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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:NEDD1-GPHN (FusionGDB2 ID:58054)

Fusion Gene Summary for NEDD1-GPHN

check button Fusion gene summary
Fusion gene informationFusion gene name: NEDD1-GPHN
Fusion gene ID: 58054
HgeneTgene
Gene symbol

NEDD1

GPHN

Gene ID

121441

10243

Gene nameNEDD1 gamma-tubulin ring complex targeting factorgephyrin
SynonymsGCP-WD|TUBGCP7GEPH|GPH|GPHRYN|HKPX1|MOCODC
Cytomap

12q23.1

14q23.3-q24.1

Type of geneprotein-codingprotein-coding
Descriptionprotein NEDD1NEDD-1neural precursor cell expressed developmentally down-regulated protein 1neural precursor cell expressed, developmentally down-regulated 1tubulin gamma complex associated protein 7gephyrin
Modification date2020031320200313
UniProtAcc.

Q9NQX3

Ensembl transtripts involved in fusion geneENST00000266742, ENST00000429527, 
ENST00000555114, ENST00000411739, 
ENST00000557644, ENST00000457368, 
ENST00000315266, ENST00000478722, 
ENST00000459628, ENST00000543237, 
ENST00000305960, ENST00000544752, 
Fusion gene scores* DoF score4 X 4 X 1=1642 X 51 X 15=32130
# samples 562
** MAII scorelog2(5/16*10)=1.64385618977472
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(62/32130*10)=-5.69550895508454
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NEDD1 [Title/Abstract] AND GPHN [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNEDD1(97301078)-GPHN(67431908), # samples:2
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
TgeneGPHN

GO:0032324

molybdopterin cofactor biosynthetic process

26613940

TgeneGPHN

GO:0097112

gamma-aminobutyric acid receptor clustering

26613940


check buttonFusion gene breakpoints across NEDD1 (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 GPHN (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
ChimerDB4SARCTCGA-DX-AB2O-01ANEDD1chr12

97301078

+GPHNchr14

67431908

+
ChimerDB4SARCTCGA-DX-AB2O-01ANEDD1chr12

97301078

-GPHNchr14

67431908

+


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Fusion Gene ORF analysis for NEDD1-GPHN

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
5UTR-3CDSENST00000266742ENST00000315266NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000266742ENST00000478722NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000266742ENST00000459628NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000266742ENST00000543237NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000266742ENST00000305960NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3UTRENST00000266742ENST00000544752NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000429527ENST00000315266NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000429527ENST00000478722NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000429527ENST00000459628NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000429527ENST00000543237NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000429527ENST00000305960NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3UTRENST00000429527ENST00000544752NEDD1chr12

97301078

+GPHNchr14

67431908

+
3UTR-3CDSENST00000555114ENST00000315266NEDD1chr12

97301078

+GPHNchr14

67431908

+
3UTR-3CDSENST00000555114ENST00000478722NEDD1chr12

97301078

+GPHNchr14

67431908

+
3UTR-3CDSENST00000555114ENST00000459628NEDD1chr12

97301078

+GPHNchr14

67431908

+
3UTR-3CDSENST00000555114ENST00000543237NEDD1chr12

97301078

+GPHNchr14

67431908

+
3UTR-3CDSENST00000555114ENST00000305960NEDD1chr12

97301078

+GPHNchr14

67431908

+
3UTR-3UTRENST00000555114ENST00000544752NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000411739ENST00000315266NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000411739ENST00000478722NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000411739ENST00000459628NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000411739ENST00000543237NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3CDSENST00000411739ENST00000305960NEDD1chr12

97301078

+GPHNchr14

67431908

+
5UTR-3UTRENST00000411739ENST00000544752NEDD1chr12

97301078

+GPHNchr14

67431908

+
intron-3CDSENST00000557644ENST00000315266NEDD1chr12

97301078

+GPHNchr14

67431908

+
intron-3CDSENST00000557644ENST00000478722NEDD1chr12

97301078

+GPHNchr14

67431908

+
intron-3CDSENST00000557644ENST00000459628NEDD1chr12

97301078

+GPHNchr14

67431908

+
intron-3CDSENST00000557644ENST00000543237NEDD1chr12

97301078

+GPHNchr14

67431908

+
intron-3CDSENST00000557644ENST00000305960NEDD1chr12

97301078

+GPHNchr14

67431908

+
intron-3UTRENST00000557644ENST00000544752NEDD1chr12

97301078

+GPHNchr14

67431908

+
intron-3CDSENST00000457368ENST00000315266NEDD1chr12

97301078

+GPHNchr14

67431908

+
intron-3CDSENST00000457368ENST00000478722NEDD1chr12

97301078

+GPHNchr14

67431908

+
intron-3CDSENST00000457368ENST00000459628NEDD1chr12

97301078

+GPHNchr14

67431908

+
intron-3CDSENST00000457368ENST00000543237NEDD1chr12

97301078

+GPHNchr14

67431908

+
intron-3CDSENST00000457368ENST00000305960NEDD1chr12

97301078

+GPHNchr14

67431908

+
intron-3UTRENST00000457368ENST00000544752NEDD1chr12

97301078

+GPHNchr14

67431908

+

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 NEDD1-GPHN


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)
NEDD1chr1297301078+GPHNchr1467431907+2.70E-050.99997294
NEDD1chr1297301078+GPHNchr1467431907+2.70E-050.99997294

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 NEDD1-GPHN


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
.GPHN

Q9NQX3

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: 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}.

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 NEDD1-GPHN


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 NEDD1-GPHN


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 NEDD1-GPHN


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneGPHNQ9NQX3DB03766Propanoic acidSmall moleculeApproved|Vet_approved
TgeneGPHNQ9NQX3DB03766Propanoic acidSmall moleculeApproved|Vet_approved
TgeneGPHNQ9NQX3DB03766Propanoic acidSmall moleculeApproved|Vet_approved

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Related Diseases for NEDD1-GPHN


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneGPHNC1854990Molybdenum Cofactor Deficiency, Complementation Group C5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneGPHNC0001956Alcohol Use Disorder1CTD_human
TgeneGPHNC0001973Alcoholic Intoxication, Chronic1CTD_human
TgeneGPHNC0009171Cocaine Abuse1CTD_human
TgeneGPHNC0085762Alcohol abuse1CTD_human
TgeneGPHNC0236736Cocaine-Related Disorders1CTD_human
TgeneGPHNC0543888Epileptic encephalopathy1GENOMICS_ENGLAND
TgeneGPHNC0600427Cocaine Dependence1CTD_human