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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:ARHGAP5-LSAMP

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ARHGAP5-LSAMP
FusionPDB ID: 6141
FusionGDB2.0 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 geneENST idsENST00000396582, ENST00000345122, 
ENST00000432921, ENST00000433497, 
ENST00000539826, ENST00000556611, 
ENST00000498645, ENST00000490035, 
ENST00000539563, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* 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 (manual curation of fusion genes in FusionPDB)

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

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ARHGAP5(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 by not retaining the major functional domain in the partially deleted in-frame ORF.
ARHGAP5-LSAMP seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
ARHGAP5-LSAMP seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
ARHGAP5-LSAMP seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
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


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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 ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
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 Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>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 Protein Functional Features


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.
- 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

- 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_124523.333333333333332238.0Compositional 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_144923.333333333333332238.0DomainRho-GAP
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+15267_32523.333333333333332238.0DomainNote=FF 1
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+15366_42023.333333333333332238.0DomainNote=FF 2
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+15427_48123.333333333333332238.0DomainNote=FF 3
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+15482_54823.333333333333332238.0DomainNote=FF 4
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+15590_76323.333333333333332238.0DomainpG1 pseudoGTPase
HgeneARHGAP5chr14:32546641chr3:116163802ENST00000396582+15779_94423.333333333333332238.0DomainpG2 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 Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
ARHGAP5
LSAMP


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to ARHGAP5-LSAMP


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to ARHGAP5-LSAMP


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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