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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:GNPDA1-GRAMD4 (FusionGDB2 ID:33810)

Fusion Gene Summary for GNPDA1-GRAMD4

check button Fusion gene summary
Fusion gene informationFusion gene name: GNPDA1-GRAMD4
Fusion gene ID: 33810
HgeneTgene
Gene symbol

GNPDA1

GRAMD4

Gene ID

10007

23151

Gene nameglucosamine-6-phosphate deaminase 1GRAM domain containing 4
SynonymsGNP1|GNPDA|GNPI|GPI|HLNDIP
Cytomap

5q31.3

22q13.31

Type of geneprotein-codingprotein-coding
Descriptionglucosamine-6-phosphate isomerase 1GNPDA 1glcN6P deaminase 1oscillinGRAM domain-containing protein 4death-inducing-protein
Modification date2020031320200313
UniProtAcc

P46926

Q6IC98

Ensembl transtripts involved in fusion geneENST00000311337, ENST00000458112, 
ENST00000500692, ENST00000503794, 
ENST00000508177, ENST00000513454, 
ENST00000542860, 		ENST00000361034, 
ENST00000406902, ENST00000408031, 
ENST00000490378, 
Fusion gene scores* DoF score5 X 6 X 2=6015 X 11 X 7=1155
# samples 616
** MAII scorelog2(6/60*10)=0log2(16/1155*10)=-2.85174904141606
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GNPDA1 [Title/Abstract] AND GRAMD4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGNPDA1(141380239)-GRAMD4(46987728), # samples:1
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 GNPDA1 (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 GRAMD4 (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/ABI493234GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+


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Fusion Gene ORF analysis for GNPDA1-GRAMD4

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-intronENST00000311337ENST00000361034GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000311337ENST00000406902GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000311337ENST00000408031GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000311337ENST00000490378GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000458112ENST00000361034GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000458112ENST00000406902GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000458112ENST00000408031GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000458112ENST00000490378GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000500692ENST00000361034GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000500692ENST00000406902GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000500692ENST00000408031GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000500692ENST00000490378GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000503794ENST00000361034GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000503794ENST00000406902GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000503794ENST00000408031GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000503794ENST00000490378GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000508177ENST00000361034GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000508177ENST00000406902GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000508177ENST00000408031GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
5CDS-intronENST00000508177ENST00000490378GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
intron-intronENST00000513454ENST00000361034GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
intron-intronENST00000513454ENST00000406902GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
intron-intronENST00000513454ENST00000408031GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
intron-intronENST00000513454ENST00000490378GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
intron-intronENST00000542860ENST00000361034GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
intron-intronENST00000542860ENST00000406902GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
intron-intronENST00000542860ENST00000408031GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+
intron-intronENST00000542860ENST00000490378GNPDA1chr5

141380239

-GRAMD4chr22

46987728

+

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 GNPDA1-GRAMD4


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 GNPDA1-GRAMD4


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/:141380239/:46987728)
- 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
GNPDA1

P46926

GRAMD4

Q6IC98

FUNCTION: Seems to trigger calcium oscillations in mammalian eggs. These oscillations serve as the essential trigger for egg activation and early development of the embryo (By similarity). {ECO:0000250}.FUNCTION: Plays a role as a mediator of E2F1-induced apoptosis in the absence of p53/TP53 (PubMed:15565177). Plays a role as a mediator of E2F1-induced apoptosis in the absence of p53/TP53. Inhibits TLR9 response to nucelic acids and regulates TLR9-mediated innate immune response (By similarity). {ECO:0000250|UniProtKB:Q8CB44, ECO:0000269|PubMed:15565177}.

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 GNPDA1-GRAMD4


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 GNPDA1-GRAMD4


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 GNPDA1-GRAMD4


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 GNPDA1-GRAMD4


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