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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:LRSAM1-DENND1A (FusionGDB2 ID:50140)

Fusion Gene Summary for LRSAM1-DENND1A

check button Fusion gene summary
Fusion gene informationFusion gene name: LRSAM1-DENND1A
Fusion gene ID: 50140
HgeneTgene
Gene symbol

LRSAM1

DENND1A

Gene ID

90678

57706

Gene nameleucine rich repeat and sterile alpha motif containing 1DENN domain containing 1A
SynonymsCMT2P|RIFLE|TALFAM31A|KIAA1608
Cytomap

9q33.3-q34.11

9q33.3

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase LRSAM1RING finger leucine repeat richRING-type E3 ubiquitin transferase LRSAM1Tsg101-associated ligaseDENN domain-containing protein 1ADENN/MADD domain containing 1Aconnecdenn 1
Modification date2020032820200320
UniProtAcc

Q6UWE0

Q8TEH3

Ensembl transtripts involved in fusion geneENST00000300417, ENST00000323301, 
ENST00000373324, ENST00000373322, 
ENST00000483302, 		ENST00000373618, 
ENST00000373620, ENST00000373624, 
ENST00000394215, ENST00000394219, 
ENST00000473039, ENST00000542603, 
Fusion gene scores* DoF score3 X 4 X 4=4822 X 22 X 12=5808
# samples 433
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(33/5808*10)=-4.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LRSAM1 [Title/Abstract] AND DENND1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLRSAM1(130214363)-DENND1A(126220176), # samples:2
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
HgeneLRSAM1

GO:0000209

protein polyubiquitination

18077552

HgeneLRSAM1

GO:0051865

protein autoubiquitination

15256501|23245322

HgeneLRSAM1

GO:0070086

ubiquitin-dependent endocytosis

15256501

TgeneDENND1A

GO:0032483

regulation of Rab protein signal transduction

20937701


check buttonFusion gene breakpoints across LRSAM1 (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 DENND1A (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-E2-A159-01ALRSAM1chr9

130214363

-DENND1Achr9

126220176

-
ChimerDB4BRCATCGA-E2-A159-01ALRSAM1chr9

130214363

+DENND1Achr9

126220176

-


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Fusion Gene ORF analysis for LRSAM1-DENND1A

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
5UTR-intronENST00000300417ENST00000373618LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000300417ENST00000373620LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000300417ENST00000373624LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000300417ENST00000394215LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000300417ENST00000394219LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000300417ENST00000473039LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000300417ENST00000542603LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000323301ENST00000373618LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000323301ENST00000373620LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000323301ENST00000373624LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000323301ENST00000394215LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000323301ENST00000394219LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000323301ENST00000473039LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000323301ENST00000542603LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000373324ENST00000373618LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000373324ENST00000373620LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000373324ENST00000373624LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000373324ENST00000394215LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000373324ENST00000394219LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000373324ENST00000473039LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
5UTR-intronENST00000373324ENST00000542603LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000373322ENST00000373618LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000373322ENST00000373620LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000373322ENST00000373624LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000373322ENST00000394215LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000373322ENST00000394219LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000373322ENST00000473039LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000373322ENST00000542603LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000483302ENST00000373618LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000483302ENST00000373620LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000483302ENST00000373624LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000483302ENST00000394215LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000483302ENST00000394219LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000483302ENST00000473039LRSAM1chr9

130214363

+DENND1Achr9

126220176

-
intron-intronENST00000483302ENST00000542603LRSAM1chr9

130214363

+DENND1Achr9

126220176

-

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 LRSAM1-DENND1A


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 LRSAM1-DENND1A


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/:130214363/:126220176)
- 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
LRSAM1

Q6UWE0

DENND1A

Q8TEH3

FUNCTION: E3 ubiquitin-protein ligase that mediates monoubiquitination of TSG101 at multiple sites, leading to inactivate the ability of TSG101 to sort endocytic (EGF receptors) and exocytic (HIV-1 viral proteins) cargos (PubMed:15256501). Bacterial recognition protein that defends the cytoplasm from invasive pathogens (PubMed:23245322). Localizes to several intracellular bacterial pathogens and generates the bacteria-associated ubiquitin signal leading to autophagy-mediated intracellular bacteria degradation (xenophagy) (PubMed:23245322, PubMed:25484098). {ECO:0000269|PubMed:15256501, ECO:0000269|PubMed:23245322, ECO:0000269|PubMed:25484098}.FUNCTION: Guanine nucleotide exchange factor (GEF) regulating clathrin-mediated endocytosis through RAB35 activation. Promotes the exchange of GDP to GTP, converting inactive GDP-bound RAB35 into its active GTP-bound form. Regulates clathrin-mediated endocytosis of synaptic vesicles and mediates exit from early endosomes (PubMed:20154091, PubMed:20937701). Binds phosphatidylinositol-phosphates (PtdInsPs), with some preference for PtdIns(3)P (By similarity). {ECO:0000250|UniProtKB:Q8K382, ECO:0000269|PubMed:20154091, ECO:0000269|PubMed:20937701}.

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 LRSAM1-DENND1A


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 LRSAM1-DENND1A


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 LRSAM1-DENND1A


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 LRSAM1-DENND1A


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