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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:MSH5-SAPCD1-AIF1 (FusionGDB2 ID:HG100532732TG199)

Fusion Gene Summary for MSH5-SAPCD1-AIF1

check button Fusion gene summary
Fusion gene informationFusion gene name: MSH5-SAPCD1-AIF1
Fusion gene ID: hg100532732tg199
HgeneTgene
Gene symbol

MSH5-SAPCD1

AIF1

Gene ID

100532732

199

Gene nameMSH5-SAPCD1 readthrough (NMD candidate)allograft inflammatory factor 1
SynonymsMSH5-C6orf26AIF-1|IBA1|IRT-1|IRT1
Cytomap('MSH5-SAPCD1')('AIF1')

6p21.33

6p21.33

Type of genencRNAprotein-coding
DescriptionMSH5-C6orf26 readthrough (non-protein coding)MSH5-SAPCD1 readthrough (non-protein coding)allograft inflammatory factor 1interferon gamma responsive transcriptionized calcium-binding adapter molecule 1protein G1
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000493662, ENST00000466318, 
ENST00000469644, ENST00000469909, 
ENST00000480223, ENST00000485553, 
ENST00000491552, ENST00000495073, 
ENST00000548094, ENST00000583103, 
Fusion gene scores* DoF score1 X 1 X 1=16 X 4 X 4=96
# samples 17
** MAII scorelog2(1/1*10)=3.32192809488736log2(7/96*10)=-0.45567948377619
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MSH5-SAPCD1 [Title/Abstract] AND AIF1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMSH5-SAPCD1(31710952)-AIF1(31584120), # samples:4
Anticipated loss of major functional domain due to fusion event.MSH5-SAPCD1-AIF1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
MSH5-SAPCD1-AIF1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
MSH5-SAPCD1-AIF1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
MSH5-SAPCD1-AIF1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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
TgeneAIF1

GO:0008284

positive regulation of cell proliferation

19745784

TgeneAIF1

GO:0030041

actin filament polymerization

16049345

TgeneAIF1

GO:0030335

positive regulation of cell migration

19745784

TgeneAIF1

GO:0034599

cellular response to oxidative stress

12887599

TgeneAIF1

GO:0042102

positive regulation of T cell proliferation

16049345

TgeneAIF1

GO:0048661

positive regulation of smooth muscle cell proliferation

15117732|22116621

TgeneAIF1

GO:0048662

negative regulation of smooth muscle cell proliferation

9614071|22116621

TgeneAIF1

GO:0050921

positive regulation of chemotaxis

24796669

TgeneAIF1

GO:0051017

actin filament bundle assembly

18699778

TgeneAIF1

GO:0071672

negative regulation of smooth muscle cell chemotaxis

22116621

TgeneAIF1

GO:0071673

positive regulation of smooth muscle cell chemotaxis

22116621

TgeneAIF1

GO:0071677

positive regulation of mononuclear cell migration

24796669

TgeneAIF1

GO:0090026

positive regulation of monocyte chemotaxis

15117732

TgeneAIF1

GO:0090197

positive regulation of chemokine secretion

24796669

TgeneAIF1

GO:0090271

positive regulation of fibroblast growth factor production

19745784

TgeneAIF1

GO:1900087

positive regulation of G1/S transition of mitotic cell cycle

11557666|15117732|19745784

TgeneAIF1

GO:2000406

positive regulation of T cell migration

16049345

TgeneAIF1

GO:2000778

positive regulation of interleukin-6 secretion

24796669


check buttonFusion gene breakpoints across MSH5-SAPCD1 (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 AIF1 (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


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Fusion Gene ORF analysis for MSH5-SAPCD1-AIF1

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

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
ENST00000493662ENST00000376059MSH5-SAPCD1chr631710952+AIF1chr631584120+0.0057115530.99428844
ENST00000493662ENST00000376049MSH5-SAPCD1chr631710952+AIF1chr631584120+0.0057115530.99428844

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Fusion Genomic Features for MSH5-SAPCD1-AIF1


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 MSH5-SAPCD1-AIF1


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/chr6:31710952/chr6:31584120)
- 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
..
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}.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
TgeneAIF1chr6:31710952chr6:31584120ENST000003760490358_691194.0Calcium binding1
TgeneAIF1chr6:31710952chr6:31584120ENST000003760490394_1051194.0Calcium binding2
TgeneAIF1chr6:31710952chr6:31584120ENST000003760593694_10565148.0Calcium binding2
TgeneAIF1chr6:31710952chr6:31584120ENST000003834730358_69094.0Calcium binding1
TgeneAIF1chr6:31710952chr6:31584120ENST000003834730394_105094.0Calcium binding2
TgeneAIF1chr6:31710952chr6:31584120ENST000003834740658_690148.0Calcium binding1
TgeneAIF1chr6:31710952chr6:31584120ENST000003834740694_1050148.0Calcium binding2
TgeneAIF1chr6:31710952chr6:31584120ENST000004133490658_690148.0Calcium binding1
TgeneAIF1chr6:31710952chr6:31584120ENST000004133490694_1050148.0Calcium binding2
TgeneAIF1chr6:31710952chr6:31584120ENST000004141490658_690148.0Calcium binding1
TgeneAIF1chr6:31710952chr6:31584120ENST000004141490694_1050148.0Calcium binding2
TgeneAIF1chr6:31710952chr6:31584120ENST000004158300358_69094.0Calcium binding1
TgeneAIF1chr6:31710952chr6:31584120ENST000004158300394_105094.0Calcium binding2
TgeneAIF1chr6:31710952chr6:31584120ENST000004164220358_69094.0Calcium binding1
TgeneAIF1chr6:31710952chr6:31584120ENST000004164220394_105094.0Calcium binding2
TgeneAIF1chr6:31710952chr6:31584120ENST000004193760358_69094.0Calcium binding1
TgeneAIF1chr6:31710952chr6:31584120ENST000004193760394_105094.0Calcium binding2
TgeneAIF1chr6:31710952chr6:31584120ENST000004249440358_69094.0Calcium binding1
TgeneAIF1chr6:31710952chr6:31584120ENST000004249440394_105094.0Calcium binding2
TgeneAIF1chr6:31710952chr6:31584120ENST000004257480658_690148.0Calcium binding1
TgeneAIF1chr6:31710952chr6:31584120ENST000004257480694_1050148.0Calcium binding2
TgeneAIF1chr6:31710952chr6:31584120ENST000004409070658_690148.0Calcium binding1
TgeneAIF1chr6:31710952chr6:31584120ENST000004409070694_1050148.0Calcium binding2
TgeneAIF1chr6:31710952chr6:31584120ENST000005494320658_69094.0Calcium binding1
TgeneAIF1chr6:31710952chr6:31584120ENST000005494320694_105094.0Calcium binding2
TgeneAIF1chr6:31710952chr6:31584120ENST000003760490345_801194.0DomainEF-hand 1
TgeneAIF1chr6:31710952chr6:31584120ENST000003760490381_1151194.0DomainEF-hand 2%3B degenerate
TgeneAIF1chr6:31710952chr6:31584120ENST000003760593681_11565148.0DomainEF-hand 2%3B degenerate
TgeneAIF1chr6:31710952chr6:31584120ENST000003834730345_80094.0DomainEF-hand 1
TgeneAIF1chr6:31710952chr6:31584120ENST000003834730381_115094.0DomainEF-hand 2%3B degenerate
TgeneAIF1chr6:31710952chr6:31584120ENST000003834740645_800148.0DomainEF-hand 1
TgeneAIF1chr6:31710952chr6:31584120ENST000003834740681_1150148.0DomainEF-hand 2%3B degenerate
TgeneAIF1chr6:31710952chr6:31584120ENST000004133490645_800148.0DomainEF-hand 1
TgeneAIF1chr6:31710952chr6:31584120ENST000004133490681_1150148.0DomainEF-hand 2%3B degenerate
TgeneAIF1chr6:31710952chr6:31584120ENST000004141490645_800148.0DomainEF-hand 1
TgeneAIF1chr6:31710952chr6:31584120ENST000004141490681_1150148.0DomainEF-hand 2%3B degenerate
TgeneAIF1chr6:31710952chr6:31584120ENST000004158300345_80094.0DomainEF-hand 1
TgeneAIF1chr6:31710952chr6:31584120ENST000004158300381_115094.0DomainEF-hand 2%3B degenerate
TgeneAIF1chr6:31710952chr6:31584120ENST000004164220345_80094.0DomainEF-hand 1
TgeneAIF1chr6:31710952chr6:31584120ENST000004164220381_115094.0DomainEF-hand 2%3B degenerate
TgeneAIF1chr6:31710952chr6:31584120ENST000004193760345_80094.0DomainEF-hand 1
TgeneAIF1chr6:31710952chr6:31584120ENST000004193760381_115094.0DomainEF-hand 2%3B degenerate
TgeneAIF1chr6:31710952chr6:31584120ENST000004249440345_80094.0DomainEF-hand 1
TgeneAIF1chr6:31710952chr6:31584120ENST000004249440381_115094.0DomainEF-hand 2%3B degenerate
TgeneAIF1chr6:31710952chr6:31584120ENST000004257480645_800148.0DomainEF-hand 1
TgeneAIF1chr6:31710952chr6:31584120ENST000004257480681_1150148.0DomainEF-hand 2%3B degenerate
TgeneAIF1chr6:31710952chr6:31584120ENST000004409070645_800148.0DomainEF-hand 1
TgeneAIF1chr6:31710952chr6:31584120ENST000004409070681_1150148.0DomainEF-hand 2%3B degenerate
TgeneAIF1chr6:31710952chr6:31584120ENST000005494320645_80094.0DomainEF-hand 1
TgeneAIF1chr6:31710952chr6:31584120ENST000005494320681_115094.0DomainEF-hand 2%3B degenerate

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneAIF1chr6:31710952chr6:31584120ENST000003760593658_6965148.0Calcium binding1
TgeneAIF1chr6:31710952chr6:31584120ENST000003760593645_8065148.0DomainEF-hand 1


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Fusion Gene Sequence for MSH5-SAPCD1-AIF1


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.
>55290_55290_1_MSH5-SAPCD1-AIF1_MSH5-SAPCD1_chr6_31710952_ENST00000493662_AIF1_chr6_31584120_ENST00000376049_length(transcript)=840nt_BP=471nt
GGCGGTCGGTCAGCGGGGCGTTCTCCCACCTGTAGCGACTCAGAGCCTCCAAGCTCATGGCCTCCTTAGGAGCGAACCCAAGGAGGACAC
CGCAGGGACCGAGACCTGGGGCGGCCTCCTCCGGCTTCCCCAGCCCGGCCCCAGTGCCGGGCCCCAGGGAGGCCGAGGAGGAGGAAGTCG
AGGAGGAGGAGGAGCTGGCCGAGATCCATCTGTGTGTGCTGTGGAATTCAGGATACTTGGGCATTGCCTACTATGATACTAGTGACTCCA
CTATCCACTTCATGCCAGATGCCCCAGACCACGAGAGCCTCAAGCTTCTCCAGAGAGTTCTGGATGAGATCAATCCCCAGTCTGTTGTTA
CGAGTGCCAAACAGGATGAGAATATGACTCGATTTCTGGGAAAGCTTGCCTCCCAGGAGCACAGAGAGCCTAAAAGACCTGAAATCATAT
TTTTGCCAAGTGTGGATTTTGATATCATGTCCCTGAAACGAATGCTGGAGAAACTTGGAGTCCCCAAGACTCACCTAGAGCTAAAGAAAT
TAATTGGAGAGGTGTCCAGTGGCTCCGGGGAGACGTTCAGCTACCCTGACTTTCTCAGGATGATGCTGGGCAAGAGATCTGCCATCCTAA
AAATGATCCTGATGTATGAGGAAAAAGCGAGAGAAAAGGAAAAGCCAACAGGCCCCCCAGCCAAGAAAGCTATCTCTGAGTTGCCCTGAT
TTGAAGGGAAAAGGGATGATGGGATTGAAGGGGCTTCTAATGACCCAGATATGGAAACAGAAGACAAAATTGTAAGCCAGAGTCAACAAA

>55290_55290_1_MSH5-SAPCD1-AIF1_MSH5-SAPCD1_chr6_31710952_ENST00000493662_AIF1_chr6_31584120_ENST00000376049_length(amino acids)=220AA_BP=138
MASLGANPRRTPQGPRPGAASSGFPSPAPVPGPREAEEEEVEEEEELAEIHLCVLWNSGYLGIAYYDTSDSTIHFMPDAPDHESLKLLQR
VLDEINPQSVVTSAKQDENMTRFLGKLASQEHREPKRPEIIFLPSVDFDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFL

--------------------------------------------------------------
>55290_55290_2_MSH5-SAPCD1-AIF1_MSH5-SAPCD1_chr6_31710952_ENST00000493662_AIF1_chr6_31584120_ENST00000376059_length(transcript)=840nt_BP=471nt
GGCGGTCGGTCAGCGGGGCGTTCTCCCACCTGTAGCGACTCAGAGCCTCCAAGCTCATGGCCTCCTTAGGAGCGAACCCAAGGAGGACAC
CGCAGGGACCGAGACCTGGGGCGGCCTCCTCCGGCTTCCCCAGCCCGGCCCCAGTGCCGGGCCCCAGGGAGGCCGAGGAGGAGGAAGTCG
AGGAGGAGGAGGAGCTGGCCGAGATCCATCTGTGTGTGCTGTGGAATTCAGGATACTTGGGCATTGCCTACTATGATACTAGTGACTCCA
CTATCCACTTCATGCCAGATGCCCCAGACCACGAGAGCCTCAAGCTTCTCCAGAGAGTTCTGGATGAGATCAATCCCCAGTCTGTTGTTA
CGAGTGCCAAACAGGATGAGAATATGACTCGATTTCTGGGAAAGCTTGCCTCCCAGGAGCACAGAGAGCCTAAAAGACCTGAAATCATAT
TTTTGCCAAGTGTGGATTTTGATATCATGTCCCTGAAACGAATGCTGGAGAAACTTGGAGTCCCCAAGACTCACCTAGAGCTAAAGAAAT
TAATTGGAGAGGTGTCCAGTGGCTCCGGGGAGACGTTCAGCTACCCTGACTTTCTCAGGATGATGCTGGGCAAGAGATCTGCCATCCTAA
AAATGATCCTGATGTATGAGGAAAAAGCGAGAGAAAAGGAAAAGCCAACAGGCCCCCCAGCCAAGAAAGCTATCTCTGAGTTGCCCTGAT
TTGAAGGGAAAAGGGATGATGGGATTGAAGGGGCTTCTAATGACCCAGATATGGAAACAGAAGACAAAATTGTAAGCCAGAGTCAACAAA

>55290_55290_2_MSH5-SAPCD1-AIF1_MSH5-SAPCD1_chr6_31710952_ENST00000493662_AIF1_chr6_31584120_ENST00000376059_length(amino acids)=220AA_BP=138
MASLGANPRRTPQGPRPGAASSGFPSPAPVPGPREAEEEEVEEEEELAEIHLCVLWNSGYLGIAYYDTSDSTIHFMPDAPDHESLKLLQR
VLDEINPQSVVTSAKQDENMTRFLGKLASQEHREPKRPEIIFLPSVDFDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFL

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Fusion Gene PPI Analysis for MSH5-SAPCD1-AIF1


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 MSH5-SAPCD1-AIF1


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 MSH5-SAPCD1-AIF1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0020429Hyperalgesia1CTD_human
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0030567Parkinson Disease1CTD_human
TgeneC0040997Trigeminal Neuralgia1CTD_human
TgeneC0393786Trigeminal Neuralgia, Idiopathic1CTD_human
TgeneC0393787Secondary Trigeminal Neuralgia1CTD_human
TgeneC0458247Allodynia1CTD_human
TgeneC0751211Hyperalgesia, Primary1CTD_human
TgeneC0751212Hyperalgesia, Secondary1CTD_human
TgeneC0751213Tactile Allodynia1CTD_human
TgeneC0751214Hyperalgesia, Thermal1CTD_human
TgeneC0752347Lewy Body Disease1CTD_human
TgeneC2936719Mechanical Allodynia1CTD_human