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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:GMNN-COL6A3 (FusionGDB2 ID:HG51053TG1293)

Fusion Gene Summary for GMNN-COL6A3

check button Fusion gene summary
Fusion gene informationFusion gene name: GMNN-COL6A3
Fusion gene ID: hg51053tg1293
HgeneTgene
Gene symbol

GMNN

COL6A3

Gene ID

51053

1293

Gene namegeminin DNA replication inhibitorcollagen type VI alpha 3 chain
SynonymsGem|MGORS6BTHLM1|DYT27|UCMD1
Cytomap('GMNN')('COL6A3')

6p22.3

2q37.3

Type of geneprotein-codingprotein-coding
Descriptiongeminincollagen alpha-3(VI) chaincollagen VI, alpha-3 polypeptidecollagen, type VI, alpha 3epididymis secretory sperm binding protein
Modification date2020031520200328
UniProtAcc

O75496

P12111

Ensembl transtripts involved in fusion geneENST00000230056, ENST00000356509, 
Fusion gene scores* DoF score5 X 5 X 3=7513 X 13 X 4=676
# samples 513
** MAII scorelog2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/676*10)=-2.37851162325373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GMNN [Title/Abstract] AND COL6A3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGMNN(24784782)-COL6A3(238294511), # 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
HgeneGMNN

GO:0008156

negative regulation of DNA replication

9635433

HgeneGMNN

GO:0035563

positive regulation of chromatin binding

11125146

HgeneGMNN

GO:0045786

negative regulation of cell cycle

9635433

HgeneGMNN

GO:0045892

negative regulation of transcription, DNA-templated

16924111

HgeneGMNN

GO:0071163

DNA replication preinitiation complex assembly

11125146

HgeneGMNN

GO:2000104

negative regulation of DNA-dependent DNA replication

11125146



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/AFN165700GMNNchr6

24784782

+COL6A3chr2

238294511

-


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Fusion Gene ORF analysis for GMNN-COL6A3

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-intronENST00000230056ENST00000295550GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000230056ENST00000346358GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000230056ENST00000347401GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000230056ENST00000353578GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000230056ENST00000392003GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000230056ENST00000392004GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000230056ENST00000409809GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000230056ENST00000472056GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000230056ENST00000473258GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000356509ENST00000295550GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000356509ENST00000346358GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000356509ENST00000347401GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000356509ENST00000353578GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000356509ENST00000392003GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000356509ENST00000392004GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000356509ENST00000409809GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000356509ENST00000472056GMNNchr6

24784782

+COL6A3chr2

238294511

-
5CDS-intronENST00000356509ENST00000473258GMNNchr6

24784782

+COL6A3chr2

238294511

-

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 GMNN-COL6A3


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)


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Fusion Protein Features for GMNN-COL6A3


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/:24784782/:238294511)
- 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
GMNN

O75496

COL6A3

P12111

FUNCTION: Inhibits DNA replication by preventing the incorporation of MCM complex into pre-replication complex (pre-RC) (PubMed:9635433, PubMed:14993212, PubMed:20129055, PubMed:24064211). It is degraded during the mitotic phase of the cell cycle (PubMed:9635433, PubMed:14993212, PubMed:24064211). Its destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle (PubMed:9635433, PubMed:14993212, PubMed:24064211). Inhibits histone acetyltransferase activity of KAT7/HBO1 in a CDT1-dependent manner, inhibiting histone H4 acetylation and DNA replication licensing (PubMed:20129055). Inhibits the transcriptional activity of a subset of Hox proteins, enrolling them in cell proliferative control (PubMed:22615398). {ECO:0000269|PubMed:14993212, ECO:0000269|PubMed:20129055, ECO:0000269|PubMed:22615398, ECO:0000269|PubMed:24064211, ECO:0000269|PubMed:9635433}.FUNCTION: Collagen VI acts as a cell-binding protein.

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 GMNN-COL6A3


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 GMNN-COL6A3


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 GMNN-COL6A3


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 GMNN-COL6A3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGMNNC4225188MEIER-GORLIN SYNDROME 62GENOMICS_ENGLAND;UNIPROT
HgeneGMNNC0013336Dwarfism1GENOMICS_ENGLAND
HgeneGMNNC0265202Seckel syndrome1GENOMICS_ENGLAND
HgeneGMNNC0342573PITUITARY DWARFISM I1GENOMICS_ENGLAND
HgeneGMNNC1292778Chronic myeloproliferative disorder1GENOMICS_ENGLAND
HgeneGMNNC1868684EAR, PATELLA, SHORT STATURE SYNDROME1CTD_human;ORPHANET
HgeneGMNNC2239176Liver carcinoma1CTD_human
TgeneC1834674BETHLEM MYOPATHY 15CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0410179Ullrich congenital muscular dystrophy 14CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC4225336DYSTONIA 272GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0000786Spontaneous abortion1CTD_human
TgeneC0000822Abortion, Tubal1CTD_human
TgeneC0027708Nephroblastoma1CTD_human
TgeneC2930471Bilateral Wilms Tumor1CTD_human
TgeneC3830362Early Pregnancy Loss1CTD_human
TgeneC4552766Miscarriage1CTD_human