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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:TNRC6B-COL18A1 (FusionGDB2 ID:92228)

Fusion Gene Summary for TNRC6B-COL18A1

check button Fusion gene summary
Fusion gene informationFusion gene name: TNRC6B-COL18A1
Fusion gene ID: 92228
HgeneTgene
Gene symbol

TNRC6B

COL18A1

Gene ID

23112

80781

Gene nametrinucleotide repeat containing adaptor 6Bcollagen type XVIII alpha 1 chain
Synonyms-KNO|KNO1|KS
Cytomap

22q13.1

21q22.3

Type of geneprotein-codingprotein-coding
Descriptiontrinucleotide repeat-containing gene 6B proteintrinucleotide repeat containing 6Bcollagen alpha-1(XVIII) chainantiangiogenic agentcollagen alpha-1(XVIII) chain isoform 1 preproproteincollagen, type XVIII, alpha 1endostatinmulti-functional protein MFP
Modification date2020031320200313
UniProtAcc.

P39060

Ensembl transtripts involved in fusion geneENST00000301923, ENST00000402203, 
ENST00000454349, ENST00000335727, 
ENST00000497559, 		ENST00000400337, 
ENST00000355480, ENST00000359759, 
ENST00000459895, 
Fusion gene scores* DoF score36 X 24 X 16=138247 X 6 X 4=168
# samples 437
** MAII scorelog2(43/13824*10)=-5.00669465257401
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/168*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TNRC6B [Title/Abstract] AND COL18A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTNRC6B(40441002)-COL18A1(46888156), # 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 TNRC6B (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 COL18A1 (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
ChimerDB4BRCATCGA-B6-A0WY-01ATNRC6Bchr22

40441002

+COL18A1chr21

46888156

+


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Fusion Gene ORF analysis for TNRC6B-COL18A1

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
5UTR-3CDSENST00000301923ENST00000400337TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
5UTR-3CDSENST00000301923ENST00000355480TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
5UTR-3CDSENST00000301923ENST00000359759TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
5UTR-intronENST00000301923ENST00000459895TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-3CDSENST00000402203ENST00000400337TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-3CDSENST00000402203ENST00000355480TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-3CDSENST00000402203ENST00000359759TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-intronENST00000402203ENST00000459895TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-3CDSENST00000454349ENST00000400337TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-3CDSENST00000454349ENST00000355480TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-3CDSENST00000454349ENST00000359759TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-intronENST00000454349ENST00000459895TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-3CDSENST00000335727ENST00000400337TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-3CDSENST00000335727ENST00000355480TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-3CDSENST00000335727ENST00000359759TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-intronENST00000335727ENST00000459895TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-3CDSENST00000497559ENST00000400337TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-3CDSENST00000497559ENST00000355480TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-3CDSENST00000497559ENST00000359759TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+
intron-intronENST00000497559ENST00000459895TNRC6Bchr22

40441002

+COL18A1chr21

46888156

+

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 TNRC6B-COL18A1


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)
TNRC6Bchr2240441002+COL18A1chr2146888155+8.71E-101
TNRC6Bchr2240441002+COL18A1chr2146888155+8.71E-101

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 TNRC6B-COL18A1


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
.COL18A1

P39060

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: Probably plays a major role in determining the retinal structure as well as in the closure of the neural tube. {ECO:0000269|PubMed:10942434}.; FUNCTION: [Non-collagenous domain 1]: May regulate extracellular matrix-dependent motility and morphogenesis of endothelial and non-endothelial cells; the function requires homotrimerization and implicates MAPK signaling. {ECO:0000269|PubMed:11257123}.; FUNCTION: [Endostatin]: Potently inhibits endothelial cell proliferation and angiogenesis (PubMed:9459295). May inhibit angiogenesis by binding to the heparan sulfate proteoglycans involved in growth factor signaling (By similarity). Inhibits VEGFA-induced endothelial cell proliferation and migration. Seems to inhibit VEGFA-mediated signaling by blocking the interaction of VEGFA to its receptor KDR/VEGFR2. Modulates endothelial cell migration in an integrin-dependent manner implicating integrin ITGA5:ITGB1 and to a lesser extent ITGAV:ITGB3 and ITGAV:ITGB5 (By similarity). May negatively regulate the activity of homotrimeric non-collagenous domain 1 (PubMed:11257123). {ECO:0000250|UniProtKB:P39061, ECO:0000269|PubMed:11257123, ECO:0000269|PubMed:9459295}.

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 TNRC6B-COL18A1


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 TNRC6B-COL18A1


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 TNRC6B-COL18A1


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 TNRC6B-COL18A1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTNRC6BC0032460Polycystic Ovary Syndrome1CTD_human
HgeneTNRC6BC1136382Sclerocystic Ovaries1CTD_human
HgeneTNRC6BC1535926Neurodevelopmental Disorders1CTD_human
TgeneCOL18A1C4551775Knobloch Syndrome, Type I3CTD_human;GENOMICS_ENGLAND
TgeneCOL18A1C1849409Knobloch syndrome2CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneCOL18A1C0006663Calcinosis1CTD_human
TgeneCOL18A1C0018824Heart valve disease1CTD_human
TgeneCOL18A1C0018923Hemangiosarcoma1CTD_human
TgeneCOL18A1C0020796Profound Mental Retardation1CTD_human
TgeneCOL18A1C0025363Mental Retardation, Psychosocial1CTD_human
TgeneCOL18A1C0263628Tumoral calcinosis1CTD_human
TgeneCOL18A1C0521174Microcalcification1CTD_human
TgeneCOL18A1C0917816Mental deficiency1CTD_human
TgeneCOL18A1C3714756Intellectual Disability1CTD_human