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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:LAMA3-TTC39C (FusionGDB2 ID:43886)

Fusion Gene Summary for LAMA3-TTC39C

check button Fusion gene summary
Fusion gene informationFusion gene name: LAMA3-TTC39C
Fusion gene ID: 43886
HgeneTgene
Gene symbol

LAMA3

TTC39C

Gene ID

3910

125488

Gene namelaminin subunit alpha 4tetratricopeptide repeat domain 39C
SynonymsCMD1JJ|LAMA3|LAMA4*-1C18orf17|HsT2697
Cytomap

6q21

18q11.2

Type of geneprotein-codingprotein-coding
Descriptionlaminin subunit alpha-4laminin alpha 4 chainlaminin, alpha 4tetratricopeptide repeat protein 39CTPR repeat protein 39C
Modification date2020031320200313
UniProtAcc

Q16787

.
Ensembl transtripts involved in fusion geneENST00000588770, ENST00000269217, 
ENST00000313654, ENST00000399516, 
ENST00000587184, 		ENST00000578150, 
ENST00000304621, ENST00000317571, 
ENST00000540918, ENST00000577185, 
ENST00000584250, 
Fusion gene scores* DoF score28 X 24 X 10=672011 X 8 X 8=704
# samples 3312
** MAII scorelog2(33/6720*10)=-4.34792330342031
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/704*10)=-2.55254102302878
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LAMA3 [Title/Abstract] AND TTC39C [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLAMA3(21529888)-TTC39C(21644104), # samples:2
TTC39C(21663045)-LAMA3(21526108), # samples:2
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 LAMA3 (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 TTC39C (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
ChimerDB4HNSCTCGA-BA-4075-01ALAMA3chr18

21529888

+TTC39Cchr18

21644104

+
ChimerDB4HNSCTCGA-BA-4075LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
ChiTaRS5.0N/ABG575748LAMA3chr18

21307399

+TTC39Cchr18

21714352

+


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Fusion Gene ORF analysis for LAMA3-TTC39C

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
3UTR-3UTRENST00000588770ENST00000578150LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
3UTR-5UTRENST00000588770ENST00000304621LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
3UTR-5UTRENST00000588770ENST00000317571LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
3UTR-intronENST00000588770ENST00000540918LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
3UTR-intronENST00000588770ENST00000577185LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
3UTR-intronENST00000588770ENST00000584250LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-3UTRENST00000269217ENST00000578150LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-3UTRENST00000313654ENST00000578150LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-3UTRENST00000399516ENST00000578150LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-3UTRENST00000587184ENST00000578150LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-5UTRENST00000269217ENST00000304621LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-5UTRENST00000269217ENST00000317571LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-5UTRENST00000313654ENST00000304621LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-5UTRENST00000313654ENST00000317571LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-5UTRENST00000399516ENST00000304621LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-5UTRENST00000399516ENST00000317571LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-5UTRENST00000587184ENST00000304621LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-5UTRENST00000587184ENST00000317571LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-intronENST00000269217ENST00000540918LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-intronENST00000269217ENST00000577185LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-intronENST00000269217ENST00000584250LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-intronENST00000313654ENST00000540918LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-intronENST00000313654ENST00000577185LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-intronENST00000313654ENST00000584250LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-intronENST00000399516ENST00000540918LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-intronENST00000399516ENST00000577185LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-intronENST00000399516ENST00000584250LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-intronENST00000587184ENST00000540918LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-intronENST00000587184ENST00000577185LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
5CDS-intronENST00000587184ENST00000584250LAMA3chr18

21529888

+TTC39Cchr18

21644104

+
intron-3UTRENST00000269217ENST00000540918LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-3UTRENST00000313654ENST00000540918LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-3UTRENST00000399516ENST00000540918LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-3UTRENST00000587184ENST00000540918LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-3UTRENST00000588770ENST00000540918LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000269217ENST00000304621LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000269217ENST00000317571LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000269217ENST00000577185LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000269217ENST00000578150LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000269217ENST00000584250LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000313654ENST00000304621LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000313654ENST00000317571LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000313654ENST00000577185LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000313654ENST00000578150LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000313654ENST00000584250LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000399516ENST00000304621LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000399516ENST00000317571LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000399516ENST00000577185LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000399516ENST00000578150LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000399516ENST00000584250LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000587184ENST00000304621LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000587184ENST00000317571LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000587184ENST00000577185LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000587184ENST00000578150LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000587184ENST00000584250LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000588770ENST00000304621LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000588770ENST00000317571LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000588770ENST00000577185LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000588770ENST00000578150LAMA3chr18

21307399

+TTC39Cchr18

21714352

+
intron-intronENST00000588770ENST00000584250LAMA3chr18

21307399

+TTC39Cchr18

21714352

+

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 LAMA3-TTC39C


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)
LAMA3chr1821529888+TTC39Cchr1821644103+0.0451146620.9548853
LAMA3chr1821529888+TTC39Cchr1821644103+0.0451146620.9548853
LAMA3chr1821529888+TTC39Cchr1821644103+0.0451146620.9548853
LAMA3chr1821529888+TTC39Cchr1821644103+0.0451146620.9548853

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.
genomic feature of top 1%

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Fusion Protein Features for LAMA3-TTC39C


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/:21529888/:21644104)
- 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
LAMA3

Q16787

.
FUNCTION: Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components.; FUNCTION: Laminin-5 is thought to be involved in (1) cell adhesion via integrin alpha-3/beta-1 in focal adhesion and integrin alpha-6/beta-4 in hemidesmosomes, (2) signal transduction via tyrosine phosphorylation of pp125-FAK and p80, (3) differentiation of keratinocytes.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 LAMA3-TTC39C


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 LAMA3-TTC39C


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 LAMA3-TTC39C


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 LAMA3-TTC39C


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource