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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:MTMR12-CARD6 (FusionGDB2 ID:55727)

Fusion Gene Summary for MTMR12-CARD6

check button Fusion gene summary
Fusion gene informationFusion gene name: MTMR12-CARD6
Fusion gene ID: 55727
HgeneTgene
Gene symbol

MTMR12

CARD6

Gene ID

54545

84674

Gene namemyotubularin related protein 12caspase recruitment domain family member 6
Synonyms3-PAP|PIP3APCINCIN1
Cytomap

5p13.3

5p13.1

Type of geneprotein-codingprotein-coding
Descriptionmyotubularin-related protein 123-phosphatase adapter protein3-phosphatase adapter subunitinactive phosphatidylinositol 3-phosphatase 12phosphatidylinositol 3 phosphate 3-phosphatase adapter subunitphosphatidylinositol-3 phosphate 3-phosphatase adaptocaspase recruitment domain-containing protein 6CARD-containing inhibitor of Nod1 and Cardiak-induced NF-kB activationcaspase recruitment domain protein 6
Modification date2020031320200313
UniProtAcc

Q9C0I1

.
Ensembl transtripts involved in fusion geneENST00000264934, ENST00000280285, 
ENST00000382142, ENST00000510216, 
ENST00000254691, ENST00000381677, 
Fusion gene scores* DoF score12 X 11 X 10=13202 X 2 X 2=8
# samples 152
** MAII scorelog2(15/1320*10)=-3.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: MTMR12 [Title/Abstract] AND CARD6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMTMR12(32312864)-CARD6(40841576), # samples:2
Anticipated loss of major functional domain due to fusion event.MTMR12-CARD6 seems lost the major protein functional domain in Hgene partner, which is a essential gene 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

check buttonFusion gene breakpoints across MTMR12 (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 CARD6 (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
ChimerDB4KIRPTCGA-2Z-A9JJ-01AMTMR12chr5

32312864

-CARD6chr5

40841576

+
ChimerDB4KIRPTCGA-2Z-A9JJMTMR12chr5

32312864

-CARD6chr5

40841576

+


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Fusion Gene ORF analysis for MTMR12-CARD6

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
Frame-shiftENST00000264934ENST00000254691MTMR12chr5

32312864

-CARD6chr5

40841576

+
Frame-shiftENST00000280285ENST00000254691MTMR12chr5

32312864

-CARD6chr5

40841576

+
Frame-shiftENST00000382142ENST00000254691MTMR12chr5

32312864

-CARD6chr5

40841576

+
In-frameENST00000264934ENST00000381677MTMR12chr5

32312864

-CARD6chr5

40841576

+
In-frameENST00000280285ENST00000381677MTMR12chr5

32312864

-CARD6chr5

40841576

+
In-frameENST00000382142ENST00000381677MTMR12chr5

32312864

-CARD6chr5

40841576

+
intron-3CDSENST00000510216ENST00000254691MTMR12chr5

32312864

-CARD6chr5

40841576

+
intron-3CDSENST00000510216ENST00000381677MTMR12chr5

32312864

-CARD6chr5

40841576

+

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)
ENST00000280285MTMR12chr532312864-ENST00000381677CARD6chr540841576+11061811761021281
ENST00000382142MTMR12chr532312864-ENST00000381677CARD6chr540841576+11772522471092281
ENST00000264934MTMR12chr532312864-ENST00000381677CARD6chr540841576+11372122071052281

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
ENST00000280285ENST00000381677MTMR12chr532312864-CARD6chr540841576+0.0014250140.998575
ENST00000382142ENST00000381677MTMR12chr532312864-CARD6chr540841576+0.0013281310.9986719
ENST00000264934ENST00000381677MTMR12chr532312864-CARD6chr540841576+0.0012540310.9987459

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Fusion Genomic Features for MTMR12-CARD6


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.

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Fusion Protein Features for MTMR12-CARD6


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/chr5:32312864/chr5:40841576)
- 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
MTMR12

Q9C0I1

.
FUNCTION: Acts as an adapter for the myotubularin-related phosphatases (PubMed:11504939, PubMed:12847286, PubMed:23818870). Regulates phosphatase MTM1 protein stability and possibly its intracellular location (PubMed:23818870). By stabilizing MTM1 protein levels, required for skeletal muscle maintenance but not for myogenesis (By similarity). {ECO:0000250|UniProtKB:Q80TA6, ECO:0000269|PubMed:11504939, ECO:0000269|PubMed:12847286, ECO:0000269|PubMed:23818870}.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}.

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
TgeneCARD6chr5:32312864chr5:40841576ENST0000025469103201_28101038.0Compositional biasNote=Asp/Glu-rich
TgeneCARD6chr5:32312864chr5:40841576ENST0000025469103957_101201038.0Compositional biasNote=Pro-rich
TgeneCARD6chr5:32312864chr5:40841576ENST00000254691033_9401038.0DomainCARD

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneMTMR12chr5:32312864chr5:40841576ENST00000264934-114205_64327638.0DomainMyotubularin phosphatase
HgeneMTMR12chr5:32312864chr5:40841576ENST00000280285-115205_64327694.0DomainMyotubularin phosphatase
HgeneMTMR12chr5:32312864chr5:40841576ENST00000382142-116205_64327748.0DomainMyotubularin phosphatase


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Fusion Gene Sequence for MTMR12-CARD6


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.
>55727_55727_1_MTMR12-CARD6_MTMR12_chr5_32312864_ENST00000264934_CARD6_chr5_40841576_ENST00000381677_length(transcript)=1137nt_BP=212nt
ATCGCGGCGGTCGCGGCCTTGGGGATGGGCGGAGCCCCAGCCGCTAGTGCTGGTGGCCGCCGCTGCTGCCCCAGCTGGAGCCCGAGCCGC
CGCCTCTGCGTCCGCGCGTCGCTGCTTCCCAGGGCGGCGGTATGCTGGGGAAAGGAGTAGTCGGCGGTGGCGGCGGCACCAAGGCCCCCA
AGCCCTCCTTCGTGTCGTACGTACGCCCTGAGCACGTTAACTTCTCGGAGGCTGATTTCTGAGGAAGAGTATGAGACTCTGGAGAATGTT
ACAGATCTCCTGAAGAAAAGTCGGAAGCTGTTAATTTTGGTACAGAAAAAGGGAGAGGCGACCTGTCAGCATTTTCTCAAGTGTTTATTT
AGTACTTTTCCACAGTCAGCTGCCATTTGCGGCTTAAGGCATGAAGTTTTAAAACATGAGAATACAGTACCTCCTCAATCTATGGGGGCA
AGCAGTAATTCAGAAGATGCTTTTTCTCCTGGAATAAAACAGCCTGAAGCCCCTGAGATCACAGTGTTCTTCAGTGAGAAGGAACACTTG
GATTTGGAAACCTCTGAGTTTTTCAGGGACAAGAAAACTAGTTATAGGGAAACAGCTTTGTCTGCCAGGAAGAATGAGAAGGAATATGAC
ACACCAGAAGTCACATTATCATATTCAGTTGAGAAAGTTGGATGTGAAGTTCCAGCAACTATTACATATATAAAAGATGGACAGAGATAT
GAGGAGCTAGATGATTCTTTATACTTAGGAAAAGAGGAATATCTAGGATCTGTTGACACCCCTGAAGATGCAGAAGCCACTGTGGAAGAG
GAGGTTTATGATGACCCAGAGCACGTTGGATATGATGGTGAAGAGGACTTCGAGAATTCAGAAACCACAGAGTTCTCTGGTGAAGAACCA
AGTTATGAGGGATCAGAAACCAGCCTTTCATTGGAGGAGGAACAGGAGAAAAGTATAGAAGGCTGGTCTCGAACTCATGGGCTTAAGCGA
TCCTCCCACGTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCCTGCCTGGCCTGAAAATTCTGCCTCAAACATCTCAAACAT

>55727_55727_1_MTMR12-CARD6_MTMR12_chr5_32312864_ENST00000264934_CARD6_chr5_40841576_ENST00000381677_length(amino acids)=281AA_BP=2
MSTLTSRRLISEEEYETLENVTDLLKKSRKLLILVQKKGEATCQHFLKCLFSTFPQSAAICGLRHEVLKHENTVPPQSMGASSNSEDAFS
PGIKQPEAPEITVFFSEKEHLDLETSEFFRDKKTSYRETALSARKNEKEYDTPEVTLSYSVEKVGCEVPATITYIKDGQRYEELDDSLYL
GKEEYLGSVDTPEDAEATVEEEVYDDPEHVGYDGEEDFENSETTEFSGEEPSYEGSETSLSLEEEQEKSIEGWSRTHGLKRSSHVGLPKC

--------------------------------------------------------------
>55727_55727_2_MTMR12-CARD6_MTMR12_chr5_32312864_ENST00000280285_CARD6_chr5_40841576_ENST00000381677_length(transcript)=1106nt_BP=181nt
GAGCCCCAGCCGCTAGTGCTGGTGGCCGCCGCTGCTGCCCCAGCTGGAGCCCGAGCCGCCGCCTCTGCGTCCGCGCGTCGCTGCTTCCCA
GGGCGGCGGTATGCTGGGGAAAGGAGTAGTCGGCGGTGGCGGCGGCACCAAGGCCCCCAAGCCCTCCTTCGTGTCGTACGTACGCCCTGA
GCACGTTAACTTCTCGGAGGCTGATTTCTGAGGAAGAGTATGAGACTCTGGAGAATGTTACAGATCTCCTGAAGAAAAGTCGGAAGCTGT
TAATTTTGGTACAGAAAAAGGGAGAGGCGACCTGTCAGCATTTTCTCAAGTGTTTATTTAGTACTTTTCCACAGTCAGCTGCCATTTGCG
GCTTAAGGCATGAAGTTTTAAAACATGAGAATACAGTACCTCCTCAATCTATGGGGGCAAGCAGTAATTCAGAAGATGCTTTTTCTCCTG
GAATAAAACAGCCTGAAGCCCCTGAGATCACAGTGTTCTTCAGTGAGAAGGAACACTTGGATTTGGAAACCTCTGAGTTTTTCAGGGACA
AGAAAACTAGTTATAGGGAAACAGCTTTGTCTGCCAGGAAGAATGAGAAGGAATATGACACACCAGAAGTCACATTATCATATTCAGTTG
AGAAAGTTGGATGTGAAGTTCCAGCAACTATTACATATATAAAAGATGGACAGAGATATGAGGAGCTAGATGATTCTTTATACTTAGGAA
AAGAGGAATATCTAGGATCTGTTGACACCCCTGAAGATGCAGAAGCCACTGTGGAAGAGGAGGTTTATGATGACCCAGAGCACGTTGGAT
ATGATGGTGAAGAGGACTTCGAGAATTCAGAAACCACAGAGTTCTCTGGTGAAGAACCAAGTTATGAGGGATCAGAAACCAGCCTTTCAT
TGGAGGAGGAACAGGAGAAAAGTATAGAAGGCTGGTCTCGAACTCATGGGCTTAAGCGATCCTCCCACGTTGGCCTCCCAAAGTGCTGGG
ATTACAGGCGTGAGCCACCCTGCCTGGCCTGAAAATTCTGCCTCAAACATCTCAAACATCCATTTATATTTTGTACAAGAAAGTAAATAA

>55727_55727_2_MTMR12-CARD6_MTMR12_chr5_32312864_ENST00000280285_CARD6_chr5_40841576_ENST00000381677_length(amino acids)=281AA_BP=2
MSTLTSRRLISEEEYETLENVTDLLKKSRKLLILVQKKGEATCQHFLKCLFSTFPQSAAICGLRHEVLKHENTVPPQSMGASSNSEDAFS
PGIKQPEAPEITVFFSEKEHLDLETSEFFRDKKTSYRETALSARKNEKEYDTPEVTLSYSVEKVGCEVPATITYIKDGQRYEELDDSLYL
GKEEYLGSVDTPEDAEATVEEEVYDDPEHVGYDGEEDFENSETTEFSGEEPSYEGSETSLSLEEEQEKSIEGWSRTHGLKRSSHVGLPKC

--------------------------------------------------------------
>55727_55727_3_MTMR12-CARD6_MTMR12_chr5_32312864_ENST00000382142_CARD6_chr5_40841576_ENST00000381677_length(transcript)=1177nt_BP=252nt
GGGGCGAGCGGTGTCAGCGGCGGAGCCGGATGCGGGCGGCATCGCGGCGGTCGCGGCCTTGGGGATGGGCGGAGCCCCAGCCGCTAGTGC
TGGTGGCCGCCGCTGCTGCCCCAGCTGGAGCCCGAGCCGCCGCCTCTGCGTCCGCGCGTCGCTGCTTCCCAGGGCGGCGGTATGCTGGGG
AAAGGAGTAGTCGGCGGTGGCGGCGGCACCAAGGCCCCCAAGCCCTCCTTCGTGTCGTACGTACGCCCTGAGCACGTTAACTTCTCGGAG
GCTGATTTCTGAGGAAGAGTATGAGACTCTGGAGAATGTTACAGATCTCCTGAAGAAAAGTCGGAAGCTGTTAATTTTGGTACAGAAAAA
GGGAGAGGCGACCTGTCAGCATTTTCTCAAGTGTTTATTTAGTACTTTTCCACAGTCAGCTGCCATTTGCGGCTTAAGGCATGAAGTTTT
AAAACATGAGAATACAGTACCTCCTCAATCTATGGGGGCAAGCAGTAATTCAGAAGATGCTTTTTCTCCTGGAATAAAACAGCCTGAAGC
CCCTGAGATCACAGTGTTCTTCAGTGAGAAGGAACACTTGGATTTGGAAACCTCTGAGTTTTTCAGGGACAAGAAAACTAGTTATAGGGA
AACAGCTTTGTCTGCCAGGAAGAATGAGAAGGAATATGACACACCAGAAGTCACATTATCATATTCAGTTGAGAAAGTTGGATGTGAAGT
TCCAGCAACTATTACATATATAAAAGATGGACAGAGATATGAGGAGCTAGATGATTCTTTATACTTAGGAAAAGAGGAATATCTAGGATC
TGTTGACACCCCTGAAGATGCAGAAGCCACTGTGGAAGAGGAGGTTTATGATGACCCAGAGCACGTTGGATATGATGGTGAAGAGGACTT
CGAGAATTCAGAAACCACAGAGTTCTCTGGTGAAGAACCAAGTTATGAGGGATCAGAAACCAGCCTTTCATTGGAGGAGGAACAGGAGAA
AAGTATAGAAGGCTGGTCTCGAACTCATGGGCTTAAGCGATCCTCCCACGTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACC
CTGCCTGGCCTGAAAATTCTGCCTCAAACATCTCAAACATCCATTTATATTTTGTACAAGAAAGTAAATAAAATTTTTCTTTTTAACATT

>55727_55727_3_MTMR12-CARD6_MTMR12_chr5_32312864_ENST00000382142_CARD6_chr5_40841576_ENST00000381677_length(amino acids)=281AA_BP=2
MSTLTSRRLISEEEYETLENVTDLLKKSRKLLILVQKKGEATCQHFLKCLFSTFPQSAAICGLRHEVLKHENTVPPQSMGASSNSEDAFS
PGIKQPEAPEITVFFSEKEHLDLETSEFFRDKKTSYRETALSARKNEKEYDTPEVTLSYSVEKVGCEVPATITYIKDGQRYEELDDSLYL
GKEEYLGSVDTPEDAEATVEEEVYDDPEHVGYDGEEDFENSETTEFSGEEPSYEGSETSLSLEEEQEKSIEGWSRTHGLKRSSHVGLPKC

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

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Fusion Gene PPI Analysis for MTMR12-CARD6


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 MTMR12-CARD6


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 MTMR12-CARD6


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