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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:COL6A3-DDX3X (FusionGDB2 ID:HG1293TG1654)

Fusion Gene Summary for COL6A3-DDX3X

check button Fusion gene summary
Fusion gene informationFusion gene name: COL6A3-DDX3X
Fusion gene ID: hg1293tg1654
HgeneTgene
Gene symbol

COL6A3

DDX3X

Gene ID

1293

1654

Gene namecollagen type VI alpha 3 chainDEAD-box helicase 3 X-linked
SynonymsBTHLM1|DYT27|UCMD1CAP-Rf|DBX|DDX14|DDX3|HLP2|MRX102
Cytomap('COL6A3')('DDX3X')

2q37.3

Xp11.4

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-3(VI) chaincollagen VI, alpha-3 polypeptidecollagen, type VI, alpha 3epididymis secretory sperm binding proteinATP-dependent RNA helicase DDX3XDEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linkedDEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linkedDEAD box protein 3, X-chromosomalDEAD box, X isoformDEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3DEAD/H box-3helicase-
Modification date2020032820200329
UniProtAcc

P12111

.
Ensembl transtripts involved in fusion geneENST00000295550, ENST00000346358, 
ENST00000347401, ENST00000353578, 
ENST00000392003, ENST00000392004, 
ENST00000409809, ENST00000472056, 
ENST00000473258, 
Fusion gene scores* DoF score13 X 12 X 6=9367 X 9 X 4=252
# samples 138
** MAII scorelog2(13/936*10)=-2.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/252*10)=-1.65535182861255
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COL6A3 [Title/Abstract] AND DDX3X [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOL6A3(238252219)-DDX3X(41209154), # 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
TgeneDDX3X

GO:0009615

response to virus

18636090

TgeneDDX3X

GO:0010501

RNA secondary structure unwinding

22872150

TgeneDDX3X

GO:0010628

positive regulation of gene expression

10074132

TgeneDDX3X

GO:0030308

negative regulation of cell growth

16818630

TgeneDDX3X

GO:0031333

negative regulation of protein complex assembly

17667941

TgeneDDX3X

GO:0031954

positive regulation of protein autophosphorylation

30341167

TgeneDDX3X

GO:0032727

positive regulation of interferon-alpha production

30341167

TgeneDDX3X

GO:0032728

positive regulation of interferon-beta production

27980081

TgeneDDX3X

GO:0034063

stress granule assembly

21883093

TgeneDDX3X

GO:0034157

positive regulation of toll-like receptor 7 signaling pathway

30341167

TgeneDDX3X

GO:0034161

positive regulation of toll-like receptor 8 signaling pathway

30341167

TgeneDDX3X

GO:0035556

intracellular signal transduction

18636090

TgeneDDX3X

GO:0045727

positive regulation of translation

18596238|22872150

TgeneDDX3X

GO:0045944

positive regulation of transcription by RNA polymerase II

16818630|18636090|28128295

TgeneDDX3X

GO:0071243

cellular response to arsenic-containing substance

21883093

TgeneDDX3X

GO:0071470

cellular response to osmotic stress

21883093

TgeneDDX3X

GO:0071902

positive regulation of protein serine/threonine kinase activity

23413191

TgeneDDX3X

GO:1902523

positive regulation of protein K63-linked ubiquitination

27980081



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
ChimerDB4PRADTCGA-KK-A8II-01ACOL6A3chr2

238252219

-DDX3XchrX

41209154

+


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Fusion Gene ORF analysis for COL6A3-DDX3X

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
intron-3UTRENST00000295550ENST00000399959COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-3UTRENST00000346358ENST00000399959COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-3UTRENST00000347401ENST00000399959COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-3UTRENST00000353578ENST00000399959COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-3UTRENST00000392003ENST00000399959COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-3UTRENST00000392004ENST00000399959COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-3UTRENST00000409809ENST00000399959COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-3UTRENST00000472056ENST00000399959COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-3UTRENST00000473258ENST00000399959COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000295550ENST00000441189COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000295550ENST00000457138COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000295550ENST00000478993COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000295550ENST00000542215COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000346358ENST00000441189COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000346358ENST00000457138COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000346358ENST00000478993COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000346358ENST00000542215COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000347401ENST00000441189COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000347401ENST00000457138COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000347401ENST00000478993COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000347401ENST00000542215COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000353578ENST00000441189COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000353578ENST00000457138COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000353578ENST00000478993COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000353578ENST00000542215COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000392003ENST00000441189COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000392003ENST00000457138COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000392003ENST00000478993COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000392003ENST00000542215COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000392004ENST00000441189COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000392004ENST00000457138COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000392004ENST00000478993COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000392004ENST00000542215COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000409809ENST00000441189COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000409809ENST00000457138COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000409809ENST00000478993COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000409809ENST00000542215COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000472056ENST00000441189COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000472056ENST00000457138COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000472056ENST00000478993COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000472056ENST00000542215COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000473258ENST00000441189COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000473258ENST00000457138COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000473258ENST00000478993COL6A3chr2

238252219

-DDX3XchrX

41209154

+
intron-intronENST00000473258ENST00000542215COL6A3chr2

238252219

-DDX3XchrX

41209154

+

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 COL6A3-DDX3X


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 COL6A3-DDX3X


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/:238252219/:41209154)
- 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
COL6A3

P12111

.
FUNCTION: Collagen VI acts as a cell-binding protein.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 COL6A3-DDX3X


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 COL6A3-DDX3X


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 COL6A3-DDX3X


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 COL6A3-DDX3X


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL6A3C1834674BETHLEM MYOPATHY 15CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCOL6A3C0410179Ullrich congenital muscular dystrophy 14CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL6A3C4225336DYSTONIA 272GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL6A3C0000786Spontaneous abortion1CTD_human
HgeneCOL6A3C0000822Abortion, Tubal1CTD_human
HgeneCOL6A3C0027708Nephroblastoma1CTD_human
HgeneCOL6A3C2930471Bilateral Wilms Tumor1CTD_human
HgeneCOL6A3C3830362Early Pregnancy Loss1CTD_human
HgeneCOL6A3C4552766Miscarriage1CTD_human
TgeneC1535926Neurodevelopmental Disorders2CTD_human
TgeneC4085582MENTAL RETARDATION, X-LINKED 1022CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0014544Epilepsy1CTD_human
TgeneC0029408Degenerative polyarthritis1CTD_human
TgeneC0079772T-Cell Lymphoma1CTD_human
TgeneC0086237Epilepsy, Cryptogenic1CTD_human
TgeneC0086743Osteoarthrosis Deformans1CTD_human
TgeneC0236018Aura1CTD_human
TgeneC0345967Malignant mesothelioma1CTD_human
TgeneC0751111Awakening Epilepsy1CTD_human
TgeneC0796184Corpus Callosum, Agenesis of, with Facial Anomalies and Robin Sequence1ORPHANET
TgeneC1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1ORPHANET
TgeneC3714756Intellectual Disability1GENOMICS_ENGLAND