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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:LSR-GRAMD1A (FusionGDB2 ID:50239)

Fusion Gene Summary for LSR-GRAMD1A

check button Fusion gene summary
Fusion gene informationFusion gene name: LSR-GRAMD1A
Fusion gene ID: 50239
HgeneTgene
Gene symbol

LSR

GRAMD1A

Gene ID

51599

57655

Gene namelipolysis stimulated lipoprotein receptorGRAM domain containing 1A
SynonymsILDR3|LISCH7KIAA1533
Cytomap

19q13.12

19q13.11

Type of geneprotein-codingprotein-coding
Descriptionlipolysis-stimulated lipoprotein receptorLISCH proteinimmunoglobulin-like domain containing receptor 3lipolysis-stimulated remnantliver-specific bHLH-Zip transcription factorprotein Aster-AGRAM domain-containing protein 1A
Modification date2020031320200313
UniProtAcc

Q86X29

Q96CP6

Ensembl transtripts involved in fusion geneENST00000597933, ENST00000347609, 
ENST00000354900, ENST00000361790, 
ENST00000602122, ENST00000360798, 
ENST00000427250, 		ENST00000317991, 
ENST00000599564, ENST00000598073, 
ENST00000411896, ENST00000424536, 
ENST00000504615, 
Fusion gene scores* DoF score10 X 6 X 6=3605 X 5 X 5=125
# samples 115
** MAII scorelog2(11/360*10)=-1.71049338280502
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/125*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LSR [Title/Abstract] AND GRAMD1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLSR(35753595)-GRAMD1A(35500023), # 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

check buttonFusion gene breakpoints across LSR (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 GRAMD1A (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
ChimerDB4LIHCTCGA-XR-A8TG-01ALSRchr19

35753595

+GRAMD1Achr19

35500023

+


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Fusion Gene ORF analysis for LSR-GRAMD1A

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
3UTR-3CDSENST00000597933ENST00000317991LSRchr19

35753595

+GRAMD1Achr19

35500023

+
3UTR-3CDSENST00000597933ENST00000599564LSRchr19

35753595

+GRAMD1Achr19

35500023

+
3UTR-3UTRENST00000597933ENST00000598073LSRchr19

35753595

+GRAMD1Achr19

35500023

+
3UTR-5UTRENST00000597933ENST00000411896LSRchr19

35753595

+GRAMD1Achr19

35500023

+
3UTR-5UTRENST00000597933ENST00000424536LSRchr19

35753595

+GRAMD1Achr19

35500023

+
3UTR-5UTRENST00000597933ENST00000504615LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-3UTRENST00000347609ENST00000598073LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-3UTRENST00000354900ENST00000598073LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-3UTRENST00000361790ENST00000598073LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-3UTRENST00000602122ENST00000598073LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-5UTRENST00000347609ENST00000411896LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-5UTRENST00000347609ENST00000424536LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-5UTRENST00000347609ENST00000504615LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-5UTRENST00000354900ENST00000411896LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-5UTRENST00000354900ENST00000424536LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-5UTRENST00000354900ENST00000504615LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-5UTRENST00000361790ENST00000411896LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-5UTRENST00000361790ENST00000424536LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-5UTRENST00000361790ENST00000504615LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-5UTRENST00000602122ENST00000411896LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-5UTRENST00000602122ENST00000424536LSRchr19

35753595

+GRAMD1Achr19

35500023

+
5CDS-5UTRENST00000602122ENST00000504615LSRchr19

35753595

+GRAMD1Achr19

35500023

+
Frame-shiftENST00000347609ENST00000317991LSRchr19

35753595

+GRAMD1Achr19

35500023

+
Frame-shiftENST00000347609ENST00000599564LSRchr19

35753595

+GRAMD1Achr19

35500023

+
Frame-shiftENST00000354900ENST00000317991LSRchr19

35753595

+GRAMD1Achr19

35500023

+
Frame-shiftENST00000354900ENST00000599564LSRchr19

35753595

+GRAMD1Achr19

35500023

+
Frame-shiftENST00000361790ENST00000317991LSRchr19

35753595

+GRAMD1Achr19

35500023

+
Frame-shiftENST00000361790ENST00000599564LSRchr19

35753595

+GRAMD1Achr19

35500023

+
Frame-shiftENST00000602122ENST00000317991LSRchr19

35753595

+GRAMD1Achr19

35500023

+
Frame-shiftENST00000602122ENST00000599564LSRchr19

35753595

+GRAMD1Achr19

35500023

+
intron-3CDSENST00000360798ENST00000317991LSRchr19

35753595

+GRAMD1Achr19

35500023

+
intron-3CDSENST00000360798ENST00000599564LSRchr19

35753595

+GRAMD1Achr19

35500023

+
intron-3CDSENST00000427250ENST00000317991LSRchr19

35753595

+GRAMD1Achr19

35500023

+
intron-3CDSENST00000427250ENST00000599564LSRchr19

35753595

+GRAMD1Achr19

35500023

+
intron-3UTRENST00000360798ENST00000598073LSRchr19

35753595

+GRAMD1Achr19

35500023

+
intron-3UTRENST00000427250ENST00000598073LSRchr19

35753595

+GRAMD1Achr19

35500023

+
intron-5UTRENST00000360798ENST00000411896LSRchr19

35753595

+GRAMD1Achr19

35500023

+
intron-5UTRENST00000360798ENST00000424536LSRchr19

35753595

+GRAMD1Achr19

35500023

+
intron-5UTRENST00000360798ENST00000504615LSRchr19

35753595

+GRAMD1Achr19

35500023

+
intron-5UTRENST00000427250ENST00000411896LSRchr19

35753595

+GRAMD1Achr19

35500023

+
intron-5UTRENST00000427250ENST00000424536LSRchr19

35753595

+GRAMD1Achr19

35500023

+
intron-5UTRENST00000427250ENST00000504615LSRchr19

35753595

+GRAMD1Achr19

35500023

+

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 LSR-GRAMD1A


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)
LSRchr1935753595+GRAMD1Achr1935500022+4.42E-050.9999558
LSRchr1935753595+GRAMD1Achr1935500022+4.42E-050.9999558

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.
genomic feature of top 1%

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Fusion Protein Features for LSR-GRAMD1A


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/:35753595/:35500023)
- 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
LSR

Q86X29

GRAMD1A

Q96CP6

FUNCTION: Probable role in the clearance of triglyceride-rich lipoprotein from blood. Binds chylomicrons, LDL and VLDL in presence of free fatty acids and allows their subsequent uptake in the cells (By similarity). {ECO:0000250}.FUNCTION: Cholesterol transporter that mediates non-vesicular transport of cholesterol from the plasma membrane (PM) to the endoplasmic reticulum (ER) (By similarity). Contains unique domains for binding cholesterol and the PM, thereby serving as a molecular bridge for the transfer of cholesterol from the PM to the ER (By similarity). Plays a crucial role in cholesterol homeostasis and has the unique ability to localize to the PM based on the level of membrane cholesterol (By similarity). In lipid-poor conditions localizes to the ER membrane and in response to excess cholesterol in the PM is recruited to the endoplasmic reticulum-plasma membrane contact sites (EPCS) which is mediated by the GRAM domain (By similarity). At the EPCS, the sterol-binding VASt/ASTER domain binds to the cholesterol in the PM and facilitates its transfer from the PM to ER (By similarity). May play a role in tumor progression (By similarity). Plays a role in autophagy regulation and is required for biogenesis of the autophagosome (PubMed:31222192). This function in autophagy requires its cholesterol-transfer activity (PubMed:31222192). {ECO:0000250|UniProtKB:Q8VEF1, ECO:0000269|PubMed:31222192}.

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 LSR-GRAMD1A


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 LSR-GRAMD1A


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 LSR-GRAMD1A


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 LSR-GRAMD1A


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