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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:ARHGAP5-LSAMP (FusionGDB2 ID:6141)

Fusion Gene Summary for ARHGAP5-LSAMP

check button Fusion gene summary
Fusion gene informationFusion gene name: ARHGAP5-LSAMP
Fusion gene ID: 6141
HgeneTgene
Gene symbol

ARHGAP5

LSAMP

Gene ID

394

4045

Gene nameRho GTPase activating protein 5limbic system associated membrane protein
SynonymsGFI2|RhoGAP5|p190-B|p190BRhoGAPIGLON3|LAMP
Cytomap

14q12

3q13.31

Type of geneprotein-codingprotein-coding
Descriptionrho GTPase-activating protein 5growth factor independent 2p100 RasGAP-associated p105 proteinp105 RhoGAPrho-type GTPase-activating protein 5limbic system-associated membrane proteinIgLON family member 3
Modification date2020031320200313
UniProtAcc

Q13017

Q13449

Ensembl transtripts involved in fusion geneENST00000396582, ENST00000345122, 
ENST00000432921, ENST00000433497, 
ENST00000539826, ENST00000556611, 
ENST00000498645, ENST00000490035, 
ENST00000539563, 
Fusion gene scores* DoF score10 X 4 X 7=28020 X 18 X 11=3960
# samples 1234
** MAII scorelog2(12/280*10)=-1.22239242133645
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(34/3960*10)=-3.54189377882927
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARHGAP5 [Title/Abstract] AND LSAMP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARHGAP5(32546641)-LSAMP(116163802), # samples:2
Anticipated loss of major functional domain due to fusion event.ARHGAP5-LSAMP seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
ARHGAP5-LSAMP seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
ARHGAP5-LSAMP seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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 buttonFusion gene breakpoints across ARHGAP5 (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 LSAMP (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 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
ChimerDB4SKCMTCGA-GF-A6C9-06AARHGAP5chr14

32546641

-LSAMPchr3

116163802

-
ChimerDB4SKCMTCGA-GF-A6C9-06AARHGAP5chr14

32546641

+LSAMPchr3

116163802

-


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Fusion Gene ORF analysis for ARHGAP5-LSAMP

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-intronENST00000396582ENST00000498645ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
5UTR-3CDSENST00000345122ENST00000490035ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
5UTR-3CDSENST00000345122ENST00000539563ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
5UTR-3CDSENST00000432921ENST00000490035ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
5UTR-3CDSENST00000432921ENST00000539563ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
5UTR-3CDSENST00000433497ENST00000490035ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
5UTR-3CDSENST00000433497ENST00000539563ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
5UTR-intronENST00000345122ENST00000498645ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
5UTR-intronENST00000432921ENST00000498645ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
5UTR-intronENST00000433497ENST00000498645ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
Frame-shiftENST00000396582ENST00000490035ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
In-frameENST00000396582ENST00000539563ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
intron-3CDSENST00000539826ENST00000490035ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
intron-3CDSENST00000539826ENST00000539563ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
intron-3CDSENST00000556611ENST00000490035ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
intron-3CDSENST00000556611ENST00000539563ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
intron-intronENST00000539826ENST00000498645ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-
intron-intronENST00000556611ENST00000498645ARHGAP5chr14

32546641

+LSAMPchr3

116163802

-

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)
ENST00000396582ARHGAP5chr1432546641+ENST00000539563LSAMPchr3116163802-13723622921371360

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
ENST00000396582ENST00000539563ARHGAP5chr1432546641+LSAMPchr3116163802-0.0028026830.9971973

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Fusion Genomic Features for ARHGAP5-LSAMP


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.

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Fusion Protein Features for ARHGAP5-LSAMP


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/chr14:32546641/chr3:116163802)
- 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
ARHGAP5

Q13017

LSAMP

Q13449

FUNCTION: GTPase-activating protein for Rho family members (PubMed:8537347). {ECO:0000269|PubMed:8537347}.FUNCTION: Mediates selective neuronal growth and axon targeting. Contributes to the guidance of developing axons and remodeling of mature circuits in the limbic system. Essential for normal growth of the hyppocampal mossy fiber projection (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
TgeneLSAMPchr14:32546641chr3:116163802ENST0000049003507132_2140339.0DomainNote=Ig-like C2-type 2
TgeneLSAMPchr14:32546641chr3:116163802ENST0000049003507219_3040339.0DomainNote=Ig-like C2-type 3
TgeneLSAMPchr14:32546641chr3:116163802ENST000004900350729_1220339.0DomainNote=Ig-like C2-type 1

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000345122+171225_124501503.0Compositional biasNote=Lys-rich
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+151225_124523238.0Compositional biasNote=Lys-rich
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000432921+171225_124501502.0Compositional biasNote=Lys-rich
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000433497+161225_12450242.0Compositional biasNote=Lys-rich
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000539826+171225_124501503.0Compositional biasNote=Lys-rich
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000556611+171225_124501502.0Compositional biasNote=Lys-rich
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000345122+171262_144901503.0DomainRho-GAP
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000345122+17267_32501503.0DomainNote=FF 1
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000345122+17366_42001503.0DomainNote=FF 2
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000345122+17427_48101503.0DomainNote=FF 3
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000345122+17482_54801503.0DomainNote=FF 4
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000345122+17590_76301503.0DomainpG1 pseudoGTPase
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000345122+17779_94401503.0DomainpG2 pseudoGTPase
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+151262_144923238.0DomainRho-GAP
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+15267_32523238.0DomainNote=FF 1
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+15366_42023238.0DomainNote=FF 2
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+15427_48123238.0DomainNote=FF 3
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+15482_54823238.0DomainNote=FF 4
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+15590_76323238.0DomainpG1 pseudoGTPase
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+15779_94423238.0DomainpG2 pseudoGTPase
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000432921+171262_144901502.0DomainRho-GAP
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000432921+17267_32501502.0DomainNote=FF 1
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000432921+17366_42001502.0DomainNote=FF 2
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000432921+17427_48101502.0DomainNote=FF 3
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000432921+17482_54801502.0DomainNote=FF 4
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000432921+17590_76301502.0DomainpG1 pseudoGTPase
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000432921+17779_94401502.0DomainpG2 pseudoGTPase
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000433497+161262_14490242.0DomainRho-GAP
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000433497+16267_3250242.0DomainNote=FF 1
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000433497+16366_4200242.0DomainNote=FF 2
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000433497+16427_4810242.0DomainNote=FF 3
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000433497+16482_5480242.0DomainNote=FF 4
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000433497+16590_7630242.0DomainpG1 pseudoGTPase
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000433497+16779_9440242.0DomainpG2 pseudoGTPase
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000539826+171262_144901503.0DomainRho-GAP
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000539826+17267_32501503.0DomainNote=FF 1
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000539826+17366_42001503.0DomainNote=FF 2
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000539826+17427_48101503.0DomainNote=FF 3
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000539826+17482_54801503.0DomainNote=FF 4
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000539826+17590_76301503.0DomainpG1 pseudoGTPase
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000539826+17779_94401503.0DomainpG2 pseudoGTPase
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000556611+171262_144901502.0DomainRho-GAP
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000556611+17267_32501502.0DomainNote=FF 1
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000556611+17366_42001502.0DomainNote=FF 2
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000556611+17427_48101502.0DomainNote=FF 3
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000556611+17482_54801502.0DomainNote=FF 4
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000556611+17590_76301502.0DomainpG1 pseudoGTPase
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000556611+17779_94401502.0DomainpG2 pseudoGTPase


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Fusion Gene Sequence for ARHGAP5-LSAMP


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.
>6141_6141_1_ARHGAP5-LSAMP_ARHGAP5_chr14_32546641_ENST00000396582_LSAMP_chr3_116163802_ENST00000539563_length(transcript)=1372nt_BP=362nt
AGAGAAATCCGTCAGCGCGAGGGAGCCCGAGTGGCCGCCATTACTGAGCCCGGCGCGGCGGCGGGCGCTGGGGAAGGGGGGAGGGACGGG
CCGCCGCTGGTGGCGGGGAGGGAGGGAGGGAGGGTGGGTGAGCTGGCTGCGGGAGCCGTGGGGCTCAGGGTTTCGGGGCGTGTGTGTCGG
GGAGGGCGGGGGGAGGTGGCTGAAGGGACGCGCCGCTCGGTGAGCGCGCCGAGGAAGAGAGGCGAGCGGAGAGTGGAGGAGGAGGCGGCG
GCGGCGGGAGCGGTCCCCAGGAATGTCGCTGCCGCCGCCACCGCCGGGGCCGCTGCCGTTGAGGAGGAGACGGAGGAGACCGACGTTGTT
AGGACTGCCTGTTCGCAGCGTGGATTTTAACCGAGGCACGGACAACATCACCGTGAGGCAGGGGGACACAGCCATCCTCAGGTGCGTTGT
AGAAGACAAGAACTCAAAGGTGGCCTGGTTGAACCGTTCTGGCATCATTTTTGCTGGACATGACAAGTGGTCTCTGGACCCACGGGTTGA
GCTGGAGAAACGCCATTCTCTGGAATACAGCCTCCGAATCCAGAAGGTGGATGTCTATGATGAGGGTTCCTACACTTGCTCAGTTCAGAC
ACAGCATGAGCCCAAGACCTCCCAAGTTTACTTGATCGTACAAGTCCCACCAAAGATCTCCAATATCTCCTCGGATGTCACTGTGAATGA
GGGCAGCAACGTGACTCTGGTCTGCATGGCCAATGGCCGTCCTGAACCTGTTATCACCTGGAGACACCTTACACCAACTGGAAGGGAATT
TGAAGGAGAAGAAGAATATCTGGAGATCCTTGGCATCACCAGGGAGCAGTCAGGCAAATATGAGTGCAAAGCTGCCAACGAGGTCTCCTC
GGCGGATGTCAAACAAGTCAAGGTCACTGTGAACTATCCTCCCACTATCACAGAATCCAAGAGCAATGAAGCCACCACAGGACGACAAGC
TTCACTCAAATGTGAGGCCTCGGCAGTGCCTGCACCTGACTTTGAGTGGTACCGGGATGACACTAGGATAAATAGTGCCAATGGCCTTGA
GATTAAGAGCACGGAGGGCCAGTCTTCCCTGACGGTGACCAACGTCACTGAGGAGCACTACGGCAACTACACCTGTGTGGCTGCCAACAA
GCTGGGGGTCACCAATGCCAGCCTAGTCCTTTTCAAACGTGTTTTACCCACAATCCCCCACCCCATTCAAGAAATTGGTACCACCGTGCA
CTTCAAGCAAAAAGGACCTGGGTCGGTGAGAGGAATAAATGGATCCATCAGTCTGGCCGTACCACTGTGGCTGCTGGCAGCATCTCTGCT

>6141_6141_1_ARHGAP5-LSAMP_ARHGAP5_chr14_32546641_ENST00000396582_LSAMP_chr3_116163802_ENST00000539563_length(amino acids)=360AA_BP=23
MSLPPPPPGPLPLRRRRRRPTLLGLPVRSVDFNRGTDNITVRQGDTAILRCVVEDKNSKVAWLNRSGIIFAGHDKWSLDPRVELEKRHSL
EYSLRIQKVDVYDEGSYTCSVQTQHEPKTSQVYLIVQVPPKISNISSDVTVNEGSNVTLVCMANGRPEPVITWRHLTPTGREFEGEEEYL
EILGITREQSGKYECKAANEVSSADVKQVKVTVNYPPTITESKSNEATTGRQASLKCEASAVPAPDFEWYRDDTRINSANGLEIKSTEGQ
SSLTVTNVTEEHYGNYTCVAANKLGVTNASLVLFKRVLPTIPHPIQEIGTTVHFKQKGPGSVRGINGSISLAVPLWLLAASLLCLLSKCX

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Fusion Gene PPI Analysis for ARHGAP5-LSAMP


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 ARHGAP5-LSAMP


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 ARHGAP5-LSAMP


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