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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:PHEX-NDUFA3 (FusionGDB2 ID:64756)

Fusion Gene Summary for PHEX-NDUFA3

check button Fusion gene summary
Fusion gene informationFusion gene name: PHEX-NDUFA3
Fusion gene ID: 64756
HgeneTgene
Gene symbol

PHEX

NDUFA3

Gene ID

5251

4696

Gene namephosphate regulating endopeptidase homolog X-linkedNADH:ubiquinone oxidoreductase subunit A3
SynonymsHPDR|HPDR1|HYP|HYP1|LXHR|PEX|XLHB9|CI-B9
Cytomap

Xp22.11

19q13.42

Type of geneprotein-codingprotein-coding
Descriptionphosphate-regulating neutral endopeptidase PHEXX-linked hypophosphatemia proteinmetalloendopeptidase homolog PEXphosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)phosphate-reNADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3, 9kDaNADH-ubiquinone oxidoreductase B9 subunitcomplex I B9 subunitcomplex I-B9
Modification date2020032220200313
UniProtAcc.

O95167

Ensembl transtripts involved in fusion geneENST00000418858, ENST00000379374, 
ENST00000475778, ENST00000535894, 
ENST00000537599, 		ENST00000391762, 
ENST00000303553, ENST00000391763, 
ENST00000391764, ENST00000471292, 
ENST00000480713, ENST00000485876, 
Fusion gene scores* DoF score3 X 3 X 3=272 X 2 X 2=8
# samples 32
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(2/8*10)=1.32192809488736
Context

PubMed: PHEX [Title/Abstract] AND NDUFA3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPHEX(22116153)-NDUFA3(54610118), # 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
HgenePHEX

GO:0006508

proteolysis

11409890


check buttonFusion gene breakpoints across PHEX (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across NDUFA3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4Non-CancerTCGA-IN-8462-11APHEXchrX

22116153

+NDUFA3chr19

54610118

+


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Fusion Gene ORF analysis for PHEX-NDUFA3

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
5CDS-3UTRENST00000418858ENST00000391762PHEXchrX

22116153

+NDUFA3chr19

54610118

+
5CDS-intronENST00000418858ENST00000303553PHEXchrX

22116153

+NDUFA3chr19

54610118

+
5CDS-intronENST00000418858ENST00000391763PHEXchrX

22116153

+NDUFA3chr19

54610118

+
5CDS-intronENST00000418858ENST00000391764PHEXchrX

22116153

+NDUFA3chr19

54610118

+
5CDS-intronENST00000418858ENST00000471292PHEXchrX

22116153

+NDUFA3chr19

54610118

+
5CDS-intronENST00000418858ENST00000480713PHEXchrX

22116153

+NDUFA3chr19

54610118

+
In-frameENST00000418858ENST00000485876PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-3CDSENST00000379374ENST00000485876PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-3CDSENST00000475778ENST00000485876PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-3CDSENST00000535894ENST00000485876PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-3CDSENST00000537599ENST00000485876PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-3UTRENST00000379374ENST00000391762PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-3UTRENST00000475778ENST00000391762PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-3UTRENST00000535894ENST00000391762PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-3UTRENST00000537599ENST00000391762PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000379374ENST00000303553PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000379374ENST00000391763PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000379374ENST00000391764PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000379374ENST00000471292PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000379374ENST00000480713PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000475778ENST00000303553PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000475778ENST00000391763PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000475778ENST00000391764PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000475778ENST00000471292PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000475778ENST00000480713PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000535894ENST00000303553PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000535894ENST00000391763PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000535894ENST00000391764PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000535894ENST00000471292PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000535894ENST00000480713PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000537599ENST00000303553PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000537599ENST00000391763PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000537599ENST00000391764PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000537599ENST00000471292PHEXchrX

22116153

+NDUFA3chr19

54610118

+
intron-intronENST00000537599ENST00000480713PHEXchrX

22116153

+NDUFA3chr19

54610118

+

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)
ENST00000418858PHEXchrX22116153+ENST00000485876NDUFA3chr1954610118+1090332771102283

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
ENST00000418858ENST00000485876PHEXchrX22116153+NDUFA3chr1954610118+0.668421570.33157846

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Fusion Genomic Features for PHEX-NDUFA3


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)
PHEXchrX22116153+NDUFA3chr1954610117+0.0262031740.9737968
PHEXchrX22116153+NDUFA3chr1954610117+0.0262031740.9737968

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.
genomic feature

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.
genomic feature of top 1%

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Fusion Protein Features for PHEX-NDUFA3


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/chrX:22116153/chr19:54610118)
- 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
.NDUFA3

O95167

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: Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. {ECO:0000269|PubMed:27626371}.

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
HgenePHEXchrX:22116153chr19:54610118ENST00000379374+12253_7490750.0DomainPeptidase M13
HgenePHEXchrX:22116153chr19:54610118ENST00000379374+1221_200750.0Topological domainCytoplasmic
HgenePHEXchrX:22116153chr19:54610118ENST00000379374+12242_6410750.0Topological domainExtracellular
HgenePHEXchrX:22116153chr19:54610118ENST00000379374+12221_410750.0TransmembraneHelical%3B Signal-anchor for type II membrane protein
TgeneNDUFA3chrX:22116153chr19:54610118ENST000004858762419_395485.0TransmembraneHelical


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Fusion Gene Sequence for PHEX-NDUFA3


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.
>64756_64756_1_PHEX-NDUFA3_PHEX_chrX_22116153_ENST00000418858_NDUFA3_chr19_54610118_ENST00000485876_length(transcript)=1090nt_BP=332nt
ACCATATGGTGTTTTAGGTAGGATAGGGATGCTCTGAAGAATGGAGGCATGTTACTTTCTGTGTTTTTATTTGTTTTTTTTTGAGACACA
GTCTTGCTGTGTCATCCAGGCTGGGGTGCAGTGGTGTGATCTTGGCTCATTGCAACCTCTGCCTCCCGGGTTCAAGTGATTCTCCTGCCT
TAGCCTCTCGAGTAGCTGGGATTACAGGTGCCGGCCACCACACCTAGCTAATTTTTGTATTTTTGATAGAGATGGGATTGGCCAGGCTGG
TCTCAAACTCCTGACCTCAAATGATCCACCTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGTGCCCGTCCGTGATGATGGGAACATGCC
CGACGTGCCCAGCCACCCCCAGGACCCTCAGGGCCCCAGCCTGGAGTGGCTGAAGAAACTGTGAGCACCTCCACTGACAGAGGCGGCCCC
TCCCACGGCTCCCAATAAAAATGTGAAAACCAACCCCCGAACGTGAGCATGTGTGTGATCAGAGGTGGGAACAAGTAGACGGTGGCCGGG
GTGAGTGTGGGGTCAGTTTATTGGGCATGCGTCAGTCAGAGGCTGGGCTGGCCAGGGTCGGGTAGGGCAGCAGTTTGTCTGGACCCCGAG
AAACCCAACTGGAATCCAGGGCCTCATCTGCTTCAAAGCCAAAGTCTTCCTCAACCTTAATCTGCAGGAGATAAGGAACAAGGTGTTAAC
AGGCCTGGGAATCTAGAAAATCCCATCAGCTTCACCATTTTTGTTTTCATTTTGTTTTGCTTTTTAAAGAGACAGGGTCTCACTCTGTTG
CCCAGGCTGGAGTGCAGTGGTGCCATCATAGTTCACTGCAGCCTCTGCCTCCCAGGCTCAAGTGATCCTCCCACCTCAGCTTCCCAAGTA
GCTGGGACTACAGGCACTTGCCAACCAAGCCTAACATGTTTTTTCTTTTTGGTAGAGATGGGGTCTCAGTATGTTGCTCAGGCAGGTCTC
AGACTCCTGGCCTCAAGTGATCCTCCCACCTAGGCCTCCCAAAGTGCCGGGATTACAGGCATGAGCCACTGCACCTGGCCAGCCTCACAG

>64756_64756_1_PHEX-NDUFA3_PHEX_chrX_22116153_ENST00000418858_NDUFA3_chr19_54610118_ENST00000485876_length(amino acids)=83AA_BP=

--------------------------------------------------------------

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Fusion Gene PPI Analysis for PHEX-NDUFA3


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 PHEX-NDUFA3


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 PHEX-NDUFA3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource