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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:COL6A1-CLCN3 (FusionGDB2 ID:HG1291TG1182)

Fusion Gene Summary for COL6A1-CLCN3

check button Fusion gene summary
Fusion gene informationFusion gene name: COL6A1-CLCN3
Fusion gene ID: hg1291tg1182
HgeneTgene
Gene symbol

COL6A1

CLCN3

Gene ID

1291

1182

Gene namecollagen type VI alpha 1 chainchloride voltage-gated channel 3
SynonymsBTHLM1|OPLL|UCHMD1CLC3|ClC-3
Cytomap('COL6A1')('CLCN3')

21q22.3

4q33

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-1(VI) chainalpha 1 (VI) chain (61 AA)collagen VI, alpha-1 polypeptidecollagen, type VI, alpha 1epididymis secretory sperm binding proteinH(+)/Cl(-) exchange transporter 3chloride channel 3chloride channel protein 3chloride channel, voltage-sensitive 3chloride transporter ClC-3
Modification date2020032820200313
UniProtAcc

P12109

P51790

Ensembl transtripts involved in fusion geneENST00000361866, ENST00000498614, 
Fusion gene scores* DoF score13 X 12 X 8=124837 X 5 X 19=3515
# samples 1537
** MAII scorelog2(15/1248*10)=-3.05658352836637
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(37/3515*10)=-3.24792751344359
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COL6A1 [Title/Abstract] AND CLCN3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOL6A1(47424962)-CLCN3(170623929), # 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
TgeneCLCN3

GO:1902476

chloride transmembrane transport

11274166



check button Fusion gene information
* 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
ChimerDB4COADTCGA-G4-6626-01ACOL6A1chr21

47424962

-CLCN3chr4

170623929

+


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Fusion Gene ORF analysis for COL6A1-CLCN3

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-intronENST00000361866ENST00000347613COL6A1chr21

47424962

-CLCN3chr4

170623929

+
5CDS-intronENST00000361866ENST00000360642COL6A1chr21

47424962

-CLCN3chr4

170623929

+
5CDS-intronENST00000361866ENST00000504131COL6A1chr21

47424962

-CLCN3chr4

170623929

+
5CDS-intronENST00000361866ENST00000506924COL6A1chr21

47424962

-CLCN3chr4

170623929

+
5CDS-intronENST00000361866ENST00000513761COL6A1chr21

47424962

-CLCN3chr4

170623929

+
5CDS-intronENST00000498614ENST00000347613COL6A1chr21

47424962

-CLCN3chr4

170623929

+
5CDS-intronENST00000498614ENST00000360642COL6A1chr21

47424962

-CLCN3chr4

170623929

+
5CDS-intronENST00000498614ENST00000504131COL6A1chr21

47424962

-CLCN3chr4

170623929

+
5CDS-intronENST00000498614ENST00000506924COL6A1chr21

47424962

-CLCN3chr4

170623929

+
5CDS-intronENST00000498614ENST00000513761COL6A1chr21

47424962

-CLCN3chr4

170623929

+

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 COL6A1-CLCN3


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 COL6A1-CLCN3


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/:47424962/:170623929)
- 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
COL6A1

P12109

CLCN3

P51790

FUNCTION: Collagen VI acts as a cell-binding protein.FUNCTION: [Isoform 1]: Strongly outwardly rectifying, electrogenic H(+)/Cl(-)exchanger which mediates the exchange of chloride ions against protons (By similarity). The CLC channel family contains both chloride channels and proton-coupled anion transporters that exchange chloride or another anion for protons (PubMed:29845874). The presence of conserved gating glutamate residues is typical for family members that function as antiporters (PubMed:29845874). {ECO:0000250|UniProtKB:P51791, ECO:0000303|PubMed:29845874}.; FUNCTION: [Isoform 2]: Strongly outwardly rectifying, electrogenic H(+)/Cl(-)exchanger which mediates the exchange of chloride ions against protons. {ECO:0000269|PubMed:11967229}.

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 COL6A1-CLCN3


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 COL6A1-CLCN3


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 COL6A1-CLCN3


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 COL6A1-CLCN3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL6A1C1834674BETHLEM MYOPATHY 17CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCOL6A1C0410179Ullrich congenital muscular dystrophy 16CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL6A1C0000786Spontaneous abortion1CTD_human
HgeneCOL6A1C0000822Abortion, Tubal1CTD_human
HgeneCOL6A1C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneCOL6A1C0024121Lung Neoplasms1CTD_human
HgeneCOL6A1C0026850Muscular Dystrophy1CTD_human
HgeneCOL6A1C0242379Malignant neoplasm of lung1CTD_human
HgeneCOL6A1C1135196Heart Failure, Diastolic1CTD_human
HgeneCOL6A1C3830362Early Pregnancy Loss1CTD_human
HgeneCOL6A1C4552766Miscarriage1CTD_human
TgeneC0017638Glioma1CTD_human
TgeneC0024623Malignant neoplasm of stomach1CTD_human
TgeneC0038356Stomach Neoplasms1CTD_human
TgeneC0235874Disease Exacerbation1CTD_human
TgeneC0259783mixed gliomas1CTD_human
TgeneC0555198Malignant Glioma1CTD_human
TgeneC1708349Hereditary Diffuse Gastric Cancer1CTD_human
TgeneC2931822Nasopharyngeal carcinoma1CTD_human