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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:GOLGA3-CHFR (FusionGDB2 ID:33754)

Fusion Gene Summary for GOLGA3-CHFR

check button Fusion gene summary
Fusion gene informationFusion gene name: GOLGA3-CHFR
Fusion gene ID: 33754
HgeneTgene
Gene symbol

GOLGA3

CHFR

Gene ID

2802

55743

Gene namegolgin A3checkpoint with forkhead and ring finger domains
SynonymsGCP170|MEA-2RNF116|RNF196
Cytomap

12q24.33

12q24.33

Type of geneprotein-codingprotein-coding
Descriptiongolgin subfamily A member 3Golgi membrane associated proteinGolgi peripheral membrane proteinSY2/SY10 proteingolgi autoantigen, golgin subfamily a, 3golgi complex-associated protein of 170 kDagolgin-160golgin-165male enhanced antigen-2E3 ubiquitin-protein ligase CHFRRING finger protein 196RING-type E3 ubiquitin transferase CHFRcheckpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase
Modification date2020031320200313
UniProtAcc.

Q96EP1

Ensembl transtripts involved in fusion geneENST00000204726, ENST00000450791, 
ENST00000456883, ENST00000537452, 
ENST00000545875, ENST00000534967, 
ENST00000315585, ENST00000266880, 
ENST00000443047, ENST00000450056, 
ENST00000537522, ENST00000541837, 
ENST00000432561, ENST00000541341, 
Fusion gene scores* DoF score15 X 51 X 17=130056 X 7 X 4=168
# samples 896
** MAII scorelog2(89/13005*10)=-3.86911725297659
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/168*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GOLGA3 [Title/Abstract] AND CHFR [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGOLGA3(133357384)-CHFR(133419669), # samples:1
Anticipated loss of major functional domain due to fusion event.GOLGA3-CHFR seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
GOLGA3-CHFR 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
TgeneCHFR

GO:0000209

protein polyubiquitination

19182791

TgeneCHFR

GO:0019941

modification-dependent protein catabolic process

19182791


check buttonFusion gene breakpoints across GOLGA3 (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 CHFR (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
ChimerDB4LUSCTCGA-33-6738-01AGOLGA3chr12

133357384

-CHFRchr12

133419669

-


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Fusion Gene ORF analysis for GOLGA3-CHFR

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
Frame-shiftENST00000204726ENST00000315585GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000204726ENST00000266880GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000204726ENST00000443047GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000204726ENST00000450056GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000204726ENST00000537522GOLGA3chr12

133357384

-CHFRchr12

133419669

-
5CDS-5UTRENST00000204726ENST00000541837GOLGA3chr12

133357384

-CHFRchr12

133419669

-
5CDS-5UTRENST00000204726ENST00000432561GOLGA3chr12

133357384

-CHFRchr12

133419669

-
5CDS-5UTRENST00000204726ENST00000541341GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000450791ENST00000315585GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000450791ENST00000266880GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000450791ENST00000443047GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000450791ENST00000450056GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000450791ENST00000537522GOLGA3chr12

133357384

-CHFRchr12

133419669

-
5CDS-5UTRENST00000450791ENST00000541837GOLGA3chr12

133357384

-CHFRchr12

133419669

-
5CDS-5UTRENST00000450791ENST00000432561GOLGA3chr12

133357384

-CHFRchr12

133419669

-
5CDS-5UTRENST00000450791ENST00000541341GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000456883ENST00000315585GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000456883ENST00000266880GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000456883ENST00000443047GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000456883ENST00000450056GOLGA3chr12

133357384

-CHFRchr12

133419669

-
Frame-shiftENST00000456883ENST00000537522GOLGA3chr12

133357384

-CHFRchr12

133419669

-
5CDS-5UTRENST00000456883ENST00000541837GOLGA3chr12

133357384

-CHFRchr12

133419669

-
5CDS-5UTRENST00000456883ENST00000432561GOLGA3chr12

133357384

-CHFRchr12

133419669

-
5CDS-5UTRENST00000456883ENST00000541341GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000537452ENST00000315585GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000537452ENST00000266880GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000537452ENST00000443047GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000537452ENST00000450056GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000537452ENST00000537522GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-5UTRENST00000537452ENST00000541837GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-5UTRENST00000537452ENST00000432561GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-5UTRENST00000537452ENST00000541341GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000545875ENST00000315585GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000545875ENST00000266880GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000545875ENST00000443047GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000545875ENST00000450056GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000545875ENST00000537522GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-5UTRENST00000545875ENST00000541837GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-5UTRENST00000545875ENST00000432561GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-5UTRENST00000545875ENST00000541341GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000534967ENST00000315585GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000534967ENST00000266880GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000534967ENST00000443047GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000534967ENST00000450056GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-3CDSENST00000534967ENST00000537522GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-5UTRENST00000534967ENST00000541837GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-5UTRENST00000534967ENST00000432561GOLGA3chr12

133357384

-CHFRchr12

133419669

-
intron-5UTRENST00000534967ENST00000541341GOLGA3chr12

133357384

-CHFRchr12

133419669

-

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 GOLGA3-CHFR


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 GOLGA3-CHFR


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.CHFR

Q96EP1

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: E3 ubiquitin-protein ligase that functions in the antephase checkpoint by actively delaying passage into mitosis in response to microtubule poisons. Acts in early prophase before chromosome condensation, when the centrosome move apart from each other along the periphery of the nucleus. Probably involved in signaling the presence of mitotic stress caused by microtubule poisons by mediating the 'Lys-48'-linked ubiquitination of target proteins, leading to their degradation by the proteasome. Promotes the ubiquitination and subsequent degradation of AURKA and PLK1. Probably acts as a tumor suppressor, possibly by mediating the polyubiquitination of HDAC1, leading to its degradation. May also promote the formation of 'Lys-63'-linked polyubiquitin chains and functions with the specific ubiquitin-conjugating UBC13-MMS2 (UBE2N-UBE2V2) heterodimer. Substrates that are polyubiquitinated at 'Lys-63' are usually not targeted for degradation, but are rather involved in signaling cellular stress. {ECO:0000269|PubMed:10935642, ECO:0000269|PubMed:11807090, ECO:0000269|PubMed:11912157, ECO:0000269|PubMed:14562038, ECO:0000269|PubMed:14694445, ECO:0000269|PubMed:18172500, ECO:0000269|PubMed:19182791}.

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 GOLGA3-CHFR


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 GOLGA3-CHFR


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 GOLGA3-CHFR


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 GOLGA3-CHFR


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCHFRC0007131Non-Small Cell Lung Carcinoma1CTD_human;UNIPROT
TgeneCHFRC0014170Endometrial Neoplasms1CTD_human
TgeneCHFRC0024623Malignant neoplasm of stomach1CTD_human
TgeneCHFRC0038356Stomach Neoplasms1CTD_human
TgeneCHFRC0476089Endometrial Carcinoma1CTD_human
TgeneCHFRC1708349Hereditary Diffuse Gastric Cancer1CTD_human