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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:CTNNA3-MGMT (FusionGDB2 ID:HG29119TG4255)

Fusion Gene Summary for CTNNA3-MGMT

check button Fusion gene summary
Fusion gene informationFusion gene name: CTNNA3-MGMT
Fusion gene ID: hg29119tg4255
HgeneTgene
Gene symbol

CTNNA3

MGMT

Gene ID

29119

4255

Gene namecatenin alpha 3O-6-methylguanine-DNA methyltransferase
SynonymsARVD13|VR22-
Cytomap('CTNNA3')('MGMT')

10q21.3

10q26.3

Type of geneprotein-codingprotein-coding
Descriptioncatenin alpha-3alpha-T-cateninalpha-catenin-like proteincatenin (cadherin-associated protein), alpha 3methylated-DNA--protein-cysteine methyltransferase6-O-methylguanine-DNA methyltransferaseO-6-methylguanine-DNA-alkyltransferaseO6-methylguanine-DNA methyltransferasemethylguanine-DNA methyltransferase
Modification date2020031320200315
UniProtAcc

Q9UI47

P16455

Ensembl transtripts involved in fusion geneENST00000373744, ENST00000433211, 
ENST00000373735, ENST00000545309, 
Fusion gene scores* DoF score16 X 15 X 3=72019 X 11 X 7=1463
# samples 1618
** MAII scorelog2(16/720*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(18/1463*10)=-3.02286095780881
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CTNNA3 [Title/Abstract] AND MGMT [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCTNNA3(68381450)-MGMT(131334505), # samples:3
Anticipated loss of major functional domain due to fusion event.CTNNA3-MGMT seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
CTNNA3-MGMT seems lost the major protein functional domain in Tgene partner, which is a CGC 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
TgeneMGMT

GO:0043066

negative regulation of apoptotic process

24147153

TgeneMGMT

GO:2000781

positive regulation of double-strand break repair

24147153


check buttonFusion gene breakpoints across CTNNA3 (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 MGMT (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
* 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
ChimerDB4BRCATCGA-AO-A03V-01ACTNNA3chr10

68381450

-MGMTchr10

131334505

+


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Fusion Gene ORF analysis for CTNNA3-MGMT

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-intronENST00000373744ENST00000462672CTNNA3chr10

68381450

-MGMTchr10

131334505

+
5CDS-intronENST00000433211ENST00000462672CTNNA3chr10

68381450

-MGMTchr10

131334505

+
Frame-shiftENST00000433211ENST00000306010CTNNA3chr10

68381450

-MGMTchr10

131334505

+
In-frameENST00000373744ENST00000306010CTNNA3chr10

68381450

-MGMTchr10

131334505

+
intron-3CDSENST00000373735ENST00000306010CTNNA3chr10

68381450

-MGMTchr10

131334505

+
intron-3CDSENST00000545309ENST00000306010CTNNA3chr10

68381450

-MGMTchr10

131334505

+
intron-intronENST00000373735ENST00000462672CTNNA3chr10

68381450

-MGMTchr10

131334505

+
intron-intronENST00000545309ENST00000462672CTNNA3chr10

68381450

-MGMTchr10

131334505

+

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)
ENST00000373744CTNNA3chr1068381450-ENST00000306010MGMTchr10131334505+3020137402009669

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
ENST00000373744ENST00000306010CTNNA3chr1068381450-MGMTchr10131334505+0.0027786670.99722135

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Fusion Genomic Features for CTNNA3-MGMT


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)
CTNNA3chr1068381449-MGMTchr10131334504+0.0003761880.9996238
CTNNA3chr1068381449-MGMTchr10131334504+0.0003761880.9996238

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 CTNNA3-MGMT


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/chr10:68381450/chr10:131334505)
- 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
CTNNA3

Q9UI47

MGMT

P16455

FUNCTION: May be involved in formation of stretch-resistant cell-cell adhesion complexes. {ECO:0000303|PubMed:11590244}.FUNCTION: Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) and O4-methylthymine (O4-MeT) in DNA. Repairs the methylated nucleobase in DNA by stoichiometrically transferring the methyl group to a cysteine residue in the enzyme. This is a suicide reaction: the enzyme is irreversibly inactivated.

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
HgeneCTNNA3chr10:68381450chr10:131334505ENST00000373744-917325_379458896.0Coiled coilOntology_term=ECO:0000255
HgeneCTNNA3chr10:68381450chr10:131334505ENST00000373744-91774_111458896.0Coiled coilOntology_term=ECO:0000255
HgeneCTNNA3chr10:68381450chr10:131334505ENST00000433211-1018325_379458896.0Coiled coilOntology_term=ECO:0000255
HgeneCTNNA3chr10:68381450chr10:131334505ENST00000433211-101874_111458896.0Coiled coilOntology_term=ECO:0000255

- 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 CTNNA3-MGMT


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.
>20297_20297_1_CTNNA3-MGMT_CTNNA3_chr10_68381450_ENST00000373744_MGMT_chr10_131334505_ENST00000306010_length(transcript)=3020nt_BP=1374nt
ATGTCAGCTGAAACACCAATCACATTGAATATCGATCCTCAGGATCTGCAGGTCCAAACATTCACCGTGGAGAAGCTACTGGAGCCTCTC
ATAATCCAGGTTACCACACTTGTAAACTGTCCCCAGAACCCTTCCAGCAGGAAAAAAGGACGTTCGAAAAGAGCCAGTGTCCTTCTAGCT
TCTGTGGAGGAAGCAACTTGGAATTTATTAGACAAGGGAGAGAAGATTGCCCAGGAAGCTACAGTTTTAAAGGATGAGCTTACGGCTTCA
CTTGAGGAAGTTCGCAAAGAAAGTGAAGCTCTGAAAGTATCAGCTGAGAGATTTACAGATGACCCCTGTTTTCTCCCAAAAAGGGAGGCT
GTGGTTCAAGCTGCCCGTGCCTTGCTGGCTGCGGTGACGAGACTCCTTATCCTTGCGGACATGATTGATGTCATGTGCCTCTTGCAACAT
GTGTCAGCTTTTCAAAGGACATTTGAGTCTCTCAAAAATGTTGCCAACAAATCTGACCTCCAGAAAACCTACCAGAAGCTTGGGAAGGAG
CTGGAAAATTTGGATTATTTAGCCTTCAAACGTCAGCAGGACTTAAAATCTCCAAATCAGAGAGATGAAATTGCAGGAGCCCGAGCTTCA
CTGAAGGAGAACTCTCCCCTCTTGCATTCAATTTGTTCAGCTTGTTTGGAGCATTCTGATGTTGCTTCCCTCAAAGCAAGCAAGGACACA
GTTTGTGAAGAAATTCAGAATGCTCTCAATGTAATTTCAAATGCTTCACAAGGGATCCAGAATATGACAACCCCACCAGAACCTCAGGCA
GCAACCCTGGGAAGTGCCCTTGATGAGCTGGAGAATTTAATTGTCCTGAATCCACTCACAGTAACTGAGGAGGAAATACGACCATCACTA
GAGAAACGCCTTGAAGCCATTATCAGTGGGGCTGCTCTGCTGGCGGATTCTTCATGTACGAGGGACTTACACCGAGAGCGGATTATCGCA
GAATGCAACGCCATTCGCCAGGCTCTTCAGGATCTGCTTTCAGAGTACATGAACAACGCTGGAAAAAAAGAAAGGAGTAATACCCTGAAT
ATTGCTTTAGACAACATGTGTAAGAAGACAAGAGACCTTCGCAGACAGCTCCGCAAGGCTATTATAGATCATGTGTCAGACTCTTTCCTG
GATACGACAGTCCCTCTTTTGGTTCTCATTGAAGCTGCTAAGAATGGCCGGGAAAAGGAAATAAAAGAATATGCTGCGATATTTCATGAA
CACACCAGCAGGCTTGTAGAGGTGGCAAATCTTGCTTGTTCCATGTCAACAAATGAAGATGGAATTAAAATTGTCAAAATTGCAGCCAAT
CATTTGGAAACCTTGTGTCCACAGGTACTTGGAAAAATGGACAAGGATTGTGAAATGAAACGCACCACACTGGACAGCCCTTTGGGGAAG
CTGGAGCTGTCTGGTTGTGAGCAGGGTCTGCACGAAATAAAGCTCCTGGGCAAGGGGACGTCTGCAGCTGATGCCGTGGAGGTCCCAGCC
CCCGCTGCGGTTCTCGGAGGTCCGGAGCCCCTGATGCAGTGCACAGCCTGGCTGAATGCCTATTTCCACCAGCCCGAGGCTATCGAAGAG
TTCCCCGTGCCGGCTCTTCACCATCCCGTTTTCCAGCAAGAGTCGTTCACCAGACAGGTGTTATGGAAGCTGCTGAAGGTTGTGAAATTC
GGAGAAGTGATTTCTTACCAGCAATTAGCAGCCCTGGCAGGCAACCCCAAAGCCGCGCGAGCAGTGGGAGGAGCAATGAGAGGCAATCCT
GTCCCCATCCTCATCCCGTGCCACAGAGTGGTCTGCAGCAGCGGAGCCGTGGGCAACTACTCCGGAGGACTGGCCGTGAAGGAATGGCTT
CTGGCCCATGAAGGCCACCGGTTGGGGAAGCCAGGCTTGGGAGGGAGCTCAGGTCTGGCAGGGGCCTGGCTCAAGGGAGCGGGAGCTACC
TCGGGCTCCCCGCCTGCTGGCCGAAACTGAGTATGTGCAGTAGGATGGATGTTTGAGCGACACACACGTGTAACACTGCATCGGATGCGG
GGCGTGGAGGCACCGCTGTATTAAAGGAAGTGGCAGTGTCCTGGGAACAAGCGTGTCTGCCCTTTCTGTTTCCATATTTTACAGCAGGAT
GAGTTCAGACGCCCGCGGTCCTGCACACATTTGTTTCCTTCTCTAACGCTGCCCTTGCTCTATTTTTCATGTCCATTAAAACAGGCCAAG
TGAGTGTGGAAGGCCTGGCTCATGTTGGGCCACAGCCCAGGATGGGGCAGTCTGGCACCCTCAGGCCACAGACGGCTGCCATAGCCGCTG
TCCAGGGCCAGCTAAGGCCCATCCCAGGCCGTCCACACTAGAAAGCTGGCCCTGCCCCATCCCCACCATGCCTCCCTTCCTGGCTGTGTC
CATGGCTGTGATGGCATTCTCCACTCAGCAGTTCCTAGCATCCCACACCCAGGTCTCACTGAAAGAAAGGGGAACAGGCCATGGCAGTCA
GTGCTTACAGAGGTTTTCTAGCTTTGTTTCCTACCTGCCAAAAAGGCTAATGCAAGATGCATCCACTTATGGTCTGTATCAGGTGAATAG
AAAATAACCATTTGCCAAGATTTGGAAAGACAGAGAGCTCTCTGGACACGGGTTCGATGGAGCTTGCACCTCTCTGAGAGCTGAAGTCAA
GTCTCACCCTCTCTCCATACTCCCTGGCCTAGTGTGCTCTGGGCAGCAGGTAGGAAGGGACAGGGACCTCTCATCTCAAGGGCTGCCCCA
AAGGGCCCTCAGGGACCATGGGCCTGTTAGGACCCCAGCACCCCAGTGTCGATCCTGGAAGTCAAAGGTCACGACTGTGGGGGGCCAGCT
CATGTCACTGATGGCAGCAGGCAGGGTTTCCAGCATGGGCGGTGCGCTGCTGTCTGATACTTCATTATTGTGTTGTCATCCTAGCTGTAT

>20297_20297_1_CTNNA3-MGMT_CTNNA3_chr10_68381450_ENST00000373744_MGMT_chr10_131334505_ENST00000306010_length(amino acids)=669AA_BP=458
MSAETPITLNIDPQDLQVQTFTVEKLLEPLIIQVTTLVNCPQNPSSRKKGRSKRASVLLASVEEATWNLLDKGEKIAQEATVLKDELTAS
LEEVRKESEALKVSAERFTDDPCFLPKREAVVQAARALLAAVTRLLILADMIDVMCLLQHVSAFQRTFESLKNVANKSDLQKTYQKLGKE
LENLDYLAFKRQQDLKSPNQRDEIAGARASLKENSPLLHSICSACLEHSDVASLKASKDTVCEEIQNALNVISNASQGIQNMTTPPEPQA
ATLGSALDELENLIVLNPLTVTEEEIRPSLEKRLEAIISGAALLADSSCTRDLHRERIIAECNAIRQALQDLLSEYMNNAGKKERSNTLN
IALDNMCKKTRDLRRQLRKAIIDHVSDSFLDTTVPLLVLIEAAKNGREKEIKEYAAIFHEHTSRLVEVANLACSMSTNEDGIKIVKIAAN
HLETLCPQVLGKMDKDCEMKRTTLDSPLGKLELSGCEQGLHEIKLLGKGTSAADAVEVPAPAAVLGGPEPLMQCTAWLNAYFHQPEAIEE
FPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYQQLAALAGNPKAARAVGGAMRGNPVPILIPCHRVVCSSGAVGNYSGGLAVKEWL

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

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Fusion Gene PPI Analysis for CTNNA3-MGMT


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 CTNNA3-MGMT


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneMGMTP16455DB14548Zinc sulfate, unspecified formStabilizationSmall moleculeApproved|Experimental
TgeneMGMTP16455DB01593ZincSmall moleculeApproved|Investigational
TgeneMGMTP16455DB14487Zinc acetateSmall moleculeApproved|Investigational
TgeneMGMTP16455DB14533Zinc chlorideStabilizationSmall moleculeApproved|Investigational
TgeneMGMTP16455DB00151CysteineSmall moleculeApproved|Nutraceutical

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Related Diseases for CTNNA3-MGMT


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCTNNA3C0004096Asthma1CTD_human
HgeneCTNNA3C0013146Drug abuse1CTD_human
HgeneCTNNA3C0013170Drug habituation1CTD_human
HgeneCTNNA3C0013222Drug Use Disorders1CTD_human
HgeneCTNNA3C0029231Organic Mental Disorders, Substance-Induced1CTD_human
HgeneCTNNA3C0038580Substance Dependence1CTD_human
HgeneCTNNA3C0038586Substance Use Disorders1CTD_human
HgeneCTNNA3C0236969Substance-Related Disorders1CTD_human
HgeneCTNNA3C0740858Substance abuse problem1CTD_human
HgeneCTNNA3C1510472Drug Dependence1CTD_human
HgeneCTNNA3C1832931ARRHYTHMOGENIC RIGHT VENTRICULAR DYSPLASIA, FAMILIAL, 21ORPHANET
HgeneCTNNA3C3810138ARRHYTHMOGENIC RIGHT VENTRICULAR DYSPLASIA, FAMILIAL, 131CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCTNNA3C4316881Prescription Drug Abuse1CTD_human
TgeneC0334588Giant Cell Glioblastoma4CTD_human;ORPHANET
TgeneC0017638Glioma3CTD_human
TgeneC0259783mixed gliomas3CTD_human
TgeneC0555198Malignant Glioma3CTD_human
TgeneC0017636Glioblastoma2CTD_human
TgeneC0206726gliosarcoma2ORPHANET
TgeneC1621958Glioblastoma Multiforme2CTD_human
TgeneC0006118Brain Neoplasms1CTD_human
TgeneC0023418leukemia1CTD_human
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0026640Mouth Neoplasms1CTD_human
TgeneC0027540Necrosis1CTD_human
TgeneC0032927Precancerous Conditions1CTD_human
TgeneC0153381Malignant neoplasm of mouth1CTD_human
TgeneC0153633Malignant neoplasm of brain1CTD_human
TgeneC0279626Squamous cell carcinoma of esophagus1CTD_human
TgeneC0282313Condition, Preneoplastic1CTD_human
TgeneC0496899Benign neoplasm of brain, unspecified1CTD_human
TgeneC0750974Brain Tumor, Primary1CTD_human
TgeneC0750977Recurrent Brain Neoplasm1CTD_human
TgeneC0750979Primary malignant neoplasm of brain1CTD_human
TgeneC1168401Squamous cell carcinoma of the head and neck1CTD_human
TgeneC1449861Micronuclei, Chromosome-Defective1CTD_human
TgeneC1449862Micronuclei, Genotoxicant-Induced1CTD_human
TgeneC1527390Neoplasms, Intracranial1CTD_human
TgeneC2314896Familial Atypical Mole Melanoma Syndrome1ORPHANET