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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:FCHSD2-LGMN (FusionGDB2 ID:30003)

Fusion Gene Summary for FCHSD2-LGMN

check button Fusion gene summary
Fusion gene informationFusion gene name: FCHSD2-LGMN
Fusion gene ID: 30003
HgeneTgene
Gene symbol

FCHSD2

LGMN

Gene ID

9873

5641

Gene nameFCH and double SH3 domains 2legumain
SynonymsNWK|NWK1|SH3MD3AEP|LGMN1|PRSC1
Cytomap

11q13.4

14q32.12

Type of geneprotein-codingprotein-coding
DescriptionF-BAR and double SH3 domains protein 2FCH and double SH3 domains protein 2SH3 multiple domains 3SH3 multiple domains protein 3caromnervous wreck homologprotein nervous wreck 1legumainasparaginyl endopeptidasecysteine protease 1protease, cysteine 1protease, cysteine, 1 (legumain)
Modification date2020031320200313
UniProtAcc

O94868

Q99538

Ensembl transtripts involved in fusion geneENST00000311172, ENST00000409263, 
ENST00000409314, ENST00000409418, 
ENST00000409853, ENST00000458644, 
ENST00000334869, ENST00000555699, 
ENST00000393218, ENST00000557034, 
ENST00000557434, 
Fusion gene scores* DoF score43 X 26 X 16=178889 X 8 X 4=288
# samples 599
** MAII scorelog2(59/17888*10)=-4.92213332859399
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/288*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FCHSD2 [Title/Abstract] AND LGMN [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFCHSD2(72794592)-LGMN(93170160), # 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
TgeneLGMN

GO:0010447

response to acidic pH

18374643

TgeneLGMN

GO:0035729

cellular response to hepatocyte growth factor stimulus

21237226

TgeneLGMN

GO:0071277

cellular response to calcium ion

21237226

TgeneLGMN

GO:0090026

positive regulation of monocyte chemotaxis

18377911

TgeneLGMN

GO:0097202

activation of cysteine-type endopeptidase activity

9821970|18374643

TgeneLGMN

GO:0097264

self proteolysis

9821970|18374643

TgeneLGMN

GO:1904646

cellular response to amyloid-beta

25326800

TgeneLGMN

GO:2001028

positive regulation of endothelial cell chemotaxis

18377911


check buttonFusion gene breakpoints across FCHSD2 (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 LGMN (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/ABI492592FCHSD2chr11

72794592

-LGMNchr14

93170160

+


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Fusion Gene ORF analysis for FCHSD2-LGMN

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
intron-3UTRENST00000311172ENST00000334869FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-3UTRENST00000311172ENST00000555699FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-3UTRENST00000409263ENST00000334869FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-3UTRENST00000409263ENST00000555699FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-3UTRENST00000409314ENST00000334869FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-3UTRENST00000409314ENST00000555699FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-3UTRENST00000409418ENST00000334869FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-3UTRENST00000409418ENST00000555699FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-3UTRENST00000409853ENST00000334869FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-3UTRENST00000409853ENST00000555699FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-3UTRENST00000458644ENST00000334869FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-3UTRENST00000458644ENST00000555699FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000311172ENST00000393218FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000311172ENST00000557034FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000311172ENST00000557434FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000409263ENST00000393218FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000409263ENST00000557034FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000409263ENST00000557434FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000409314ENST00000393218FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000409314ENST00000557034FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000409314ENST00000557434FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000409418ENST00000393218FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000409418ENST00000557034FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000409418ENST00000557434FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000409853ENST00000393218FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000409853ENST00000557034FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000409853ENST00000557434FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000458644ENST00000393218FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000458644ENST00000557034FCHSD2chr11

72794592

-LGMNchr14

93170160

+
intron-intronENST00000458644ENST00000557434FCHSD2chr11

72794592

-LGMNchr14

93170160

+

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 FCHSD2-LGMN


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 FCHSD2-LGMN


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/:72794592/:93170160)
- 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
FCHSD2

O94868

LGMN

Q99538

FUNCTION: Adapter protein that plays a role in endocytosis via clathrin-coated pits. Contributes to the internalization of cell surface receptors, such as integrin ITGB1 and transferrin receptor (PubMed:29887380). Promotes endocytosis of EGFR in cancer cells, and thereby contributes to the down-regulation of EGFR signaling (PubMed:30249660). Recruited to clathrin-coated pits during a mid-to-late stage of assembly, where it is required for normal progress from U-shaped intermediate stage pits to terminal, omega-shaped pits (PubMed:29887380). Binds to membranes enriched in phosphatidylinositol 3,4-bisphosphate or phosphatidylinositol 3,4,5-trisphosphate (PubMed:29887380). When bound to membranes, promotes actin polymerization via its interaction with WAS and/or WASL which leads to the activation of the Arp2/3 complex. Does not promote actin polymerisation in the absence of membranes (PubMed:29887380). {ECO:0000269|PubMed:29887380, ECO:0000269|PubMed:30249660}.FUNCTION: Has a strict specificity for hydrolysis of asparaginyl bonds. Can also cleave aspartyl bonds slowly, especially under acidic conditions. Required for normal lysosomal protein degradation in renal proximal tubules. Required for normal degradation of internalized EGFR. Plays a role in the regulation of cell proliferation via its role in EGFR degradation (By similarity). May be involved in the processing of proteins for MHC class II antigen presentation in the lysosomal/endosomal system. {ECO:0000250, ECO:0000269|PubMed:23776206}.

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 FCHSD2-LGMN


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 FCHSD2-LGMN


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 FCHSD2-LGMN


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 FCHSD2-LGMN


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