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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:GPHN-CDH13 (FusionGDB2 ID:HG10243TG1012)

Fusion Gene Summary for GPHN-CDH13

check button Fusion gene summary
Fusion gene informationFusion gene name: GPHN-CDH13
Fusion gene ID: hg10243tg1012
HgeneTgene
Gene symbol

GPHN

CDH13

Gene ID

10243

1012

Gene namegephyrincadherin 13
SynonymsGEPH|GPH|GPHRYN|HKPX1|MOCODCCDHH|P105
Cytomap('GPHN')('CDH13')

14q23.3-q24.1

16q23.3

Type of geneprotein-codingprotein-coding
Descriptiongephyrincadherin-13H-cadherin (heart)T-cadT-cadherincadherin 13, H-cadherin (heart)heart cadherin
Modification date2020031320200315
UniProtAcc

Q9NQX3

.
Ensembl transtripts involved in fusion geneENST00000305960, ENST00000315266, 
ENST00000459628, ENST00000478722, 
ENST00000543237, ENST00000544752, 
Fusion gene scores* DoF score38 X 33 X 10=1254015 X 16 X 5=1200
# samples 4016
** MAII scorelog2(40/12540*10)=-4.97039353791468
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1200*10)=-2.90689059560852
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

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

Most frequent breakpointGPHN(67724948)-CDH13(82858461), # 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
HgeneGPHN

GO:0032324

molybdopterin cofactor biosynthetic process

26613940

HgeneGPHN

GO:0097112

gamma-aminobutyric acid receptor clustering

26613940

TgeneCDH13

GO:0002040

sprouting angiogenesis

16873731

TgeneCDH13

GO:0007156

homophilic cell adhesion via plasma membrane adhesion molecules

10601632

TgeneCDH13

GO:0007162

negative regulation of cell adhesion

14729458

TgeneCDH13

GO:0008285

negative regulation of cell proliferation

10737605

TgeneCDH13

GO:0016339

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

10601632

TgeneCDH13

GO:0030032

lamellipodium assembly

15703273

TgeneCDH13

GO:0030335

positive regulation of cell migration

14729458

TgeneCDH13

GO:0043542

endothelial cell migration

14729458

TgeneCDH13

GO:0043616

keratinocyte proliferation

15816843

TgeneCDH13

GO:0050850

positive regulation of calcium-mediated signaling

16013438

TgeneCDH13

GO:0050927

positive regulation of positive chemotaxis

16013438

TgeneCDH13

GO:0055096

low-density lipoprotein particle mediated signaling

16013438



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 GPHN-CDH13

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 GPHN-CDH13


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 GPHN-CDH13


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/:67724948/:82858461)
- 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
GPHN

Q9NQX3

.
FUNCTION: Microtubule-associated protein involved in membrane protein-cytoskeleton interactions. It is thought to anchor the inhibitory glycine receptor (GLYR) to subsynaptic microtubules (By similarity). Acts as a major instructive molecule at inhibitory synapses, where it also clusters GABA type A receptors (PubMed:25025157, PubMed:26613940). {ECO:0000250|UniProtKB:Q03555, ECO:0000269|PubMed:25025157, ECO:0000269|PubMed:26613940}.; FUNCTION: Has also a catalytic activity and catalyzes two steps in the biosynthesis of the molybdenum cofactor. In the first step, molybdopterin is adenylated. Subsequently, molybdate is inserted into adenylated molybdopterin and AMP is released. {ECO:0000269|PubMed:26613940}.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 GPHN-CDH13


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 GPHN-CDH13


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 GPHN-CDH13


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneGPHNQ9NQX3DB03766Propanoic acidSmall moleculeApproved|Vet_approved
HgeneGPHNQ9NQX3DB03766Propanoic acidSmall moleculeApproved|Vet_approved
HgeneGPHNQ9NQX3DB03766Propanoic acidSmall moleculeApproved|Vet_approved

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Related Diseases for GPHN-CDH13


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGPHNC1854990Molybdenum Cofactor Deficiency, Complementation Group C5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneGPHNC0001956Alcohol Use Disorder1CTD_human
HgeneGPHNC0001973Alcoholic Intoxication, Chronic1CTD_human
HgeneGPHNC0009171Cocaine Abuse1CTD_human
HgeneGPHNC0085762Alcohol abuse1CTD_human
HgeneGPHNC0236736Cocaine-Related Disorders1CTD_human
HgeneGPHNC0543888Epileptic encephalopathy1GENOMICS_ENGLAND
HgeneGPHNC0600427Cocaine Dependence1CTD_human
TgeneC0001973Alcoholic Intoxication, Chronic3PSYGENET
TgeneC2239176Liver carcinoma3CTD_human
TgeneC0033578Prostatic Neoplasms2CTD_human
TgeneC0376358Malignant neoplasm of prostate2CTD_human
TgeneC0004763Barrett Esophagus1CTD_human
TgeneC0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneC0011570Mental Depression1PSYGENET
TgeneC0011581Depressive disorder1PSYGENET
TgeneC0013146Drug abuse1CTD_human
TgeneC0013170Drug habituation1CTD_human
TgeneC0013222Drug Use Disorders1CTD_human
TgeneC0014859Esophageal Neoplasms1CTD_human
TgeneC0024121Lung Neoplasms1CTD_human
TgeneC0029231Organic Mental Disorders, Substance-Induced1CTD_human
TgeneC0038580Substance Dependence1CTD_human
TgeneC0038586Substance Use Disorders1CTD_human
TgeneC0236733Amphetamine-Related Disorders1CTD_human
TgeneC0236804Amphetamine Addiction1CTD_human
TgeneC0236807Amphetamine Abuse1CTD_human
TgeneC0236969Substance-Related Disorders1CTD_human
TgeneC0242379Malignant neoplasm of lung1CTD_human
TgeneC0546837Malignant neoplasm of esophagus1CTD_human
TgeneC0740858Substance abuse problem1CTD_human
TgeneC1258085Barrett Epithelium1CTD_human
TgeneC1510472Drug Dependence1CTD_human
TgeneC4316881Prescription Drug Abuse1CTD_human