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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:TGFBR3-LRTM1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: TGFBR3-LRTM1
FusionPDB ID: 90477
FusionGDB2.0 ID: 90477
HgeneTgene
Gene symbol

TGFBR3

LRTM1

Gene ID

7049

57408

Gene nametransforming growth factor beta receptor 3leucine rich repeats and transmembrane domains 1
SynonymsBGCAN|betaglycanHT017
Cytomap

1p22.1

3p14.3

Type of geneprotein-codingprotein-coding
Descriptiontransforming growth factor beta receptor type 3TGF-beta receptor type 3TGF-beta receptor type IIITGFR-3betaglycan proteoglycantransforming growth factor beta receptor IIIleucine-rich repeat and transmembrane domain-containing protein 1
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000212355, ENST00000370399, 
ENST00000525962, ENST00000468996, 
ENST00000493075, ENST00000273286, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 13 X 6=10923 X 2 X 3=18
# samples 154
** MAII scorelog2(15/1092*10)=-2.86393845042397
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/18*10)=1.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: TGFBR3 [Title/Abstract] AND LRTM1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)TGFBR3(92174220)-LRTM1(54959242), # samples:2
Anticipated loss of major functional domain due to fusion event.TGFBR3-LRTM1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
TGFBR3-LRTM1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
TGFBR3-LRTM1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
TGFBR3-LRTM1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
* 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
HgeneTGFBR3

GO:0001837

epithelial to mesenchymal transition

18184661

HgeneTGFBR3

GO:0007179

transforming growth factor beta receptor signaling pathway

12958365

HgeneTGFBR3

GO:0030509

BMP signaling pathway

18184661

HgeneTGFBR3

GO:0032354

response to follicle-stimulating hormone

14557487

HgeneTGFBR3

GO:0034695

response to prostaglandin E

14557487

HgeneTGFBR3

GO:0034699

response to luteinizing hormone

14557487

HgeneTGFBR3

GO:0051271

negative regulation of cellular component movement

17999987

HgeneTGFBR3

GO:0060317

cardiac epithelial to mesenchymal transition

18184661


check buttonFusion gene breakpoints across TGFBR3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across LRTM1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4OVTCGA-30-1861-01ATGFBR3chr1

92174220

-LRTM1chr3

54959242

-
ChimerDB4OVTCGA-30-1861TGFBR3chr1

92174219

-LRTM1chr3

54959242

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000525962TGFBR3chr192174220-ENST00000273286LRTM1chr354959242-360223496233791105
ENST00000525962TGFBR3chr192174219-ENST00000273286LRTM1chr354959242-360223496233791105

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
ENST00000525962ENST00000273286TGFBR3chr192174220-LRTM1chr354959242-0.0002319260.9997681
ENST00000525962ENST00000273286TGFBR3chr192174219-LRTM1chr354959242-0.0002319260.9997681

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>90477_90477_1_TGFBR3-LRTM1_TGFBR3_chr1_92174219_ENST00000525962_LRTM1_chr3_54959242_ENST00000273286_length(amino acids)=1105AA_BP=762
MTSHYVIAIFALMSSCLATAGPEPGALCELSPVSASHPVQALMESFTVLSGCASRGTTGLPQEVHVLNLRTAGQGPGQLQREVTLHLNPI
SSVHIHHKSVVFLLNSPHPLVWHLKTERLATGVSRLFLVSEGSVVQFSSANFSLTAETEERNFPHGNEHLLNWARKEYGAVTSFTELKIA
RNIYIKVGEDQVFPPKCNIGKNFLSLNYLAEYLQPKAAEGCVMSSQPQNEEVHIIELITPNSNPYSAFQVDITIDIRPSQEDLEVVKNLI
LILKCKKSVNWVIKSFDVKGSLKIIAPNSIGFGKESERSMTMTKSIRDDIPSTQGNLVKWALDNGYSPITSYTMAPVANRFHLRLENNAE
EMGDEEVHTIPPELRILLDPGALPALQNPPIRGGEGQNGGLPFPFPDISRRVWNEEGEDGLPRPKDPVIPSIQLFPGLREPEEVQGSVDI
ALSVKCDNEKMIVAVEKDSFQASGYSGMDVTLLDPTCKAKMNGTHFVLESPLNGCGTRPRWSALDGVVYYNSIVIQVPALGDSSGWPDGY
EDLESGDNGFPGDMDEGDASLFTRPEIVVFNCSLQQVRNPSSFQEQPHGNITFNMELYNTDLFLVPSQGVFSVPENGHVYVEVSVTKAEQ
ELGFAIQTCFISPYSNPDRMSHYTIIENICPKDESVKFYSPKRVHFPIPQADMDKKRFSFVFKPVFNTSLLFLQCELTLCTKMEKHPQKL
PKCVPPDEACTSLDASIIWAMMQNKKTFTKPLAVIHHEAESKGELLLFSSVIVLLQVVCSCPDKCYCQSSTNFVDCSQQGLAEIPSHLPP
QTRTLHLQDNQIHHLPAFAFRSVPWLMTLNLSNNSLSNLAPGAFHGLQHLQVLNLTQNSLLSLESRLFHSLPQLRELDLSSNNISHLPTS
LGETWENLTILAVQQNQLQQLDRALLESMPSVRLLLLKDNLWKCNCHLLGLKLWLEKFVYKGGLTDGIICESPDTWKGKDLLRIPHELYQ
PCPLPAPDPVSSQAQWPGSAHGVVLRPPENHNAGERELLECELKPKPRPANLRHAIATVIITGVVCGIVCLMMLAAAIYGCTYAAITAQY

--------------------------------------------------------------

>90477_90477_2_TGFBR3-LRTM1_TGFBR3_chr1_92174220_ENST00000525962_LRTM1_chr3_54959242_ENST00000273286_length(amino acids)=1105AA_BP=762
MTSHYVIAIFALMSSCLATAGPEPGALCELSPVSASHPVQALMESFTVLSGCASRGTTGLPQEVHVLNLRTAGQGPGQLQREVTLHLNPI
SSVHIHHKSVVFLLNSPHPLVWHLKTERLATGVSRLFLVSEGSVVQFSSANFSLTAETEERNFPHGNEHLLNWARKEYGAVTSFTELKIA
RNIYIKVGEDQVFPPKCNIGKNFLSLNYLAEYLQPKAAEGCVMSSQPQNEEVHIIELITPNSNPYSAFQVDITIDIRPSQEDLEVVKNLI
LILKCKKSVNWVIKSFDVKGSLKIIAPNSIGFGKESERSMTMTKSIRDDIPSTQGNLVKWALDNGYSPITSYTMAPVANRFHLRLENNAE
EMGDEEVHTIPPELRILLDPGALPALQNPPIRGGEGQNGGLPFPFPDISRRVWNEEGEDGLPRPKDPVIPSIQLFPGLREPEEVQGSVDI
ALSVKCDNEKMIVAVEKDSFQASGYSGMDVTLLDPTCKAKMNGTHFVLESPLNGCGTRPRWSALDGVVYYNSIVIQVPALGDSSGWPDGY
EDLESGDNGFPGDMDEGDASLFTRPEIVVFNCSLQQVRNPSSFQEQPHGNITFNMELYNTDLFLVPSQGVFSVPENGHVYVEVSVTKAEQ
ELGFAIQTCFISPYSNPDRMSHYTIIENICPKDESVKFYSPKRVHFPIPQADMDKKRFSFVFKPVFNTSLLFLQCELTLCTKMEKHPQKL
PKCVPPDEACTSLDASIIWAMMQNKKTFTKPLAVIHHEAESKGELLLFSSVIVLLQVVCSCPDKCYCQSSTNFVDCSQQGLAEIPSHLPP
QTRTLHLQDNQIHHLPAFAFRSVPWLMTLNLSNNSLSNLAPGAFHGLQHLQVLNLTQNSLLSLESRLFHSLPQLRELDLSSNNISHLPTS
LGETWENLTILAVQQNQLQQLDRALLESMPSVRLLLLKDNLWKCNCHLLGLKLWLEKFVYKGGLTDGIICESPDTWKGKDLLRIPHELYQ
PCPLPAPDPVSSQAQWPGSAHGVVLRPPENHNAGERELLECELKPKPRPANLRHAIATVIITGVVCGIVCLMMLAAAIYGCTYAAITAQY

--------------------------------------------------------------

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Fusion Protein Functional Features


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/chr1:92174220/chr3:54959242)
- 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
..
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: 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.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTGFBR3chr1:92174219chr3:54959242ENST00000212355-1417455_730762.3333333333334852.0DomainZP
HgeneTGFBR3chr1:92174219chr3:54959242ENST00000370399-1518455_730761.3333333333334851.0DomainZP
HgeneTGFBR3chr1:92174219chr3:54959242ENST00000525962-1316455_730762.3333333333334852.0DomainZP
HgeneTGFBR3chr1:92174220chr3:54959242ENST00000212355-1417455_730762.3333333333334852.0DomainZP
HgeneTGFBR3chr1:92174220chr3:54959242ENST00000370399-1518455_730761.3333333333334851.0DomainZP
HgeneTGFBR3chr1:92174220chr3:54959242ENST00000525962-1316455_730762.3333333333334852.0DomainZP
TgeneLRTM1chr1:92174219chr3:54959242ENST0000027328603180_2342.3333333333333335346.0DomainNote=LRRCT
TgeneLRTM1chr1:92174219chr3:54959242ENST000002732860328_502.3333333333333335346.0DomainNote=LRRNT
TgeneLRTM1chr1:92174219chr3:54959242ENST0000049307503180_2340270.0DomainNote=LRRCT
TgeneLRTM1chr1:92174219chr3:54959242ENST000004930750328_500270.0DomainNote=LRRNT
TgeneLRTM1chr1:92174220chr3:54959242ENST0000027328603180_2342.3333333333333335346.0DomainNote=LRRCT
TgeneLRTM1chr1:92174220chr3:54959242ENST000002732860328_502.3333333333333335346.0DomainNote=LRRNT
TgeneLRTM1chr1:92174220chr3:54959242ENST0000049307503180_2340270.0DomainNote=LRRCT
TgeneLRTM1chr1:92174220chr3:54959242ENST000004930750328_500270.0DomainNote=LRRNT
TgeneLRTM1chr1:92174219chr3:54959242ENST0000027328603123_1442.3333333333333335346.0RepeatNote=LRR 4
TgeneLRTM1chr1:92174219chr3:54959242ENST0000027328603147_1682.3333333333333335346.0RepeatNote=LRR 5
TgeneLRTM1chr1:92174219chr3:54959242ENST000002732860351_722.3333333333333335346.0RepeatNote=LRR 1
TgeneLRTM1chr1:92174219chr3:54959242ENST000002732860375_962.3333333333333335346.0RepeatNote=LRR 2
TgeneLRTM1chr1:92174219chr3:54959242ENST000002732860399_1202.3333333333333335346.0RepeatNote=LRR 3
TgeneLRTM1chr1:92174219chr3:54959242ENST0000049307503123_1440270.0RepeatNote=LRR 4
TgeneLRTM1chr1:92174219chr3:54959242ENST0000049307503147_1680270.0RepeatNote=LRR 5
TgeneLRTM1chr1:92174219chr3:54959242ENST000004930750351_720270.0RepeatNote=LRR 1
TgeneLRTM1chr1:92174219chr3:54959242ENST000004930750375_960270.0RepeatNote=LRR 2
TgeneLRTM1chr1:92174219chr3:54959242ENST000004930750399_1200270.0RepeatNote=LRR 3
TgeneLRTM1chr1:92174220chr3:54959242ENST0000027328603123_1442.3333333333333335346.0RepeatNote=LRR 4
TgeneLRTM1chr1:92174220chr3:54959242ENST0000027328603147_1682.3333333333333335346.0RepeatNote=LRR 5
TgeneLRTM1chr1:92174220chr3:54959242ENST000002732860351_722.3333333333333335346.0RepeatNote=LRR 1
TgeneLRTM1chr1:92174220chr3:54959242ENST000002732860375_962.3333333333333335346.0RepeatNote=LRR 2
TgeneLRTM1chr1:92174220chr3:54959242ENST000002732860399_1202.3333333333333335346.0RepeatNote=LRR 3
TgeneLRTM1chr1:92174220chr3:54959242ENST0000049307503123_1440270.0RepeatNote=LRR 4
TgeneLRTM1chr1:92174220chr3:54959242ENST0000049307503147_1680270.0RepeatNote=LRR 5
TgeneLRTM1chr1:92174220chr3:54959242ENST000004930750351_720270.0RepeatNote=LRR 1
TgeneLRTM1chr1:92174220chr3:54959242ENST000004930750375_960270.0RepeatNote=LRR 2
TgeneLRTM1chr1:92174220chr3:54959242ENST000004930750399_1200270.0RepeatNote=LRR 3
TgeneLRTM1chr1:92174219chr3:54959242ENST000002732860328_2882.3333333333333335346.0Topological domainExtracellular
TgeneLRTM1chr1:92174219chr3:54959242ENST0000027328603310_3452.3333333333333335346.0Topological domainCytoplasmic
TgeneLRTM1chr1:92174219chr3:54959242ENST000004930750328_2880270.0Topological domainExtracellular
TgeneLRTM1chr1:92174219chr3:54959242ENST0000049307503310_3450270.0Topological domainCytoplasmic
TgeneLRTM1chr1:92174220chr3:54959242ENST000002732860328_2882.3333333333333335346.0Topological domainExtracellular
TgeneLRTM1chr1:92174220chr3:54959242ENST0000027328603310_3452.3333333333333335346.0Topological domainCytoplasmic
TgeneLRTM1chr1:92174220chr3:54959242ENST000004930750328_2880270.0Topological domainExtracellular
TgeneLRTM1chr1:92174220chr3:54959242ENST0000049307503310_3450270.0Topological domainCytoplasmic
TgeneLRTM1chr1:92174219chr3:54959242ENST0000027328603289_3092.3333333333333335346.0TransmembraneHelical
TgeneLRTM1chr1:92174219chr3:54959242ENST0000049307503289_3090270.0TransmembraneHelical
TgeneLRTM1chr1:92174220chr3:54959242ENST0000027328603289_3092.3333333333333335346.0TransmembraneHelical
TgeneLRTM1chr1:92174220chr3:54959242ENST0000049307503289_3090270.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTGFBR3chr1:92174219chr3:54959242ENST00000212355-141721_787762.3333333333334852.0Topological domainExtracellular
HgeneTGFBR3chr1:92174219chr3:54959242ENST00000212355-1417810_851762.3333333333334852.0Topological domainCytoplasmic
HgeneTGFBR3chr1:92174219chr3:54959242ENST00000370399-151821_787761.3333333333334851.0Topological domainExtracellular
HgeneTGFBR3chr1:92174219chr3:54959242ENST00000370399-1518810_851761.3333333333334851.0Topological domainCytoplasmic
HgeneTGFBR3chr1:92174219chr3:54959242ENST00000525962-131621_787762.3333333333334852.0Topological domainExtracellular
HgeneTGFBR3chr1:92174219chr3:54959242ENST00000525962-1316810_851762.3333333333334852.0Topological domainCytoplasmic
HgeneTGFBR3chr1:92174220chr3:54959242ENST00000212355-141721_787762.3333333333334852.0Topological domainExtracellular
HgeneTGFBR3chr1:92174220chr3:54959242ENST00000212355-1417810_851762.3333333333334852.0Topological domainCytoplasmic
HgeneTGFBR3chr1:92174220chr3:54959242ENST00000370399-151821_787761.3333333333334851.0Topological domainExtracellular
HgeneTGFBR3chr1:92174220chr3:54959242ENST00000370399-1518810_851761.3333333333334851.0Topological domainCytoplasmic
HgeneTGFBR3chr1:92174220chr3:54959242ENST00000525962-131621_787762.3333333333334852.0Topological domainExtracellular
HgeneTGFBR3chr1:92174220chr3:54959242ENST00000525962-1316810_851762.3333333333334852.0Topological domainCytoplasmic
HgeneTGFBR3chr1:92174219chr3:54959242ENST00000212355-1417788_809762.3333333333334852.0TransmembraneHelical
HgeneTGFBR3chr1:92174219chr3:54959242ENST00000370399-1518788_809761.3333333333334851.0TransmembraneHelical
HgeneTGFBR3chr1:92174219chr3:54959242ENST00000525962-1316788_809762.3333333333334852.0TransmembraneHelical
HgeneTGFBR3chr1:92174220chr3:54959242ENST00000212355-1417788_809762.3333333333334852.0TransmembraneHelical
HgeneTGFBR3chr1:92174220chr3:54959242ENST00000370399-1518788_809761.3333333333334851.0TransmembraneHelical
HgeneTGFBR3chr1:92174220chr3:54959242ENST00000525962-1316788_809762.3333333333334852.0TransmembraneHelical


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
TGFBR3
LRTM1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to TGFBR3-LRTM1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to TGFBR3-LRTM1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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