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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-APBB2 (FusionGDB2 ID:44692)

Fusion Gene Summary for LIMCH1-APBB2

check button Fusion gene summary
Fusion gene informationFusion gene name: LIMCH1-APBB2
Fusion gene ID: 44692
HgeneTgene
Gene symbol

LIMCH1

APBB2

Gene ID

22998

323

Gene nameLIM and calponin homology domains 1amyloid beta precursor protein binding family B member 2
SynonymsLIMCH1A|LMO7BFE65L|FE65L1
Cytomap

4p13

4p14-p13

Type of geneprotein-codingprotein-coding
DescriptionLIM and calponin homology domains-containing protein 1amyloid-beta A4 precursor protein-binding family B member 2Fe65-like 1protein Fe65-like 1
Modification date2020031320200327
UniProtAcc

Q9UPQ0

Q92870

Ensembl transtripts involved in fusion geneENST00000313860, ENST00000508501, 
ENST00000512632, ENST00000512820, 
ENST00000512946, ENST00000509638, 
ENST00000513024, ENST00000381753, 
ENST00000396595, ENST00000503057, 
ENST00000509277, ENST00000509454, 
ENST00000511496, ENST00000514096, 
ENST00000515785, 		ENST00000295974, 
ENST00000506352, ENST00000508593, 
ENST00000511572, ENST00000513140, 
ENST00000502841, ENST00000504305, 
ENST00000543538, 
Fusion gene scores* DoF score14 X 12 X 9=151212 X 12 X 9=1296
# samples 1917
** MAII scorelog2(19/1512*10)=-2.99238681589013
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/1296*10)=-2.93045906674692
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LIMCH1 [Title/Abstract] AND APBB2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLIMCH1(41526495)-APBB2(41102767), # samples:4
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

check buttonFusion gene breakpoints across LIMCH1 (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 APBB2 (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
ChimerDB4BRCATCGA-D8-A1X5-01ALIMCH1chr4

41526495

-APBB2chr4

41102767

-
ChimerDB4BRCATCGA-D8-A1X5-01ALIMCH1chr4

41526495

+APBB2chr4

41102767

-
ChimerDB4BRCATCGA-D8-A1X5LIMCH1chr4

41526495

+APBB2chr4

41102767

-


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Fusion Gene ORF analysis for LIMCH1-APBB2

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-5UTRENST00000313860ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000313860ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000313860ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000313860ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000313860ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000508501ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000508501ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000508501ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000508501ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000508501ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512632ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512632ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512632ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512632ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512632ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512820ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512820ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512820ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512820ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512820ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512946ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512946ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512946ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512946ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-5UTRENST00000512946ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000313860ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000313860ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000313860ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000508501ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000508501ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000508501ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000512632ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000512632ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000512632ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000512820ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000512820ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000512820ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000512946ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000512946ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5CDS-intronENST00000512946ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-5UTRENST00000509638ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-5UTRENST00000509638ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-5UTRENST00000509638ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-5UTRENST00000509638ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-5UTRENST00000509638ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-5UTRENST00000513024ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-5UTRENST00000513024ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-5UTRENST00000513024ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-5UTRENST00000513024ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-5UTRENST00000513024ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-intronENST00000509638ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-intronENST00000509638ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-intronENST00000509638ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-intronENST00000513024ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-intronENST00000513024ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
5UTR-intronENST00000513024ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000381753ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000381753ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000381753ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000381753ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000381753ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000396595ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000396595ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000396595ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000396595ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000396595ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000503057ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000503057ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000503057ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000503057ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000503057ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000509277ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000509277ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000509277ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000509277ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000509277ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000509454ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000509454ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000509454ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000509454ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000509454ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000511496ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000511496ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000511496ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000511496ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000511496ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000514096ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000514096ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000514096ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000514096ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000514096ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000515785ENST00000295974LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000515785ENST00000506352LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000515785ENST00000508593LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000515785ENST00000511572LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-5UTRENST00000515785ENST00000513140LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000381753ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000381753ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000381753ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000396595ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000396595ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000396595ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000503057ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000503057ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000503057ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000509277ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000509277ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000509277ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000509454ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000509454ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000509454ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000511496ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000511496ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000511496ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000514096ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000514096ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000514096ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000515785ENST00000502841LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000515785ENST00000504305LIMCH1chr4

41526495

+APBB2chr4

41102767

-
intron-intronENST00000515785ENST00000543538LIMCH1chr4

41526495

+APBB2chr4

41102767

-

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-APBB2


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 LIMCH1-APBB2


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/:41526495/:41102767)
- 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
LIMCH1

Q9UPQ0

APBB2

Q92870

FUNCTION: Actin stress fibers-associated protein that activates non-muscle myosin IIa. Activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. Through the activation of non-muscle myosin IIa, positively regulates actin stress fibers assembly and stabilizes focal adhesions. It therefore negatively regulates cell spreading and cell migration. {ECO:0000269|PubMed:28228547}.FUNCTION: May modulate the internalization of amyloid-beta precursor protein.

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-APBB2


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-APBB2


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-APBB2


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-APBB2


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