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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:LIMCH1-NSUN7 (FusionGDB2 ID:HG22998TG79730)

Fusion Gene Summary for LIMCH1-NSUN7

check button Fusion gene summary
Fusion gene informationFusion gene name: LIMCH1-NSUN7
Fusion gene ID: hg22998tg79730
HgeneTgene
Gene symbol

LIMCH1

NSUN7

Gene ID

22998

79730

Gene nameLIM and calponin homology domains 1NOP2/Sun RNA methyltransferase family member 7
SynonymsLIMCH1A|LMO7B-
Cytomap('LIMCH1')('NSUN7')

4p13

4p14

Type of geneprotein-codingprotein-coding
DescriptionLIM and calponin homology domains-containing protein 1putative methyltransferase NSUN7NOL1/NOP2/Sun domain family member 7NOP2/Sun domain family, member 7
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000313860, ENST00000508501, 
ENST00000512632, ENST00000512820, 
ENST00000512946, ENST00000509638, 
ENST00000381753, ENST00000396595, 
ENST00000503057, ENST00000509277, 
ENST00000509454, ENST00000511496, 
ENST00000513024, ENST00000514096, 
ENST00000515785, 
Fusion gene scores* DoF score14 X 12 X 9=15123 X 3 X 2=18
# samples 193
** MAII scorelog2(19/1512*10)=-2.99238681589013
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: LIMCH1 [Title/Abstract] AND NSUN7 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLIMCH1(41362953)-NSUN7(40776282), # samples:1
Anticipated loss of major functional domain due to fusion event.LIMCH1-NSUN7 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 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
ChimerDB4STADTCGA-FP-8211-01ALIMCH1chr4

41362953

+NSUN7chr4

40776282

+


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Fusion Gene ORF analysis for LIMCH1-NSUN7

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-3UTRENST00000313860ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
5CDS-3UTRENST00000508501ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
5CDS-3UTRENST00000512632ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
5CDS-3UTRENST00000512820ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
5CDS-3UTRENST00000512946ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
5UTR-3CDSENST00000509638ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
5UTR-3CDSENST00000509638ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
5UTR-3UTRENST00000509638ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
Frame-shiftENST00000313860ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
Frame-shiftENST00000313860ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
Frame-shiftENST00000508501ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
Frame-shiftENST00000508501ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
Frame-shiftENST00000512632ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
Frame-shiftENST00000512632ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
Frame-shiftENST00000512820ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
Frame-shiftENST00000512820ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
Frame-shiftENST00000512946ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
Frame-shiftENST00000512946ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000381753ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000381753ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000396595ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000396595ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000503057ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000503057ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000509277ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000509277ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000509454ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000509454ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000511496ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000511496ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000513024ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000513024ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000514096ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000514096ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000515785ENST00000316607LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3CDSENST00000515785ENST00000381782LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3UTRENST00000381753ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3UTRENST00000396595ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3UTRENST00000503057ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3UTRENST00000509277ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3UTRENST00000509454ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3UTRENST00000511496ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3UTRENST00000513024ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3UTRENST00000514096ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+
intron-3UTRENST00000515785ENST00000463952LIMCH1chr4

41362953

+NSUN7chr4

40776282

+

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 LIMCH1-NSUN7


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)
LIMCH1chr441362953+NSUN7chr440776281+4.25E-050.99995744
LIMCH1chr441362953+NSUN7chr440776281+4.25E-050.99995744


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 LIMCH1-NSUN7


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/:41362953/:40776282)
- 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

- 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 LIMCH1-NSUN7


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 LIMCH1-NSUN7


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 LIMCH1-NSUN7


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 LIMCH1-NSUN7


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLIMCH1C0013146Drug abuse1CTD_human
HgeneLIMCH1C0013170Drug habituation1CTD_human
HgeneLIMCH1C0013222Drug Use Disorders1CTD_human
HgeneLIMCH1C0029231Organic Mental Disorders, Substance-Induced1CTD_human
HgeneLIMCH1C0038580Substance Dependence1CTD_human
HgeneLIMCH1C0038586Substance Use Disorders1CTD_human
HgeneLIMCH1C0236969Substance-Related Disorders1CTD_human
HgeneLIMCH1C0345967Malignant mesothelioma1CTD_human
HgeneLIMCH1C0740858Substance abuse problem1CTD_human
HgeneLIMCH1C1510472Drug Dependence1CTD_human
HgeneLIMCH1C4316881Prescription Drug Abuse1CTD_human
TgeneC0021364Male infertility1CTD_human
TgeneC0848676Subfertility, Male1CTD_human
TgeneC0917731Male sterility1CTD_human