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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:MSH6-MSH6 (FusionGDB2 ID:55292)

Fusion Gene Summary for MSH6-MSH6

check button Fusion gene summary
Fusion gene informationFusion gene name: MSH6-MSH6
Fusion gene ID: 55292
HgeneTgene
Gene symbol

MSH6

MSH6

Gene ID

2956

2956

Gene namemutS homolog 6mutS homolog 6
SynonymsGTBP|GTMBP|HNPCC5|HSAP|p160GTBP|GTMBP|HNPCC5|HSAP|p160
Cytomap

2p16.3

2p16.3

Type of geneprotein-codingprotein-coding
DescriptionDNA mismatch repair protein Msh6G/T mismatch-binding proteinmutS protein homolog 6mutS-alpha 160 kDa subunitsperm-associated proteinDNA mismatch repair protein Msh6G/T mismatch-binding proteinmutS protein homolog 6mutS-alpha 160 kDa subunitsperm-associated protein
Modification date2020031320200313
UniProtAcc

P52701

P52701

Ensembl transtripts involved in fusion geneENST00000234420, ENST00000538136, 
ENST00000540021, ENST00000607272, 
ENST00000234420, ENST00000538136, 
ENST00000540021, ENST00000607272, 
Fusion gene scores* DoF score5 X 13 X 5=3256 X 8 X 3=144
# samples 138
** MAII scorelog2(13/325*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/144*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MSH6 [Title/Abstract] AND MSH6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMSH6(48018264)-MSH6(48028979), # samples:1
MSH6(48028064)-MSH6(48028122), # samples:1
MSH6(48027303)-MSH6(48027238), # 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
HgeneMSH6

GO:0006281

DNA repair

8942985

HgeneMSH6

GO:0006298

mismatch repair

10871409|23622243

HgeneMSH6

GO:0045910

negative regulation of DNA recombination

17715146

HgeneMSH6

GO:0051096

positive regulation of helicase activity

17715146

TgeneMSH6

GO:0006281

DNA repair

8942985

TgeneMSH6

GO:0006298

mismatch repair

10871409|23622243

TgeneMSH6

GO:0045910

negative regulation of DNA recombination

17715146

TgeneMSH6

GO:0051096

positive regulation of helicase activity

17715146


check buttonFusion gene breakpoints across MSH6 (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 MSH6 (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
ChiTaRS5.0N/AAA001996MSH6chr2

48018264

+MSH6chr2

48028979

-
ChiTaRS5.0N/AAW805096MSH6chr2

48028064

-MSH6chr2

48028122

+
ChiTaRS5.0N/AAW875091MSH6chr2

48027303

-MSH6chr2

48027238

+


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Fusion Gene ORF analysis for MSH6-MSH6

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-intronENST00000234420ENST00000234420MSH6chr2

48018264

+MSH6chr2

48028979

-
5CDS-intronENST00000234420ENST00000234420MSH6chr2

48028064

-MSH6chr2

48028122

+
5CDS-intronENST00000234420ENST00000234420MSH6chr2

48027303

-MSH6chr2

48027238

+
5CDS-intronENST00000234420ENST00000538136MSH6chr2

48018264

+MSH6chr2

48028979

-
5CDS-intronENST00000234420ENST00000538136MSH6chr2

48028064

-MSH6chr2

48028122

+
5CDS-intronENST00000234420ENST00000538136MSH6chr2

48027303

-MSH6chr2

48027238

+
5CDS-intronENST00000234420ENST00000540021MSH6chr2

48018264

+MSH6chr2

48028979

-
5CDS-intronENST00000234420ENST00000540021MSH6chr2

48028064

-MSH6chr2

48028122

+
5CDS-intronENST00000234420ENST00000540021MSH6chr2

48027303

-MSH6chr2

48027238

+
5CDS-intronENST00000234420ENST00000607272MSH6chr2

48018264

+MSH6chr2

48028979

-
5CDS-intronENST00000234420ENST00000607272MSH6chr2

48028064

-MSH6chr2

48028122

+
5CDS-intronENST00000234420ENST00000607272MSH6chr2

48027303

-MSH6chr2

48027238

+
5CDS-intronENST00000538136ENST00000234420MSH6chr2

48028064

-MSH6chr2

48028122

+
5CDS-intronENST00000538136ENST00000234420MSH6chr2

48027303

-MSH6chr2

48027238

+
5CDS-intronENST00000538136ENST00000538136MSH6chr2

48028064

-MSH6chr2

48028122

+
5CDS-intronENST00000538136ENST00000538136MSH6chr2

48027303

-MSH6chr2

48027238

+
5CDS-intronENST00000538136ENST00000540021MSH6chr2

48028064

-MSH6chr2

48028122

+
5CDS-intronENST00000538136ENST00000540021MSH6chr2

48027303

-MSH6chr2

48027238

+
5CDS-intronENST00000538136ENST00000607272MSH6chr2

48028064

-MSH6chr2

48028122

+
5CDS-intronENST00000538136ENST00000607272MSH6chr2

48027303

-MSH6chr2

48027238

+
5CDS-intronENST00000540021ENST00000234420MSH6chr2

48028064

-MSH6chr2

48028122

+
5CDS-intronENST00000540021ENST00000234420MSH6chr2

48027303

-MSH6chr2

48027238

+
5CDS-intronENST00000540021ENST00000538136MSH6chr2

48028064

-MSH6chr2

48028122

+
5CDS-intronENST00000540021ENST00000538136MSH6chr2

48027303

-MSH6chr2

48027238

+
5CDS-intronENST00000540021ENST00000540021MSH6chr2

48028064

-MSH6chr2

48028122

+
5CDS-intronENST00000540021ENST00000540021MSH6chr2

48027303

-MSH6chr2

48027238

+
5CDS-intronENST00000540021ENST00000607272MSH6chr2

48028064

-MSH6chr2

48028122

+
5CDS-intronENST00000540021ENST00000607272MSH6chr2

48027303

-MSH6chr2

48027238

+
5UTR-intronENST00000538136ENST00000234420MSH6chr2

48018264

+MSH6chr2

48028979

-
5UTR-intronENST00000538136ENST00000538136MSH6chr2

48018264

+MSH6chr2

48028979

-
5UTR-intronENST00000538136ENST00000540021MSH6chr2

48018264

+MSH6chr2

48028979

-
5UTR-intronENST00000538136ENST00000607272MSH6chr2

48018264

+MSH6chr2

48028979

-
intron-intronENST00000540021ENST00000234420MSH6chr2

48018264

+MSH6chr2

48028979

-
intron-intronENST00000540021ENST00000538136MSH6chr2

48018264

+MSH6chr2

48028979

-
intron-intronENST00000540021ENST00000540021MSH6chr2

48018264

+MSH6chr2

48028979

-
intron-intronENST00000540021ENST00000607272MSH6chr2

48018264

+MSH6chr2

48028979

-
intron-intronENST00000607272ENST00000234420MSH6chr2

48018264

+MSH6chr2

48028979

-
intron-intronENST00000607272ENST00000234420MSH6chr2

48028064

-MSH6chr2

48028122

+
intron-intronENST00000607272ENST00000234420MSH6chr2

48027303

-MSH6chr2

48027238

+
intron-intronENST00000607272ENST00000538136MSH6chr2

48018264

+MSH6chr2

48028979

-
intron-intronENST00000607272ENST00000538136MSH6chr2

48028064

-MSH6chr2

48028122

+
intron-intronENST00000607272ENST00000538136MSH6chr2

48027303

-MSH6chr2

48027238

+
intron-intronENST00000607272ENST00000540021MSH6chr2

48018264

+MSH6chr2

48028979

-
intron-intronENST00000607272ENST00000540021MSH6chr2

48028064

-MSH6chr2

48028122

+
intron-intronENST00000607272ENST00000540021MSH6chr2

48027303

-MSH6chr2

48027238

+
intron-intronENST00000607272ENST00000607272MSH6chr2

48018264

+MSH6chr2

48028979

-
intron-intronENST00000607272ENST00000607272MSH6chr2

48028064

-MSH6chr2

48028122

+
intron-intronENST00000607272ENST00000607272MSH6chr2

48027303

-MSH6chr2

48027238

+

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 MSH6-MSH6


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.

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 MSH6-MSH6


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/:48018264/:48028979)
- 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
MSH6

P52701

MSH6

P52701

FUNCTION: Component of the post-replicative DNA mismatch repair system (MMR). Heterodimerizes with MSH2 to form MutS alpha, which binds to DNA mismatches thereby initiating DNA repair. When bound, MutS alpha bends the DNA helix and shields approximately 20 base pairs, and recognizes single base mismatches and dinucleotide insertion-deletion loops (IDL) in the DNA. After mismatch binding, forms a ternary complex with the MutL alpha heterodimer, which is thought to be responsible for directing the downstream MMR events, including strand discrimination, excision, and resynthesis. ATP binding and hydrolysis play a pivotal role in mismatch repair functions. The ATPase activity associated with MutS alpha regulates binding similar to a molecular switch: mismatched DNA provokes ADP-->ATP exchange, resulting in a discernible conformational transition that converts MutS alpha into a sliding clamp capable of hydrolysis-independent diffusion along the DNA backbone. This transition is crucial for mismatch repair. MutS alpha may also play a role in DNA homologous recombination repair. Recruited on chromatin in G1 and early S phase via its PWWP domain that specifically binds trimethylated 'Lys-36' of histone H3 (H3K36me3): early recruitment to chromatin to be replicated allowing a quick identification of mismatch repair to initiate the DNA mismatch repair reaction. {ECO:0000269|PubMed:10078208, ECO:0000269|PubMed:10660545, ECO:0000269|PubMed:15064730, ECO:0000269|PubMed:21120944, ECO:0000269|PubMed:23622243, ECO:0000269|PubMed:9564049, ECO:0000269|PubMed:9822679, ECO:0000269|PubMed:9822680}.FUNCTION: Component of the post-replicative DNA mismatch repair system (MMR). Heterodimerizes with MSH2 to form MutS alpha, which binds to DNA mismatches thereby initiating DNA repair. When bound, MutS alpha bends the DNA helix and shields approximately 20 base pairs, and recognizes single base mismatches and dinucleotide insertion-deletion loops (IDL) in the DNA. After mismatch binding, forms a ternary complex with the MutL alpha heterodimer, which is thought to be responsible for directing the downstream MMR events, including strand discrimination, excision, and resynthesis. ATP binding and hydrolysis play a pivotal role in mismatch repair functions. The ATPase activity associated with MutS alpha regulates binding similar to a molecular switch: mismatched DNA provokes ADP-->ATP exchange, resulting in a discernible conformational transition that converts MutS alpha into a sliding clamp capable of hydrolysis-independent diffusion along the DNA backbone. This transition is crucial for mismatch repair. MutS alpha may also play a role in DNA homologous recombination repair. Recruited on chromatin in G1 and early S phase via its PWWP domain that specifically binds trimethylated 'Lys-36' of histone H3 (H3K36me3): early recruitment to chromatin to be replicated allowing a quick identification of mismatch repair to initiate the DNA mismatch repair reaction. {ECO:0000269|PubMed:10078208, ECO:0000269|PubMed:10660545, ECO:0000269|PubMed:15064730, ECO:0000269|PubMed:21120944, ECO:0000269|PubMed:23622243, ECO:0000269|PubMed:9564049, ECO:0000269|PubMed:9822679, ECO:0000269|PubMed:9822680}.

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 MSH6-MSH6


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 MSH6-MSH6


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 MSH6-MSH6


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 MSH6-MSH6


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