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level2

	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:TFE3-PRCC

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: TFE3-PRCC
	FusionPDB ID: 90319
	FusionGDB2.0 ID: 90319
		Hgene	Tgene
	Gene symbol	TFE3	PRCC
	Gene ID	7030	5546
	Gene name	transcription factor binding to IGHM enhancer 3	proline rich mitotic checkpoint control factor
	Synonyms	RCCP2\|RCCX1\|TFEA\|bHLHe33	RCCP1\|TPRC
	Cytomap	Xp11.23	1q23.1
	Type of gene	protein-coding	protein-coding
	Description	transcription factor E3class E basic helix-loop-helix protein 33transcription factor E family, member Atranscription factor for IgH enhancertranscription factor for immunoglobulin heavy-chain enhancer 3	proline-rich protein PRCCPRCC, proline rich mitotic checkpoint control factorpapillary renal cell carcinoma (translocation-associated)papillary renal cell carcinoma translocation-associated gene protein
	Modification date	20200327	20200313
	UniProtAcc	P19532	Q92733
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000315869, ENST00000487451,	ENST00000491853, ENST00000271526, ENST00000353233,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	9 X 12 X 6=648	7 X 10 X 4=280
	# samples	12	12
	** MAII score	log2(12/648*10)=-2.43295940727611 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(12/280*10)=-1.22239242133645 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: TFE3 [Title/Abstract] AND PRCC [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PRCC(156738031)-TFE3(48895967), # samples:12 TFE3(48896632)-PRCC(156752074), # samples:3
Anticipated loss of major functional domain due to fusion event.	PRCC-TFE3 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. PRCC-TFE3 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. TFE3-PRCC 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. TFE3-PRCC 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. TFE3-PRCC 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. TFE3-PRCC 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. PRCC-TFE3 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. PRCC-TFE3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. PRCC-TFE3 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF. PRCC-TFE3 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. PRCC-TFE3 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	PRCC	GO:0007093	mitotic cell cycle checkpoint	11717438

Fusion gene breakpoints across TFE3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	KIRP	TCGA-BQ-5882-01A	TFE3	chrX	48896632	-	PRCC	chr1	156752074	+
ChimerDB4	KIRP	TCGA-BQ-5882	TFE3	chrX	48896631	-	PRCC	chr1	156752073	+
ChimerDB4	KIRP	TCGA-BQ-5882	TFE3	chrX	48896632	-	PRCC	chr1	156752074	+
ChimerDB4	KIRP	TCGA-BQ-5887-01A	TFE3	chrX	48896632	-	PRCC	chr1	156756400	+
ChimerDB4	KIRP	TCGA-BQ-5887	TFE3	chrX	48896631	-	PRCC	chr1	156756399	+
ChimerKB3	.	.	TFE3	chrX	156738031	-	PRCC	chr1	48895967	+

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000315869	TFE3	chrX	48896632	-	ENST00000271526	PRCC	chr1	156752074	+	2157	794	260	1801	513
ENST00000315869	TFE3	chrX	48896632	-	ENST00000353233	PRCC	chr1	156752074	+	2056	794	260	1705	481
ENST00000315869	TFE3	chrX	48896632	-	ENST00000271526	PRCC	chr1	156756400	+	2109	794	260	1753	497
ENST00000315869	TFE3	chrX	48896632	-	ENST00000353233	PRCC	chr1	156756400	+	2008	794	260	1657	465
ENST00000315869	TFE3	chrX	48896631	-	ENST00000271526	PRCC	chr1	156752073	+	2157	794	260	1801	513
ENST00000315869	TFE3	chrX	48896631	-	ENST00000353233	PRCC	chr1	156752073	+	2056	794	260	1705	481
ENST00000315869	TFE3	chrX	48896631	-	ENST00000271526	PRCC	chr1	156756399	+	2109	794	260	1753	497
ENST00000315869	TFE3	chrX	48896631	-	ENST00000353233	PRCC	chr1	156756399	+	2008	794	260	1657	465

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000315869	ENST00000271526	TFE3	chrX	48896632	-	PRCC	chr1	156752074	+	0.007903203	0.9920968
ENST00000315869	ENST00000353233	TFE3	chrX	48896632	-	PRCC	chr1	156752074	+	0.00957593	0.9904241
ENST00000315869	ENST00000271526	TFE3	chrX	48896632	-	PRCC	chr1	156756400	+	0.009882505	0.9901175
ENST00000315869	ENST00000353233	TFE3	chrX	48896632	-	PRCC	chr1	156756400	+	0.012539086	0.9874609
ENST00000315869	ENST00000271526	TFE3	chrX	48896631	-	PRCC	chr1	156752073	+	0.007903203	0.9920968
ENST00000315869	ENST00000353233	TFE3	chrX	48896631	-	PRCC	chr1	156752073	+	0.00957593	0.9904241
ENST00000315869	ENST00000271526	TFE3	chrX	48896631	-	PRCC	chr1	156756399	+	0.009882505	0.9901175
ENST00000315869	ENST00000353233	TFE3	chrX	48896631	-	PRCC	chr1	156756399	+	0.012539086	0.9874609

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Fusion Amino Acid Sequences

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

>90319_90319_1_TFE3-PRCC_TFE3_chrX_48896631_ENST00000315869_PRCC_chr1_156752073_ENST00000271526_length(amino acids)=513AA_BP=57
MSHAAEPARDGVEASAEGPRAVFVLLEERRPADSAQLLSLNSLLPESGIVADIELENVLDPDSFYELKSQPLPLRSSLPISLQATPATPA
TLSASSSAGGSRTPAMSSSSSSRVLLRQQLMRAQAQEQERRERREQAAAAPFPSPAPASPAISVVGVSAGGHTLSRPPPAQVPREVLKSD
SEEDEPTKKKTILQGSSEGTGLSALLPQPKNLTVKETNRLLLPHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAA
AKSAALQVTKQITQEEDDSDEEVAPENFFSLPEKAEPPGVEPYPYPIPTVPEELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKP
GDDYSYNQFSTYGDANAAGAYYQDYYSGGYYPAQDPALVPPQEIAPDASFIDDEAFKRLQGKRNRGREEINFVEIKGDDQLSGAQQWMTK

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

>90319_90319_2_TFE3-PRCC_TFE3_chrX_48896631_ENST00000315869_PRCC_chr1_156752073_ENST00000353233_length(amino acids)=481AA_BP=57
MSHAAEPARDGVEASAEGPRAVFVLLEERRPADSAQLLSLNSLLPESGIVADIELENVLDPDSFYELKSQPLPLRSSLPISLQATPATPA
TLSASSSAGGSRTPAMSSSSSSRVLLRQQLMRAQAQEQERRERREQAAAAPFPSPAPASPAISVVGVSAGGHTLSRPPPAQVPREVLKSD
SEEDEPTKKKTILQGSSEGTGLSALLPQPKNLTVKETNRLLLPHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAA
AKSAALQVTKQITQEEDDSDEEVAPENFFSLPEKAEPPGVEPYPYPIPTVPEELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKP
GDDYSYNQFSTYGDANAAGAYYQFKRLQGKRNRGREEINFVEIKGDDQLSGAQQWMTKSLTEEKTMKSFSKKKGEQPTGQQRRKHQITYL

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

>90319_90319_3_TFE3-PRCC_TFE3_chrX_48896631_ENST00000315869_PRCC_chr1_156756399_ENST00000271526_length(amino acids)=497AA_BP=57
MSHAAEPARDGVEASAEGPRAVFVLLEERRPADSAQLLSLNSLLPESGIVADIELENVLDPDSFYELKSQPLPLRSSLPISLQATPATPA
TLSASSSAGGSRTPAMSSSSSSRVLLRQQLMRAQAQEQERRERREQAAAAPFPSPAPASPAISVVGVSAGGHTLSRPPPAQVPREVLKGS
SEGTGLSALLPQPKNLTVKETNRLLLPHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAAAKSAALQVTKQITQEE
DDSDEEVAPENFFSLPEKAEPPGVEPYPYPIPTVPEELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKPGDDYSYNQFSTYGDAN
AAGAYYQDYYSGGYYPAQDPALVPPQEIAPDASFIDDEAFKRLQGKRNRGREEINFVEIKGDDQLSGAQQWMTKSLTEEKTMKSFSKKKG

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

>90319_90319_4_TFE3-PRCC_TFE3_chrX_48896631_ENST00000315869_PRCC_chr1_156756399_ENST00000353233_length(amino acids)=465AA_BP=57
MSHAAEPARDGVEASAEGPRAVFVLLEERRPADSAQLLSLNSLLPESGIVADIELENVLDPDSFYELKSQPLPLRSSLPISLQATPATPA
TLSASSSAGGSRTPAMSSSSSSRVLLRQQLMRAQAQEQERRERREQAAAAPFPSPAPASPAISVVGVSAGGHTLSRPPPAQVPREVLKGS
SEGTGLSALLPQPKNLTVKETNRLLLPHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAAAKSAALQVTKQITQEE
DDSDEEVAPENFFSLPEKAEPPGVEPYPYPIPTVPEELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKPGDDYSYNQFSTYGDAN
AAGAYYQFKRLQGKRNRGREEINFVEIKGDDQLSGAQQWMTKSLTEEKTMKSFSKKKGEQPTGQQRRKHQITYLIHQAKERELELKNTWS

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

>90319_90319_5_TFE3-PRCC_TFE3_chrX_48896632_ENST00000315869_PRCC_chr1_156752074_ENST00000271526_length(amino acids)=513AA_BP=57
MSHAAEPARDGVEASAEGPRAVFVLLEERRPADSAQLLSLNSLLPESGIVADIELENVLDPDSFYELKSQPLPLRSSLPISLQATPATPA
TLSASSSAGGSRTPAMSSSSSSRVLLRQQLMRAQAQEQERRERREQAAAAPFPSPAPASPAISVVGVSAGGHTLSRPPPAQVPREVLKSD
SEEDEPTKKKTILQGSSEGTGLSALLPQPKNLTVKETNRLLLPHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAA
AKSAALQVTKQITQEEDDSDEEVAPENFFSLPEKAEPPGVEPYPYPIPTVPEELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKP
GDDYSYNQFSTYGDANAAGAYYQDYYSGGYYPAQDPALVPPQEIAPDASFIDDEAFKRLQGKRNRGREEINFVEIKGDDQLSGAQQWMTK

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

>90319_90319_6_TFE3-PRCC_TFE3_chrX_48896632_ENST00000315869_PRCC_chr1_156752074_ENST00000353233_length(amino acids)=481AA_BP=57
MSHAAEPARDGVEASAEGPRAVFVLLEERRPADSAQLLSLNSLLPESGIVADIELENVLDPDSFYELKSQPLPLRSSLPISLQATPATPA
TLSASSSAGGSRTPAMSSSSSSRVLLRQQLMRAQAQEQERRERREQAAAAPFPSPAPASPAISVVGVSAGGHTLSRPPPAQVPREVLKSD
SEEDEPTKKKTILQGSSEGTGLSALLPQPKNLTVKETNRLLLPHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAA
AKSAALQVTKQITQEEDDSDEEVAPENFFSLPEKAEPPGVEPYPYPIPTVPEELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKP
GDDYSYNQFSTYGDANAAGAYYQFKRLQGKRNRGREEINFVEIKGDDQLSGAQQWMTKSLTEEKTMKSFSKKKGEQPTGQQRRKHQITYL

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

>90319_90319_7_TFE3-PRCC_TFE3_chrX_48896632_ENST00000315869_PRCC_chr1_156756400_ENST00000271526_length(amino acids)=497AA_BP=57
MSHAAEPARDGVEASAEGPRAVFVLLEERRPADSAQLLSLNSLLPESGIVADIELENVLDPDSFYELKSQPLPLRSSLPISLQATPATPA
TLSASSSAGGSRTPAMSSSSSSRVLLRQQLMRAQAQEQERRERREQAAAAPFPSPAPASPAISVVGVSAGGHTLSRPPPAQVPREVLKGS
SEGTGLSALLPQPKNLTVKETNRLLLPHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAAAKSAALQVTKQITQEE
DDSDEEVAPENFFSLPEKAEPPGVEPYPYPIPTVPEELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKPGDDYSYNQFSTYGDAN
AAGAYYQDYYSGGYYPAQDPALVPPQEIAPDASFIDDEAFKRLQGKRNRGREEINFVEIKGDDQLSGAQQWMTKSLTEEKTMKSFSKKKG

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

>90319_90319_8_TFE3-PRCC_TFE3_chrX_48896632_ENST00000315869_PRCC_chr1_156756400_ENST00000353233_length(amino acids)=465AA_BP=57
MSHAAEPARDGVEASAEGPRAVFVLLEERRPADSAQLLSLNSLLPESGIVADIELENVLDPDSFYELKSQPLPLRSSLPISLQATPATPA
TLSASSSAGGSRTPAMSSSSSSRVLLRQQLMRAQAQEQERRERREQAAAAPFPSPAPASPAISVVGVSAGGHTLSRPPPAQVPREVLKGS
SEGTGLSALLPQPKNLTVKETNRLLLPHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAAAKSAALQVTKQITQEE
DDSDEEVAPENFFSLPEKAEPPGVEPYPYPIPTVPEELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKPGDDYSYNQFSTYGDAN
AAGAYYQFKRLQGKRNRGREEINFVEIKGDDQLSGAQQWMTKSLTEEKTMKSFSKKKGEQPTGQQRRKHQITYLIHQAKERELELKNTWS

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

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chrX:156738031/chr1:48895967)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
TFE3 P19532	PRCC Q92733
FUNCTION: Transcription factor that acts as a master regulator of lysosomal biogenesis and immune response (PubMed:2338243, PubMed:29146937, PubMed:30733432, PubMed:31672913). Specifically recognizes and binds E-box sequences (5'-CANNTG-3'); efficient DNA-binding requires dimerization with itself or with another MiT/TFE family member such as TFEB or MITF (By similarity). Involved in the cellular response to amino acid availability by acting downstream of MTOR: in the presence of nutrients, TFE3 phosphorylation by MTOR promotes its cytosolic retention and subsequent inactivation (PubMed:31672913). Upon starvation or lysosomal stress, inhibition of MTOR induces TFE3 dephosphorylation, resulting in nuclear localization and transcription factor activity (PubMed:31672913). In association with TFEB, activates the expression of CD40L in T-cells, thereby playing a role in T-cell-dependent antibody responses in activated CD4(+) T-cells and thymus-dependent humoral immunity (By similarity). Specifically recognizes the MUE3 box, a subset of E-boxes, present in the immunoglobulin enhancer (PubMed:2338243). It also binds very well to a USF/MLTF site (PubMed:2338243). May regulate lysosomal positioning in response to nutrient deprivation by promoting the expression of PIP4P1 (PubMed:29146937). Acts as a positive regulator of browning of adipose tissue by promoting expression of target genes; mTOR-dependent phosphorylation promotes cytoplasmic retention of TFE3 and inhibits browning of adipose tissue (By similarity). Maintains the pluripotent state of embryonic stem cells by promoting the expression of genes such as ESRRB; mTOR-dependent nuclear exclusion promotes exit from pluripotency (By similarity). Required to maintain the naive pluripotent state of hematopoietic stem cell; mTOR-dependent cytoplasmic retention of TFE3 promotes the exit of hematopoietic stem cell from pluripotency (PubMed:30733432). {ECO:0000250\|UniProtKB:Q64092, ECO:0000269\|PubMed:2338243, ECO:0000269\|PubMed:29146937, ECO:0000269\|PubMed:30733432, ECO:0000269\|PubMed:31672913}.	FUNCTION: May regulate cell cycle progression through interaction with MAD2L2. {ECO:0000269\|PubMed:11717438}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Tgene

PRCC

chrX:48896631

chr1:156752073

ENST00000271526

235_239

156.0

492.0

Compositional bias

Note=Poly-Thr

Tgene

PRCC

chrX:48896631

chr1:156756399

ENST00000271526

235_239

172.0

492.0

Compositional bias

Note=Poly-Thr

Tgene

PRCC

chrX:48896632

chr1:156752074

ENST00000271526

235_239

156.0

492.0

Compositional bias

Note=Poly-Thr

Tgene

PRCC

chrX:48896632

chr1:156756400

ENST00000271526

235_239

172.0

492.0

Compositional bias

Note=Poly-Thr

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

TFE3

chrX:48896631

chr1:156752073

ENST00000315869

346_399

178.0

576.0

Domain

bHLH

Hgene

TFE3

chrX:48896631

chr1:156756399

ENST00000315869

346_399

178.0

576.0

Domain

bHLH

Hgene

TFE3

chrX:48896632

chr1:156752074

ENST00000315869

346_399

178.0

576.0

Domain

bHLH

Hgene

TFE3

chrX:48896632

chr1:156756400

ENST00000315869

346_399

178.0

576.0

Domain

bHLH

Hgene

TFE3

chrX:48896631

chr1:156752073

ENST00000315869

260_271

178.0

576.0

Region

Strong transcription activation domain

Hgene

TFE3

chrX:48896631

chr1:156752073

ENST00000315869

409_430

178.0

576.0

Region

Note=Leucine-zipper

Hgene

TFE3

chrX:48896631

chr1:156756399

ENST00000315869

260_271

178.0

576.0

Region

Strong transcription activation domain

Hgene

TFE3

chrX:48896631

chr1:156756399

ENST00000315869

409_430

178.0

576.0

Region

Note=Leucine-zipper

Hgene

TFE3

chrX:48896632

chr1:156752074

ENST00000315869

260_271

178.0

576.0

Region

Strong transcription activation domain

Hgene

TFE3

chrX:48896632

chr1:156752074

ENST00000315869

409_430

178.0

576.0

Region

Note=Leucine-zipper

Hgene

TFE3

chrX:48896632

chr1:156756400

ENST00000315869

260_271

178.0

576.0

Region

Strong transcription activation domain

Hgene

TFE3

chrX:48896632

chr1:156756400

ENST00000315869

409_430

178.0

576.0

Region

Note=Leucine-zipper

Tgene

PRCC

chrX:48896631

chr1:156752073

ENST00000271526

18_25

156.0

492.0

Compositional bias

Note=Poly-Glu

Tgene

PRCC

chrX:48896631

chr1:156752073

ENST00000271526

52_55

156.0

492.0

Compositional bias

Note=Poly-Pro

Tgene

PRCC

chrX:48896631

chr1:156752073

ENST00000271526

79_84

156.0

492.0

Compositional bias

Note=Poly-Pro

Tgene

PRCC

chrX:48896631

chr1:156752073

ENST00000271526

91_94

156.0

492.0

Compositional bias

Note=Poly-Pro

Tgene

PRCC

chrX:48896631

chr1:156756399

ENST00000271526

18_25

172.0

492.0

Compositional bias

Note=Poly-Glu

Tgene

PRCC

chrX:48896631

chr1:156756399

ENST00000271526

52_55

172.0

492.0

Compositional bias

Note=Poly-Pro

Tgene

PRCC

chrX:48896631

chr1:156756399

ENST00000271526

79_84

172.0

492.0

Compositional bias

Note=Poly-Pro

Tgene

PRCC

chrX:48896631

chr1:156756399

ENST00000271526

91_94

172.0

492.0

Compositional bias

Note=Poly-Pro

Tgene

PRCC

chrX:48896632

chr1:156752074

ENST00000271526

18_25

156.0

492.0

Compositional bias

Note=Poly-Glu

Tgene

PRCC

chrX:48896632

chr1:156752074

ENST00000271526

52_55

156.0

492.0

Compositional bias

Note=Poly-Pro

Tgene

PRCC

chrX:48896632

chr1:156752074

ENST00000271526

79_84

156.0

492.0

Compositional bias

Note=Poly-Pro

Tgene

PRCC

chrX:48896632

chr1:156752074

ENST00000271526

91_94

156.0

492.0

Compositional bias

Note=Poly-Pro

Tgene

PRCC

chrX:48896632

chr1:156756400

ENST00000271526

18_25

172.0

492.0

Compositional bias

Note=Poly-Glu

Tgene

PRCC

chrX:48896632

chr1:156756400

ENST00000271526

52_55

172.0

492.0

Compositional bias

Note=Poly-Pro

Tgene

PRCC

chrX:48896632

chr1:156756400

ENST00000271526

79_84

172.0

492.0

Compositional bias

Note=Poly-Pro

Tgene

PRCC

chrX:48896632

chr1:156756400

ENST00000271526

91_94

172.0

492.0

Compositional bias

Note=Poly-Pro

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>1091_TFE3_48896632_PRCC_156752074_1091_TFE3_48896632_PRCC_156752074_ranked_0.pdb	TFE3	48896631	48896632	ENST00000353233	PRCC	chr1	156752074	+	MSHAAEPARDGVEASAEGPRAVFVLLEERRPADSAQLLSLNSLLPESGIVADIELENVLDPDSFYELKSQPLPLRSSLPISLQATPATPA TLSASSSAGGSRTPAMSSSSSSRVLLRQQLMRAQAQEQERRERREQAAAAPFPSPAPASPAISVVGVSAGGHTLSRPPPAQVPREVLKSD SEEDEPTKKKTILQGSSEGTGLSALLPQPKNLTVKETNRLLLPHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAA AKSAALQVTKQITQEEDDSDEEVAPENFFSLPEKAEPPGVEPYPYPIPTVPEELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKP GDDYSYNQFSTYGDANAAGAYYQDYYSGGYYPAQDPALVPPQEIAPDASFIDDEAFKRLQGKRNRGREEINFVEIKGDDQLSGAQQWMTK	513

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

TFE3_pLDDT.png

PRCC_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene	PPI interactors
PRCC	EGFR, SF3A2, MAD2L2, NABP2, RBM10, LSM2, PRPF19, PPIL2, TOE1, CSNK2A1, WRAP73, EWSR1, XPO1, HSF2, PCK2, SORT1, SOD1, YWHAZ, LRP8, PIM2, ZNF281, IWS1, CEP170P1, Crnkl1, Bcas2, CDC5L, C19orf57, F11, TKTL2, BCAM, FAF1, BCAS2, HSPA9, FKBP9, CARM1, CRNKL1, SCYL2, SH3GLB1, CDK5, SEPT7, DIS3, CHORDC1, SUB1, SARNP, COPZ1, GORASP2, SEPT11, DRG1, TRIM25, NTC20, HOMER3, ESR2, TP53BP1, ACTC1, PLEKHA4, DNAJC10, ELAVL1, LSM4, DNAJB1, CBX3, DHX8, HIST1H2BG, NUP50, PRPF8, TERF2IP, NAA40, HSPA12A, PLOD3, EP300, SP7,
TFE3	AKR1B1, CLTC, PHB2, ACLY, CUL2, EPRS, PFAS, VARS, NEDD8, RPL38, TRIM28, EIF3A, RPA3, E2F3, SMARCE1, MITF, TFE3, SMAD3, SMAD4, TFEC, EWSR1, XPO1, TFEB, Arrb2, TARDBP, HIST1H4A, LAMTOR3, nsp2, nsp7, AIM2, NR3C1, DDX58, YWHAG, YWHAQ, HDAC5, BTF3, nsp16, IRF8, KLF12, KLF16, KLF3, KLF5, KLF8, SOX2, TLX3, VSX1,

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
TFE3
PRCC

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to TFE3-PRCC

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

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to TFE3-PRCC

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

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	TFE3	C4518356	MiT family translocation renal cell carcinoma	2	ORPHANET
Hgene	TFE3	C0206657	Alveolar Soft Part Sarcoma	1	ORPHANET
Hgene	TFE3	C0206732	Epithelioid hemangioendothelioma	1	ORPHANET
Tgene	PRCC	C4518356	MiT family translocation renal cell carcinoma	3	ORPHANET