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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:MT2A-MT3 (FusionGDB2 ID:55473)

Fusion Gene Summary for MT2A-MT3

check button Fusion gene summary
Fusion gene informationFusion gene name: MT2A-MT3
Fusion gene ID: 55473
HgeneTgene
Gene symbol

MT2A

MT3

Gene ID

4502

4504

Gene namemetallothionein 2Ametallothionein 3
SynonymsMT-2|MT-II|MT2GIF|GIFB|GRIF|ZnMT3
Cytomap

16q13

16q13

Type of geneprotein-codingprotein-coding
Descriptionmetallothionein-2metallothionein-IImetallothionein-3growth inhibitory factormetallothionein 3 (growth inhibitory factor (neurotrophic))metallothionein-III
Modification date2020031320200320
UniProtAcc

P02795

P25713

Ensembl transtripts involved in fusion geneENST00000563985, ENST00000245185, 
ENST00000561491, 		ENST00000200691, 
ENST00000561640, ENST00000565838, 
ENST00000570176, ENST00000566576, 
Fusion gene scores* DoF score4 X 4 X 3=489 X 6 X 3=162
# samples 511
** MAII scorelog2(5/48*10)=0.0588936890535686
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
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: MT2A [Title/Abstract] AND MT3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMT2A(56642969)-MT3(56624752), # samples:30
Anticipated loss of major functional domain due to fusion event.MT2A-MT3 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
* 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
HgeneMT2A

GO:0035690

cellular response to drug

19536566

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 MT2A (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 MT3 (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
ChimerDB4GBMTCGA-02-2485-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-06-0138-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-06-0141-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-06-0184-01AMT2Achr16

56642595

+MT3chr16

56623782

+
ChimerDB4GBMTCGA-06-0184-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-06-0187-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-06-0210-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-06-0211-01BMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-06-0745-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-06-1804-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-06-5408-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-06-5411-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-06-5412-01AMT2Achr16

56642595

+MT3chr16

56623782

+
ChimerDB4GBMTCGA-06-5415-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-12-0619-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-12-1597-01BMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-12-3652-01AMT2Achr16

56642595

+MT3chr16

56623782

+
ChimerDB4GBMTCGA-12-3652-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-12-5299-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-14-0790-01BMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-14-1829-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-14-2554-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-19-0957-02AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-19-2620-01AMT2Achr16

56642595

+MT3chr16

56623782

+
ChimerDB4GBMTCGA-19-2620-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-19-2625-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-26-5133-01AMT2Achr16

56642595

+MT3chr16

56623782

+
ChimerDB4GBMTCGA-27-2526-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-28-2499-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-28-2509-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-28-2514-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-28-5204-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-32-1970-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-32-2615-01AMT2Achr16

56642969

+MT3chr16

56624752

+
ChimerDB4GBMTCGA-41-2572-01AMT2Achr16

56642595

+MT3chr16

56623782

+
ChimerDB4GBMTCGA-76-4928-01BMT2Achr16

56642595

+MT3chr16

56623782

+
ChimerDB4GBMTCGA-76-4932-01AMT2Achr16

56642595

+MT3chr16

56623782

+
ChimerDB4GBMTCGA-76-4932-01AMT2Achr16

56642969

+MT3chr16

56624752

+


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Fusion Gene ORF analysis for MT2A-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
3UTR-3CDSENST00000563985ENST00000200691MT2Achr16

56642595

+MT3chr16

56623782

+
3UTR-3CDSENST00000563985ENST00000200691MT2Achr16

56642969

+MT3chr16

56624752

+
3UTR-3CDSENST00000563985ENST00000561640MT2Achr16

56642595

+MT3chr16

56623782

+
3UTR-3CDSENST00000563985ENST00000561640MT2Achr16

56642969

+MT3chr16

56624752

+
3UTR-3CDSENST00000563985ENST00000565838MT2Achr16

56642595

+MT3chr16

56623782

+
3UTR-3CDSENST00000563985ENST00000565838MT2Achr16

56642969

+MT3chr16

56624752

+
3UTR-3CDSENST00000563985ENST00000570176MT2Achr16

56642595

+MT3chr16

56623782

+
3UTR-3UTRENST00000563985ENST00000566576MT2Achr16

56642595

+MT3chr16

56623782

+
3UTR-3UTRENST00000563985ENST00000566576MT2Achr16

56642969

+MT3chr16

56624752

+
3UTR-intronENST00000563985ENST00000570176MT2Achr16

56642969

+MT3chr16

56624752

+
5CDS-3UTRENST00000245185ENST00000566576MT2Achr16

56642595

+MT3chr16

56623782

+
5CDS-3UTRENST00000245185ENST00000566576MT2Achr16

56642969

+MT3chr16

56624752

+
5CDS-3UTRENST00000561491ENST00000566576MT2Achr16

56642595

+MT3chr16

56623782

+
5CDS-3UTRENST00000561491ENST00000566576MT2Achr16

56642969

+MT3chr16

56624752

+
5CDS-intronENST00000245185ENST00000570176MT2Achr16

56642969

+MT3chr16

56624752

+
5CDS-intronENST00000561491ENST00000570176MT2Achr16

56642969

+MT3chr16

56624752

+
Frame-shiftENST00000245185ENST00000200691MT2Achr16

56642969

+MT3chr16

56624752

+
Frame-shiftENST00000245185ENST00000561640MT2Achr16

56642969

+MT3chr16

56624752

+
Frame-shiftENST00000245185ENST00000565838MT2Achr16

56642969

+MT3chr16

56624752

+
Frame-shiftENST00000245185ENST00000570176MT2Achr16

56642595

+MT3chr16

56623782

+
Frame-shiftENST00000561491ENST00000200691MT2Achr16

56642969

+MT3chr16

56624752

+
Frame-shiftENST00000561491ENST00000570176MT2Achr16

56642595

+MT3chr16

56623782

+
In-frameENST00000245185ENST00000200691MT2Achr16

56642595

+MT3chr16

56623782

+
In-frameENST00000245185ENST00000561640MT2Achr16

56642595

+MT3chr16

56623782

+
In-frameENST00000245185ENST00000565838MT2Achr16

56642595

+MT3chr16

56623782

+
In-frameENST00000561491ENST00000200691MT2Achr16

56642595

+MT3chr16

56623782

+
In-frameENST00000561491ENST00000561640MT2Achr16

56642595

+MT3chr16

56623782

+
In-frameENST00000561491ENST00000561640MT2Achr16

56642969

+MT3chr16

56624752

+
In-frameENST00000561491ENST00000565838MT2Achr16

56642595

+MT3chr16

56623782

+
In-frameENST00000561491ENST00000565838MT2Achr16

56642969

+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 MT2A-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)

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 MT2A-MT3


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/chr16:56642969/chr16:56624752)
- 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
MT2A

P02795

MT3

P25713

FUNCTION: Metallothioneins have a high content of cysteine residues that bind various heavy metals; these proteins are transcriptionally regulated by both heavy metals and glucocorticoids.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
HgeneMT2Achr16:56642969chr16:56624752ENST00000245185+231_293162.0RegionNote=Beta
TgeneMT3chr16:56642595chr16:56623782ENST000002006910331_681069.0RegionNote=Alpha
TgeneMT3chr16:56642969chr16:56624752ENST000002006911331_683269.0RegionNote=Alpha

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneMT2Achr16:56642595chr16:56623782ENST00000245185+131_29962.0RegionNote=Beta
HgeneMT2Achr16:56642595chr16:56623782ENST00000245185+1330_61962.0RegionNote=Alpha
HgeneMT2Achr16:56642969chr16:56624752ENST00000245185+2330_613162.0RegionNote=Alpha
TgeneMT3chr16:56642595chr16:56623782ENST00000200691031_301069.0RegionNote=Beta
TgeneMT3chr16:56642969chr16:56624752ENST00000200691131_303269.0RegionNote=Beta


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Fusion Gene Sequence for MT2A-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 MT2A-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 MT2A-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

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Related Diseases for MT2A-MT3


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