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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-LGMN (FusionGDB2 ID:18460)

Fusion Gene Summary for COL6A3-LGMN

check button Fusion gene summary
Fusion gene informationFusion gene name: COL6A3-LGMN
Fusion gene ID: 18460
HgeneTgene
Gene symbol

COL6A3

LGMN

Gene ID

1293

5641

Gene namecollagen type VI alpha 3 chainlegumain
SynonymsBTHLM1|DYT27|UCMD1AEP|LGMN1|PRSC1
Cytomap

2q37.3

14q32.12

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-3(VI) chaincollagen VI, alpha-3 polypeptidecollagen, type VI, alpha 3epididymis secretory sperm binding proteinlegumainasparaginyl endopeptidasecysteine protease 1protease, cysteine 1protease, cysteine, 1 (legumain)
Modification date2020032820200313
UniProtAcc.

Q99538

Ensembl transtripts involved in fusion geneENST00000347401, ENST00000353578, 
ENST00000295550, ENST00000472056, 
ENST00000409809, ENST00000346358, 
ENST00000392004, ENST00000392003, 
ENST00000473258, 		ENST00000555699, 
ENST00000334869, ENST00000557434, 
ENST00000393218, ENST00000557034, 
Fusion gene scores* DoF score13 X 12 X 6=9369 X 8 X 4=288
# samples 139
** MAII scorelog2(13/936*10)=-2.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/288*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

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

Most frequent breakpointCOL6A3(238232742)-LGMN(93178236), # 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
TgeneLGMN

GO:0010447

response to acidic pH

18374643

TgeneLGMN

GO:0035729

cellular response to hepatocyte growth factor stimulus

21237226

TgeneLGMN

GO:0071277

cellular response to calcium ion

21237226

TgeneLGMN

GO:0090026

positive regulation of monocyte chemotaxis

18377911

TgeneLGMN

GO:0097202

activation of cysteine-type endopeptidase activity

9821970|18374643

TgeneLGMN

GO:0097264

self proteolysis

9821970|18374643

TgeneLGMN

GO:1904646

cellular response to amyloid-beta

25326800

TgeneLGMN

GO:2001028

positive regulation of endothelial cell chemotaxis

18377911


check buttonFusion gene breakpoints across COL6A3 (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 LGMN (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
ChiTaRS5.0N/AAW450755COL6A3chr2

238232742

+LGMNchr14

93178236

+


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Fusion Gene ORF analysis for COL6A3-LGMN

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-3CDSENST00000347401ENST00000555699COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000347401ENST00000334869COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000347401ENST00000557434COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000347401ENST00000393218COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-intronENST00000347401ENST00000557034COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000353578ENST00000555699COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000353578ENST00000334869COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000353578ENST00000557434COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000353578ENST00000393218COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-intronENST00000353578ENST00000557034COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000295550ENST00000555699COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000295550ENST00000334869COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000295550ENST00000557434COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000295550ENST00000393218COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-intronENST00000295550ENST00000557034COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000472056ENST00000555699COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000472056ENST00000334869COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000472056ENST00000557434COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000472056ENST00000393218COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-intronENST00000472056ENST00000557034COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000409809ENST00000555699COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000409809ENST00000334869COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000409809ENST00000557434COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000409809ENST00000393218COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-intronENST00000409809ENST00000557034COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000346358ENST00000555699COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000346358ENST00000334869COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000346358ENST00000557434COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000346358ENST00000393218COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-intronENST00000346358ENST00000557034COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000392004ENST00000555699COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000392004ENST00000334869COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000392004ENST00000557434COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000392004ENST00000393218COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-intronENST00000392004ENST00000557034COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000392003ENST00000555699COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000392003ENST00000334869COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000392003ENST00000557434COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000392003ENST00000393218COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-intronENST00000392003ENST00000557034COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000473258ENST00000555699COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000473258ENST00000334869COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000473258ENST00000557434COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-3CDSENST00000473258ENST00000393218COL6A3chr2

238232742

+LGMNchr14

93178236

+
intron-intronENST00000473258ENST00000557034COL6A3chr2

238232742

+LGMNchr14

93178236

+

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-LGMN


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 COL6A3-LGMN


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
.LGMN

Q99538

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: Has a strict specificity for hydrolysis of asparaginyl bonds. Can also cleave aspartyl bonds slowly, especially under acidic conditions. Required for normal lysosomal protein degradation in renal proximal tubules. Required for normal degradation of internalized EGFR. Plays a role in the regulation of cell proliferation via its role in EGFR degradation (By similarity). May be involved in the processing of proteins for MHC class II antigen presentation in the lysosomal/endosomal system. {ECO:0000250, ECO:0000269|PubMed:23776206}.

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-LGMN


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-LGMN


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-LGMN


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-LGMN


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
TgeneLGMNC0023893Liver Cirrhosis, Experimental1CTD_human