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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:PLEKHA6-MT3 (FusionGDB2 ID:65796)

Fusion Gene Summary for PLEKHA6-MT3

check button Fusion gene summary
Fusion gene informationFusion gene name: PLEKHA6-MT3
Fusion gene ID: 65796
HgeneTgene
Gene symbol

PLEKHA6

MT3

Gene ID

22874

4504

Gene namepleckstrin homology domain containing A6metallothionein 3
SynonymsPEPP-3|PEPP3GIF|GIFB|GRIF|ZnMT3
Cytomap

1q32.1

16q13

Type of geneprotein-codingprotein-coding
Descriptionpleckstrin homology domain-containing family A member 6PH domain-containing family A member 6phosphoinositol 3-phosphate-binding protein 3metallothionein-3growth inhibitory factormetallothionein 3 (growth inhibitory factor (neurotrophic))metallothionein-III
Modification date2020031320200320
UniProtAcc.

P25713

Ensembl transtripts involved in fusion geneENST00000272203, ENST00000414478, 
ENST00000485632, 		ENST00000561640, 
ENST00000565838, ENST00000200691, 
ENST00000570176, ENST00000566576, 
Fusion gene scores* DoF score15 X 17 X 8=20409 X 6 X 3=162
# samples 1911
** MAII scorelog2(19/2040*10)=-3.42449782852791
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/162*10)=-0.558490289359965
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PLEKHA6 [Title/Abstract] AND MT3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPLEKHA6(204328822)-MT3(56624752), # 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
TgeneMT3

GO:0001666

response to hypoxia

12763630

TgeneMT3

GO:0001934

positive regulation of protein phosphorylation

18295594

TgeneMT3

GO:0010628

positive regulation of gene expression

18295594

TgeneMT3

GO:0010940

positive regulation of necrotic cell death

15129022|16387743

TgeneMT3

GO:0010942

positive regulation of cell death

16387743

TgeneMT3

GO:0019430

removal of superoxide radicals

12383939

TgeneMT3

GO:0030308

negative regulation of cell growth

16601975|17712581

TgeneMT3

GO:0030517

negative regulation of axon extension

16601975|17712581

TgeneMT3

GO:0030949

positive regulation of vascular endothelial growth factor receptor signaling pathway

18295594

TgeneMT3

GO:0032148

activation of protein kinase B activity

18295594

TgeneMT3

GO:0035690

cellular response to drug

19536566

TgeneMT3

GO:0036091

positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress

18554677

TgeneMT3

GO:0043066

negative regulation of apoptotic process

15129022|18554677

TgeneMT3

GO:0043154

negative regulation of cysteine-type endopeptidase activity involved in apoptotic process

16387743

TgeneMT3

GO:0043491

protein kinase B signaling

18554677

TgeneMT3

GO:0045893

positive regulation of transcription, DNA-templated

18295594

TgeneMT3

GO:0050821

protein stabilization

18295594

TgeneMT3

GO:0051354

negative regulation of oxidoreductase activity

21320589

TgeneMT3

GO:0055069

zinc ion homeostasis

18157556

TgeneMT3

GO:0055073

cadmium ion homeostasis

18157556

TgeneMT3

GO:0060547

negative regulation of necrotic cell death

18554677

TgeneMT3

GO:0070371

ERK1 and ERK2 cascade

18554677

TgeneMT3

GO:0070374

positive regulation of ERK1 and ERK2 cascade

18295594

TgeneMT3

GO:0071276

cellular response to cadmium ion

16387743

TgeneMT3

GO:0071732

cellular response to nitric oxide

18157556

TgeneMT3

GO:2000117

negative regulation of cysteine-type endopeptidase activity

18554677

TgeneMT3

GO:2000378

negative regulation of reactive oxygen species metabolic process

18554677


check buttonFusion gene breakpoints across PLEKHA6 (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 MT3 (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
ChimerDB4LGGTCGA-HT-8104-01APLEKHA6chr1

204328822

-MT3chr16

56624752

+


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Fusion Gene ORF analysis for PLEKHA6-MT3

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-3CDSENST00000272203ENST00000561640PLEKHA6chr1

204328822

-MT3chr16

56624752

+
5UTR-3CDSENST00000272203ENST00000565838PLEKHA6chr1

204328822

-MT3chr16

56624752

+
5UTR-3CDSENST00000272203ENST00000200691PLEKHA6chr1

204328822

-MT3chr16

56624752

+
5UTR-intronENST00000272203ENST00000570176PLEKHA6chr1

204328822

-MT3chr16

56624752

+
5UTR-3UTRENST00000272203ENST00000566576PLEKHA6chr1

204328822

-MT3chr16

56624752

+
5UTR-3CDSENST00000414478ENST00000561640PLEKHA6chr1

204328822

-MT3chr16

56624752

+
5UTR-3CDSENST00000414478ENST00000565838PLEKHA6chr1

204328822

-MT3chr16

56624752

+
5UTR-3CDSENST00000414478ENST00000200691PLEKHA6chr1

204328822

-MT3chr16

56624752

+
5UTR-intronENST00000414478ENST00000570176PLEKHA6chr1

204328822

-MT3chr16

56624752

+
5UTR-3UTRENST00000414478ENST00000566576PLEKHA6chr1

204328822

-MT3chr16

56624752

+
intron-3CDSENST00000485632ENST00000561640PLEKHA6chr1

204328822

-MT3chr16

56624752

+
intron-3CDSENST00000485632ENST00000565838PLEKHA6chr1

204328822

-MT3chr16

56624752

+
intron-3CDSENST00000485632ENST00000200691PLEKHA6chr1

204328822

-MT3chr16

56624752

+
intron-intronENST00000485632ENST00000570176PLEKHA6chr1

204328822

-MT3chr16

56624752

+
intron-3UTRENST00000485632ENST00000566576PLEKHA6chr1

204328822

-MT3chr16

56624752

+

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 PLEKHA6-MT3


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)
PLEKHA6chr1204328821-MT3chr1656624751+0.37844560.62155443
PLEKHA6chr1204328821-MT3chr1656624751+0.37844560.62155443

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 PLEKHA6-MT3


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
.MT3

P25713

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: Binds heavy metals. Contains three zinc and three copper atoms per polypeptide chain and only a negligible amount of cadmium. Inhibits survival and neurite formation of cortical neurons in vitro.

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 PLEKHA6-MT3


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 PLEKHA6-MT3


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 PLEKHA6-MT3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneMT3P25713DB14548Zinc sulfate, unspecified formCofactorSmall moleculeApproved|Experimental
TgeneMT3P25713DB01593ZincSmall moleculeApproved|Investigational
TgeneMT3P25713DB14487Zinc acetateSmall moleculeApproved|Investigational
TgeneMT3P25713DB14533Zinc chlorideCofactorSmall moleculeApproved|Investigational

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Related Diseases for PLEKHA6-MT3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePLEKHA6C0036341Schizophrenia1PSYGENET
TgeneMT3C0005684Malignant neoplasm of urinary bladder1CTD_human
TgeneMT3C0005695Bladder Neoplasm1CTD_human
TgeneMT3C0006142Malignant neoplasm of breast1CTD_human
TgeneMT3C0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneMT3C0022333Jacksonian Seizure1CTD_human
TgeneMT3C0027626Neoplasm Invasiveness1CTD_human
TgeneMT3C0035222Respiratory Distress Syndrome, Adult1CTD_human
TgeneMT3C0036572Seizures1CTD_human
TgeneMT3C0149958Complex partial seizures1CTD_human
TgeneMT3C0234533Generalized seizures1CTD_human
TgeneMT3C0234535Clonic Seizures1CTD_human
TgeneMT3C0270824Visual seizure1CTD_human
TgeneMT3C0270844Tonic Seizures1CTD_human
TgeneMT3C0270846Epileptic drop attack1CTD_human
TgeneMT3C0422850Seizures, Somatosensory1CTD_human
TgeneMT3C0422852Seizures, Auditory1CTD_human
TgeneMT3C0422853Olfactory seizure1CTD_human
TgeneMT3C0422854Gustatory seizure1CTD_human
TgeneMT3C0422855Vertiginous seizure1CTD_human
TgeneMT3C0494475Tonic - clonic seizures1CTD_human
TgeneMT3C0678222Breast Carcinoma1CTD_human
TgeneMT3C0751056Non-epileptic convulsion1CTD_human
TgeneMT3C0751110Single Seizure1CTD_human
TgeneMT3C0751123Atonic Absence Seizures1CTD_human
TgeneMT3C0751494Convulsive Seizures1CTD_human
TgeneMT3C0751495Seizures, Focal1CTD_human
TgeneMT3C0751496Seizures, Sensory1CTD_human
TgeneMT3C1257931Mammary Neoplasms, Human1CTD_human
TgeneMT3C1458155Mammary Neoplasms1CTD_human
TgeneMT3C3495874Nonepileptic Seizures1CTD_human
TgeneMT3C4048158Convulsions1CTD_human
TgeneMT3C4316903Absence Seizures1CTD_human
TgeneMT3C4317109Epileptic Seizures1CTD_human
TgeneMT3C4317123Myoclonic Seizures1CTD_human
TgeneMT3C4505436Generalized Absence Seizures1CTD_human
TgeneMT3C4704874Mammary Carcinoma, Human1CTD_human