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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:L1CAM-ARHGAP4 (FusionGDB2 ID:43779)

Fusion Gene Summary for L1CAM-ARHGAP4

check button Fusion gene summary
Fusion gene informationFusion gene name: L1CAM-ARHGAP4
Fusion gene ID: 43779
HgeneTgene
Gene symbol

L1CAM

ARHGAP4

Gene ID

3897

393

Gene nameL1 cell adhesion moleculeRho GTPase activating protein 4
SynonymsCAML1|CD171|HSAS|HSAS1|MASA|MIC5|N-CAM-L1|N-CAML1|NCAM-L1|S10|SPG1C1|RGC1|RhoGAP4|SrGAP4|p115
Cytomap

Xq28

Xq28

Type of geneprotein-codingprotein-coding
Descriptionneural cell adhesion molecule L1antigen identified by monoclonal antibody R1rho GTPase-activating protein 4Rho-GAP hematopoietic protein C1rho-type GTPase-activating protein 4
Modification date2020032220200320
UniProtAcc

P32004

Q92619

Ensembl transtripts involved in fusion geneENST00000361699, ENST00000361981, 
ENST00000370055, ENST00000370057, 
ENST00000370060, ENST00000484587, 
ENST00000538883, ENST00000543994, 
ENST00000350060, ENST00000370016, 
ENST00000370028, ENST00000393721, 
ENST00000467421, ENST00000537206, 
Fusion gene scores* DoF score2 X 2 X 1=44 X 6 X 3=72
# samples 27
** MAII scorelog2(2/4*10)=2.32192809488736log2(7/72*10)=-0.0406419844973459
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: L1CAM [Title/Abstract] AND ARHGAP4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointL1CAM(153130578)-ARHGAP4(153185153), # 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
HgeneL1CAM

GO:0007160

cell-matrix adhesion

22973895

HgeneL1CAM

GO:0007411

axon guidance

24155914

HgeneL1CAM

GO:0016477

cell migration

22973895

HgeneL1CAM

GO:0031175

neuron projection development

22973895

HgeneL1CAM

GO:0050808

synapse organization

24155914

HgeneL1CAM

GO:0061564

axon development

20621658


check buttonFusion gene breakpoints across L1CAM (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 ARHGAP4 (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
ChimerDB4OVTCGA-13-1512-01AL1CAMchrX

153130578

-ARHGAP4chrX

153185153

-


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Fusion Gene ORF analysis for L1CAM-ARHGAP4

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-intronENST00000361699ENST00000350060L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000361699ENST00000370016L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000361699ENST00000370028L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000361699ENST00000393721L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000361699ENST00000467421L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000361699ENST00000537206L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000361981ENST00000350060L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000361981ENST00000370016L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000361981ENST00000370028L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000361981ENST00000393721L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000361981ENST00000467421L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000361981ENST00000537206L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370055ENST00000350060L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370055ENST00000370016L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370055ENST00000370028L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370055ENST00000393721L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370055ENST00000467421L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370055ENST00000537206L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370057ENST00000350060L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370057ENST00000370016L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370057ENST00000370028L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370057ENST00000393721L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370057ENST00000467421L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370057ENST00000537206L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370060ENST00000350060L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370060ENST00000370016L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370060ENST00000370028L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370060ENST00000393721L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370060ENST00000467421L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000370060ENST00000537206L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000484587ENST00000350060L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000484587ENST00000370016L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000484587ENST00000370028L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000484587ENST00000393721L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000484587ENST00000467421L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000484587ENST00000537206L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000538883ENST00000350060L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000538883ENST00000370016L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000538883ENST00000370028L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000538883ENST00000393721L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000538883ENST00000467421L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000538883ENST00000537206L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000543994ENST00000350060L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000543994ENST00000370016L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000543994ENST00000370028L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000543994ENST00000393721L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000543994ENST00000467421L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-
intron-intronENST00000543994ENST00000537206L1CAMchrX

153130578

-ARHGAP4chrX

153185153

-

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 L1CAM-ARHGAP4


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 L1CAM-ARHGAP4


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/:153130578/:153185153)
- 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
L1CAM

P32004

ARHGAP4

Q92619

FUNCTION: Neural cell adhesion molecule involved in the dynamics of cell adhesion and in the generation of transmembrane signals at tyrosine kinase receptors. During brain development, critical in multiple processes, including neuronal migration, axonal growth and fasciculation, and synaptogenesis. In the mature brain, plays a role in the dynamics of neuronal structure and function, including synaptic plasticity. {ECO:0000269|PubMed:20621658, ECO:0000305}.FUNCTION: Contains a GTPase activator for the Rho-type GTPases (RhoGAP) domain that would be able to negatively regulate the actin cytoskeleton as well as cell spreading. However, also contains N-terminally a BAR-domin which is able to play an autoinhibitory effect on this RhoGAP activity. {ECO:0000269|PubMed:24086303}.; FUNCTION: Precursor of the histocompatibility antigen HA-1. More generally, minor histocompatibility antigens (mHags) refer to immunogenic peptide which, when complexed with MHC, can generate an immune response after recognition by specific T-cells. The peptides are derived from polymorphic intracellular proteins, which are cleaved by normal pathways of antigen processing. The binding of these peptides to MHC class I or class II molecules and its expression on the cell surface can stimulate T-cell responses and thereby trigger graft rejection or graft-versus-host disease (GVHD) after hematopoietic stem cell transplantation from HLA-identical sibling donor. GVHD is a frequent complication after bone marrow transplantation (BMT), due to mismatch of minor histocompatibility antigen in HLA-matched sibling marrow transplants. Specifically, mismatching for mHag HA-1 which is recognized as immunodominant, is shown to be associated with the development of severe GVHD after HLA-identical BMT. HA-1 is presented to the cell surface by MHC class I HLA-A*0201, but also by other HLA-A alleles. This complex specifically elicits donor-cytotoxic T-lymphocyte (CTL) reactivity against hematologic malignancies after treatment by HLA-identical allogenic BMT. It induces cell recognition and lysis by CTL. {ECO:0000269|PubMed:12601144, ECO:0000269|PubMed:8260714, ECO:0000269|PubMed:8532022, ECO:0000269|PubMed:9798702}.

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 L1CAM-ARHGAP4


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 L1CAM-ARHGAP4


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 L1CAM-ARHGAP4


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 L1CAM-ARHGAP4


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