MULTIPLE TYPES1UNIPROT
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0009402Colorectal Carcinoma1CTD_human
TgeneC0009404Colorectal Neoplasms1CTD_human
TgeneC0013221Drug toxicity1CTD_human
TgeneC0018799Heart Diseases1CTD_human
TgeneC0019193Hepatitis, Toxic1CTD_human
TgeneC0020538Hypertensive disease1CTD_human
TgeneC0041755Adverse reaction to drug1CTD_human
TgeneC0235874Disease Exacerbation1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC0860207Drug-Induced Liver Disease1CTD_human
TgeneC1168401Squamous cell carcinoma of the head and neck1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1262760Hepatitis, Drug-Induced1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC3658290Drug-Induced Acute Liver Injury1CTD_human
TgeneC4277682Chemical and Drug Induced Liver Injury1CTD_human
TgeneC4279912Chemically-Induced Liver Toxicity1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human
TgeneC4721453Peripheral Nervous System Diseases1CTD_human