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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:GRAMD1A-CARS (FusionGDB2 ID:34572)

Fusion Gene Summary for GRAMD1A-CARS

check button Fusion gene summary
Fusion gene informationFusion gene name: GRAMD1A-CARS
Fusion gene ID: 34572
HgeneTgene
Gene symbol

GRAMD1A

CARS

Gene ID

57655

833

Gene nameGRAM domain containing 1Acysteinyl-tRNA synthetase 1
SynonymsKIAA1533CARS|CYSRS|MGC:11246
Cytomap

19q13.11

11p15.4

Type of geneprotein-codingprotein-coding
Descriptionprotein Aster-AGRAM domain-containing protein 1Acysteine--tRNA ligase, cytoplasmiccysteine tRNA ligase 1, cytoplasmiccysteine translase
Modification date2020031320200313
UniProtAcc

Q96CP6

Q9HA77

Ensembl transtripts involved in fusion geneENST00000317991, ENST00000411896, 
ENST00000424536, ENST00000504615, 
ENST00000598073, ENST00000599564, 
ENST00000397114, ENST00000401769, 
ENST00000470221, ENST00000278224, 
ENST00000380525, ENST00000397111, 
Fusion gene scores* DoF score5 X 3 X 5=7511 X 12 X 6=792
# samples 612
** MAII scorelog2(6/75*10)=-0.321928094887362
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/792*10)=-2.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

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

Most frequent breakpointGRAMD1A(35491390)-CARS(3039741), # samples:1
Anticipated loss of major functional domain due to fusion event.GRAMD1A-CARS seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
GRAMD1A-CARS seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
TgeneCARS

GO:0006423

cysteinyl-tRNA aminoacylation

10908348|17303165


check buttonFusion gene breakpoints across GRAMD1A (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 CARS (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
ChiTaRS5.0N/AAI300436GRAMD1Achr19

35491390

+CARSchr11

3039741

-


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Fusion Gene ORF analysis for GRAMD1A-CARS

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-intronENST00000317991ENST00000397114GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5CDS-intronENST00000317991ENST00000401769GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5CDS-intronENST00000317991ENST00000470221GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5CDS-intronENST00000411896ENST00000397114GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5CDS-intronENST00000411896ENST00000401769GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5CDS-intronENST00000411896ENST00000470221GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5CDS-intronENST00000424536ENST00000397114GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5CDS-intronENST00000424536ENST00000401769GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5CDS-intronENST00000424536ENST00000470221GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5UTR-3CDSENST00000504615ENST00000278224GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5UTR-3CDSENST00000504615ENST00000380525GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5UTR-3CDSENST00000504615ENST00000397111GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5UTR-intronENST00000504615ENST00000397114GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5UTR-intronENST00000504615ENST00000401769GRAMD1Achr19

35491390

+CARSchr11

3039741

-
5UTR-intronENST00000504615ENST00000470221GRAMD1Achr19

35491390

+CARSchr11

3039741

-
Frame-shiftENST00000317991ENST00000278224GRAMD1Achr19

35491390

+CARSchr11

3039741

-
Frame-shiftENST00000317991ENST00000380525GRAMD1Achr19

35491390

+CARSchr11

3039741

-
Frame-shiftENST00000317991ENST00000397111GRAMD1Achr19

35491390

+CARSchr11

3039741

-
Frame-shiftENST00000411896ENST00000278224GRAMD1Achr19

35491390

+CARSchr11

3039741

-
Frame-shiftENST00000411896ENST00000380525GRAMD1Achr19

35491390

+CARSchr11

3039741

-
Frame-shiftENST00000411896ENST00000397111GRAMD1Achr19

35491390

+CARSchr11

3039741

-
Frame-shiftENST00000424536ENST00000278224GRAMD1Achr19

35491390

+CARSchr11

3039741

-
Frame-shiftENST00000424536ENST00000380525GRAMD1Achr19

35491390

+CARSchr11

3039741

-
Frame-shiftENST00000424536ENST00000397111GRAMD1Achr19

35491390

+CARSchr11

3039741

-
intron-3CDSENST00000598073ENST00000278224GRAMD1Achr19

35491390

+CARSchr11

3039741

-
intron-3CDSENST00000598073ENST00000380525GRAMD1Achr19

35491390

+CARSchr11

3039741

-
intron-3CDSENST00000598073ENST00000397111GRAMD1Achr19

35491390

+CARSchr11

3039741

-
intron-3CDSENST00000599564ENST00000278224GRAMD1Achr19

35491390

+CARSchr11

3039741

-
intron-3CDSENST00000599564ENST00000380525GRAMD1Achr19

35491390

+CARSchr11

3039741

-
intron-3CDSENST00000599564ENST00000397111GRAMD1Achr19

35491390

+CARSchr11

3039741

-
intron-intronENST00000598073ENST00000397114GRAMD1Achr19

35491390

+CARSchr11

3039741

-
intron-intronENST00000598073ENST00000401769GRAMD1Achr19

35491390

+CARSchr11

3039741

-
intron-intronENST00000598073ENST00000470221GRAMD1Achr19

35491390

+CARSchr11

3039741

-
intron-intronENST00000599564ENST00000397114GRAMD1Achr19

35491390

+CARSchr11

3039741

-
intron-intronENST00000599564ENST00000401769GRAMD1Achr19

35491390

+CARSchr11

3039741

-
intron-intronENST00000599564ENST00000470221GRAMD1Achr19

35491390

+CARSchr11

3039741

-

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 GRAMD1A-CARS


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 GRAMD1A-CARS


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/:35491390/:3039741)
- 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
GRAMD1A

Q96CP6

CARS

Q9HA77

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 GRAMD1A-CARS


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 GRAMD1A-CARS


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 GRAMD1A-CARS


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 GRAMD1A-CARS


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