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Center for Computational Systems Medicine level3
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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 Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Potential Active Site Information

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Potentially Interacting Small Molecules through Virtual Screening

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Biochemical Features of Small Molecules with ADME

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Drug Toxicity Information

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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:PRCC-TFE3

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PRCC-TFE3
FusionPDB ID: 68410
FusionGDB2.0 ID: 68410
HgeneTgene
Gene symbol

PRCC

TFE3

Gene ID

5546

7030

Gene nameproline rich mitotic checkpoint control factortranscription factor binding to IGHM enhancer 3
SynonymsRCCP1|TPRCRCCP2|RCCX1|TFEA|bHLHe33
Cytomap

1q23.1

Xp11.23

Type of geneprotein-codingprotein-coding
Descriptionproline-rich protein PRCCPRCC, proline rich mitotic checkpoint control factorpapillary renal cell carcinoma (translocation-associated)papillary renal cell carcinoma translocation-associated gene proteintranscription 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
Modification date2020031320200327
UniProtAcc

Q92733

P19532

Ensembl transtripts involved in fusion geneENST idsENST00000491853, ENST00000271526, 
ENST00000353233, 		ENST00000315869, 
ENST00000487451, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score12 X 6 X 10=72014 X 15 X 6=1260
# samples 1415
** MAII scorelog2(14/720*10)=-2.36257007938471
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/1260*10)=-3.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: PRCC [Title/Abstract] AND TFE3 [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 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.
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 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgenePRCC

GO:0007093

mitotic cell cycle checkpoint

11717438


check buttonFusion gene breakpoints across PRCC (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 TFE3 (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
ChimerDB4KIRPTCGA-BQ-5882-01APRCCchr1

156738031

-TFE3chrX

48895967

-
ChimerDB4KIRPTCGA-BQ-5882-01APRCCchr1

156738031

+TFE3chrX

48895967

-
ChimerDB4KIRPTCGA-BQ-5882PRCCchr1

156738031

+TFE3chrX

48895967

-
ChimerDB4KIRPTCGA-BQ-5887-01APRCCchr1

156738031

-TFE3chrX

48895967

-
ChimerDB4KIRPTCGA-BQ-5887-01APRCCchr1

156738031

+TFE3chrX

48895967

-
ChimerDB4KIRPTCGA-BQ-5887PRCCchr1

156738031

+TFE3chrX

48895967

-
ChimerDB4KIRPTCGA-BQ-7050-01APRCCchr1

156738031

-TFE3chrX

48895967

-
ChimerDB4KIRPTCGA-BQ-7050-01APRCCchr1

156738031

+TFE3chrX

48895967

-
ChimerDB4KIRPTCGA-BQ-7050PRCCchr1

156738031

+TFE3chrX

48895967

-
ChimerDB4READTCGA-AG-3605PRCCchr1

156738031

+TFE3chrX

48895967

-
ChimerKB3..PRCCchr1

156738031

+TFE3chrX

48895967

-
ChimerKB3..PRCCchr1

156756966

+TFE3chrX

48895967

-
ChimerKB3..PRCCchr1

156761584

+TFE3chrX

48895639

-


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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)
ENST00000271526PRCCchr1156738031+ENST00000315869TFE3chrX48895967-33617402721933553
ENST00000353233PRCCchr1156738031+ENST00000315869TFE3chrX48895967-33076862181879553
ENST00000271526PRCCchr1156756966+ENST00000315869TFE3chrX48895967-397613552722548758
ENST00000353233PRCCchr1156756966+ENST00000315869TFE3chrX48895967-392213012182494758
ENST00000271526PRCCchr1156761584+ENST00000315869TFE3chrX48895639-382614512722398708
ENST00000271526PRCCchr1156738031+ENST00000315869TFE3chrX48895967-33617402721933553
ENST00000353233PRCCchr1156738031+ENST00000315869TFE3chrX48895967-33076862181879553

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
ENST00000271526ENST00000315869PRCCchr1156738031+TFE3chrX48895967-0.038983770.96101624
ENST00000353233ENST00000315869PRCCchr1156738031+TFE3chrX48895967-0.0410405360.95895946

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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

>68410_68410_1_PRCC-TFE3_PRCC_chr1_156738031_ENST00000271526_TFE3_chrX_48895967_ENST00000315869_length(amino acids)=553AA_BP=104
MSLVAYASSDESEPDEAEPEPEEEEAVAPTSGPALGGLFASLPAPKGPALLPPPPQMLAPAFPPPLLLPPPTGDPRLQPPPPLPFGLGGF
PPPPGVSPAEAAGVGEGLGLGLPSPRGPGLNLPPPIGGAGPPLGLPKPKKRKEPVKIAAPELHKGDVQTHLENPTRYHLQQARRQQVKQY
LSTTLGPKLASQALTPPPGPASAQPLPAPEAAHTTGPTGSAPNSPMALLTIGSSSEKEIDDVIDEIISLESSYNDEMLSYLPGGTTGLQL
PSTLPVSGNLLDVYSSQGVATPAITVSNSCPAELPNIKREISETEAKALLKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSSDPEMR
WNKGTILKASVDYIRKLQKEQQRSKDLESRQRSLEQANRSLQLRIQELELQAQIHGLPVPPTPGLLSLATTSASDSLKPEQLDIEEEGRP
GAATFHVGGGPAQNAPHQQPPAPPSDALLDLHFPSDHLGDLGDPFHLGLEDILMEEEEGVVGGLSGGALSPLRAASDPLLSSVSPAVSKA

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

>68410_68410_2_PRCC-TFE3_PRCC_chr1_156738031_ENST00000353233_TFE3_chrX_48895967_ENST00000315869_length(amino acids)=553AA_BP=104
MSLVAYASSDESEPDEAEPEPEEEEAVAPTSGPALGGLFASLPAPKGPALLPPPPQMLAPAFPPPLLLPPPTGDPRLQPPPPLPFGLGGF
PPPPGVSPAEAAGVGEGLGLGLPSPRGPGLNLPPPIGGAGPPLGLPKPKKRKEPVKIAAPELHKGDVQTHLENPTRYHLQQARRQQVKQY
LSTTLGPKLASQALTPPPGPASAQPLPAPEAAHTTGPTGSAPNSPMALLTIGSSSEKEIDDVIDEIISLESSYNDEMLSYLPGGTTGLQL
PSTLPVSGNLLDVYSSQGVATPAITVSNSCPAELPNIKREISETEAKALLKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSSDPEMR
WNKGTILKASVDYIRKLQKEQQRSKDLESRQRSLEQANRSLQLRIQELELQAQIHGLPVPPTPGLLSLATTSASDSLKPEQLDIEEEGRP
GAATFHVGGGPAQNAPHQQPPAPPSDALLDLHFPSDHLGDLGDPFHLGLEDILMEEEEGVVGGLSGGALSPLRAASDPLLSSVSPAVSKA

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

>68410_68410_3_PRCC-TFE3_PRCC_chr1_156756966_ENST00000271526_TFE3_chrX_48895967_ENST00000315869_length(amino acids)=758AA_BP=360
MSLVAYASSDESEPDEAEPEPEEEEAVAPTSGPALGGLFASLPAPKGPALLPPPPQMLAPAFPPPLLLPPPTGDPRLQPPPPLPFGLGGF
PPPPGVSPAEAAGVGEGLGLGLPSPRGPGLNLPPPIGGAGPPLGLPKPKKRKEPVKIAAPELHKGDSDSEEDEPTKKKTILQGSSEGTGL
SALLPQPKNLTVKETNRLLLPHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAAAKSAALQVTKQITQEEDDSDEE
VAPENFFSLPEKAEPPGVEPYPYPIPTVPEELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKPGDDYSYNQFSTYGDANAAGAYY
QVQTHLENPTRYHLQQARRQQVKQYLSTTLGPKLASQALTPPPGPASAQPLPAPEAAHTTGPTGSAPNSPMALLTIGSSSEKEIDDVIDE
IISLESSYNDEMLSYLPGGTTGLQLPSTLPVSGNLLDVYSSQGVATPAITVSNSCPAELPNIKREISETEAKALLKERQKKDNHNLIERR
RRFNINDRIKELGTLIPKSSDPEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRQRSLEQANRSLQLRIQELELQAQIHGLPVPPTPGL
LSLATTSASDSLKPEQLDIEEEGRPGAATFHVGGGPAQNAPHQQPPAPPSDALLDLHFPSDHLGDLGDPFHLGLEDILMEEEEGVVGGLS

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

>68410_68410_4_PRCC-TFE3_PRCC_chr1_156756966_ENST00000353233_TFE3_chrX_48895967_ENST00000315869_length(amino acids)=758AA_BP=360
MSLVAYASSDESEPDEAEPEPEEEEAVAPTSGPALGGLFASLPAPKGPALLPPPPQMLAPAFPPPLLLPPPTGDPRLQPPPPLPFGLGGF
PPPPGVSPAEAAGVGEGLGLGLPSPRGPGLNLPPPIGGAGPPLGLPKPKKRKEPVKIAAPELHKGDSDSEEDEPTKKKTILQGSSEGTGL
SALLPQPKNLTVKETNRLLLPHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAAAKSAALQVTKQITQEEDDSDEE
VAPENFFSLPEKAEPPGVEPYPYPIPTVPEELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKPGDDYSYNQFSTYGDANAAGAYY
QVQTHLENPTRYHLQQARRQQVKQYLSTTLGPKLASQALTPPPGPASAQPLPAPEAAHTTGPTGSAPNSPMALLTIGSSSEKEIDDVIDE
IISLESSYNDEMLSYLPGGTTGLQLPSTLPVSGNLLDVYSSQGVATPAITVSNSCPAELPNIKREISETEAKALLKERQKKDNHNLIERR
RRFNINDRIKELGTLIPKSSDPEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRQRSLEQANRSLQLRIQELELQAQIHGLPVPPTPGL
LSLATTSASDSLKPEQLDIEEEGRPGAATFHVGGGPAQNAPHQQPPAPPSDALLDLHFPSDHLGDLGDPFHLGLEDILMEEEEGVVGGLS

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

>68410_68410_5_PRCC-TFE3_PRCC_chr1_156761584_ENST00000271526_TFE3_chrX_48895639_ENST00000315869_length(amino acids)=708AA_BP=393
MSLVAYASSDESEPDEAEPEPEEEEAVAPTSGPALGGLFASLPAPKGPALLPPPPQMLAPAFPPPLLLPPPTGDPRLQPPPPLPFGLGGF
PPPPGVSPAEAAGVGEGLGLGLPSPRGPGLNLPPPIGGAGPPLGLPKPKKRKEPVKIAAPELHKGDSDSEEDEPTKKKTILQGSSEGTGL
SALLPQPKNLTVKETNRLLLPHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAAAKSAALQVTKQITQEEDDSDEE
VAPENFFSLPEKAEPPGVEPYPYPIPTVPEELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKPGDDYSYNQFSTYGDANAAGAYY
QDYYSGGYYPAQDPALVPPQEIAPDASFIDDEAIDDVIDEIISLESSYNDEMLSYLPGGTTGLQLPSTLPVSGNLLDVYSSQGVATPAIT
VSNSCPAELPNIKREISETEAKALLKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSSDPEMRWNKGTILKASVDYIRKLQKEQQRSK
DLESRQRSLEQANRSLQLRIQELELQAQIHGLPVPPTPGLLSLATTSASDSLKPEQLDIEEEGRPGAATFHVGGGPAQNAPHQQPPAPPS

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

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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/chr1:156738031/chrX: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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PRCC

Q92733

TFE3

P19532

FUNCTION: May regulate cell cycle progression through interaction with MAD2L2. {ECO:0000269|PubMed:11717438}.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}.

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
HgenePRCCchr1:156738031chrX:48895967ENST00000271526+1718_25156.0492.0Compositional biasNote=Poly-Glu
HgenePRCCchr1:156738031chrX:48895967ENST00000271526+1752_55156.0492.0Compositional biasNote=Poly-Pro
HgenePRCCchr1:156738031chrX:48895967ENST00000271526+1779_84156.0492.0Compositional biasNote=Poly-Pro
HgenePRCCchr1:156738031chrX:48895967ENST00000271526+1791_94156.0492.0Compositional biasNote=Poly-Pro
TgeneTFE3chr1:156738031chrX:48895967ENST00000315869210346_399178.0576.0DomainbHLH
TgeneTFE3chr1:156738031chrX:48895967ENST00000315869210260_271178.0576.0RegionStrong transcription activation domain
TgeneTFE3chr1:156738031chrX:48895967ENST00000315869210409_430178.0576.0RegionNote=Leucine-zipper

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePRCCchr1:156738031chrX:48895967ENST00000271526+17235_239156.0492.0Compositional biasNote=Poly-Thr


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Fusion Protein Structures

check button 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)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file (396) >>>396.pdbFusion protein BP residue: 104
CIF file (396) >>>396.cif		PRCCchr1156738031+TFE3chrX48895967-
MSLVAYASSDESEPDEAEPEPEEEEAVAPTSGPALGGLFASLPAPKGPAL
LPPPPQMLAPAFPPPLLLPPPTGDPRLQPPPPLPFGLGGFPPPPGVSPAE
AAGVGEGLGLGLPSPRGPGLNLPPPIGGAGPPLGLPKPKKRKEPVKIAAP
ELHKGDVQTHLENPTRYHLQQARRQQVKQYLSTTLGPKLASQALTPPPGP
ASAQPLPAPEAAHTTGPTGSAPNSPMALLTIGSSSEKEIDDVIDEIISLE
SSYNDEMLSYLPGGTTGLQLPSTLPVSGNLLDVYSSQGVATPAITVSNSC
PAELPNIKREISETEAKALLKERQKKDNHNLIERRRRFNINDRIKELGTL
IPKSSDPEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRQRSLEQANRS
LQLRIQELELQAQIHGLPVPPTPGLLSLATTSASDSLKPEQLDIEEEGRP
GAATFHVGGGPAQNAPHQQPPAPPSDALLDLHFPSDHLGDLGDPFHLGLE
DILMEEEEGVVGGLSGGALSPLRAASDPLLSSVSPAVSKASSRRSSFSME
553
3D view using mol* of 396 (AA BP:104)
PDB file (581) >>>581.pdbFusion protein BP residue: 393
CIF file (581) >>>581.cif		PRCCchr1156761584+TFE3chrX48895639-
MSLVAYASSDESEPDEAEPEPEEEEAVAPTSGPALGGLFASLPAPKGPAL
LPPPPQMLAPAFPPPLLLPPPTGDPRLQPPPPLPFGLGGFPPPPGVSPAE
AAGVGEGLGLGLPSPRGPGLNLPPPIGGAGPPLGLPKPKKRKEPVKIAAP
ELHKGDSDSEEDEPTKKKTILQGSSEGTGLSALLPQPKNLTVKETNRLLL
PHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAAAK
SAALQVTKQITQEEDDSDEEVAPENFFSLPEKAEPPGVEPYPYPIPTVPE
ELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKPGDDYSYNQFSTY
GDANAAGAYYQDYYSGGYYPAQDPALVPPQEIAPDASFIDDEAIDDVIDE
IISLESSYNDEMLSYLPGGTTGLQLPSTLPVSGNLLDVYSSQGVATPAIT
VSNSCPAELPNIKREISETEAKALLKERQKKDNHNLIERRRRFNINDRIK
ELGTLIPKSSDPEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRQRSLE
QANRSLQLRIQELELQAQIHGLPVPPTPGLLSLATTSASDSLKPEQLDIE
EEGRPGAATFHVGGGPAQNAPHQQPPAPPSDALLDLHFPSDHLGDLGDPF
HLGLEDILMEEEEGVVGGLSGGALSPLRAASDPLLSSVSPAVSKASSRRS
708
3D view using mol* of 581 (AA BP:393)
PDB file (620) >>>620.pdbFusion protein BP residue: 360
CIF file (620) >>>620.cif		PRCCchr1156756966+TFE3chrX48895967-
MSLVAYASSDESEPDEAEPEPEEEEAVAPTSGPALGGLFASLPAPKGPAL
LPPPPQMLAPAFPPPLLLPPPTGDPRLQPPPPLPFGLGGFPPPPGVSPAE
AAGVGEGLGLGLPSPRGPGLNLPPPIGGAGPPLGLPKPKKRKEPVKIAAP
ELHKGDSDSEEDEPTKKKTILQGSSEGTGLSALLPQPKNLTVKETNRLLL
PHAFSRKPSDGSPDTKPSRLASKTKTSSLAPVVGTTTTTPSPSAIKAAAK
SAALQVTKQITQEEDDSDEEVAPENFFSLPEKAEPPGVEPYPYPIPTVPE
ELPPGTEPEPAFQDDAANAPLEFKMAAGSSGAPWMPKPGDDYSYNQFSTY
GDANAAGAYYQVQTHLENPTRYHLQQARRQQVKQYLSTTLGPKLASQALT
PPPGPASAQPLPAPEAAHTTGPTGSAPNSPMALLTIGSSSEKEIDDVIDE
IISLESSYNDEMLSYLPGGTTGLQLPSTLPVSGNLLDVYSSQGVATPAIT
VSNSCPAELPNIKREISETEAKALLKERQKKDNHNLIERRRRFNINDRIK
ELGTLIPKSSDPEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRQRSLE
QANRSLQLRIQELELQAQIHGLPVPPTPGLLSLATTSASDSLKPEQLDIE
EEGRPGAATFHVGGGPAQNAPHQQPPAPPSDALLDLHFPSDHLGDLGDPF
HLGLEDILMEEEEGVVGGLSGGALSPLRAASDPLLSSVSPAVSKASSRRS
758
3D view using mol* of 620 (AA BP:360)


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pLDDT score distribution

check button 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.
PRCC_pLDDT.png
all structure
all structure
TFE3_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
PRCC_TFE3_396_pLDDT.png (AA BP:104)
all structure
PRCC_TFE3_396_pLDDT_and_active_sites.png (AA BP:104)
all structure
PRCC_TFE3_396_violinplot.png (AA BP:104)
all structure
PRCC_TFE3_581_pLDDT.png (AA BP:393)
all structure
PRCC_TFE3_581_pLDDT_and_active_sites.png (AA BP:393)
all structure
PRCC_TFE3_581_violinplot.png (AA BP:393)
all structure
PRCC_TFE3_620_pLDDT.png (AA BP:360)
all structure
PRCC_TFE3_620_pLDDT_and_active_sites.png (AA BP:360)
all structure
PRCC_TFE3_620_violinplot.png (AA BP:360)
all structure


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Ramachandran Plot of Fusion Protein Structure


check button 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
PRCC_TFE3_396.png
all structure
PRCC_TFE3_581.png
all structure
PRCC_TFE3_620.png
all structure

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Potential Active Site Information


check button The potential binding sites of these fusion proteins were identified using SiteMap, a module of the Schrodinger suite.
Fusion AA seq ID in FusionPDBSite scoreSizeD scoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues
3960.694460.665132.0550.7110.5720.8190.290.9690.30.651Chain A: 399,402,403,406,409,413,419,421,422,424,4
25,426,427,428,429
5810.639200.64282.320.8360.5720.7081.2820.3733.4361.077Chain A: 506,509,514,516,520,523,524,527,528
6200.871620.914158.8090.6370.6060.8431.0420.5821.7911.909Chain A: 458,461,462,465,466,516,518,521,522,524,5
25,526

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Potentially Interacting Small Molecules through Virtual Screening


check button The FDA-approved small molecule library molecules were subjected to virtual screening using the Glide.
Fusion AA seq ID in FusionPDBZINC IDDrugBank IDDrug nameDocking scoreGlide gscore
581ZINC000019632917DB00475Chlordiazepoxide-7.10488-7.15278
581ZINC000000018635DB00998Frovatriptan-6.38435-6.38485
581ZINC000000083315DB00150Tryptophan-6.11603-6.11603
581ZINC000002015035DB06262Droxidopa-5.95238-5.95238
581ZINC000000105216DB00788Naproxen-5.90984-5.91074
581ZINC000003842753DB00432Trifluridine-5.74572-5.83042
581ZINC000003813010DB00322Floxuridine-5.79677-5.82657
581ZINC000000001735DB00350Minoxidil-5.77866-5.77866
581ZINC000004099200DB00213Pantoprazole-3.67824-5.76404
581ZINC000000020243DB00861Diflunisal-5.71309-5.71309
581ZINC000000008492DB11145Oxyquinoline-5.60495-5.62295
581ZINC000001530948DB01041Thalidomide-5.59848-5.59848
581ZINC000000896546DB01099Flucytosine-5.57595-5.57645
581ZINC000084843283DB00356Chlorzoxazone-5.50066-5.53396
581ZINC000000000922DB00233Aminosalicylic acid-5.46925-5.47015
581ZINC000018203737DB12243Edaravone-5.05436-5.40576
581ZINC000001482184DB00853Temozolomide-5.39607-5.39767
581ZINC000016929327DB01262Decitabine-4.97026-5.38966
581ZINC000006382803DB00352Tioguanine-5.23754-5.38794
581ZINC000000000882DB00173Adenine-5.36198-5.38268

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check button Drug information from DrugBank of the top 20 interacting small molecules.
ZINC IDDrugBank IDDrug nameDrug typeSMILESDrug group
ZINC000019632917DB00475ChlordiazepoxideSmall moleculeCNC1=NC2=C(C=C(Cl)C=C2)C(C2=CC=CC=C2)=[N+]([O-])C1Approved|Illicit|Investigational
ZINC000000018635DB00998FrovatriptanSmall moleculeCN[C@@H]1CCC2=C(C1)C1=C(N2)C=CC(=C1)C(N)=OApproved|Investigational
ZINC000000083315DB00150TryptophanSmall moleculeN[C@@H](CC1=CNC2=C1C=CC=C2)C(O)=OApproved|Nutraceutical|Withdrawn
ZINC000002015035DB06262DroxidopaSmall moleculeN[C@@H]([C@H](O)C1=CC(O)=C(O)C=C1)C(O)=OApproved|Investigational
ZINC000000105216DB00788NaproxenSmall moleculeCOC1=CC2=C(C=C1)C=C(C=C2)[C@H](C)C(O)=OApproved|Vet_approved
ZINC000003842753DB00432TrifluridineSmall moleculeOC[C@H]1O[C@H](C[C@@H]1O)N1C=C(C(=O)NC1=O)C(F)(F)FApproved|Investigational
ZINC000003813010DB00322FloxuridineSmall moleculeOC[C@H]1O[C@H](C[C@@H]1O)N1C=C(F)C(=O)NC1=OApproved
ZINC000000001735DB00350MinoxidilSmall moleculeNC1=CC(=NC(N)=[N+]1[O-])N1CCCCC1Approved|Investigational
ZINC000000020243DB00861DiflunisalSmall moleculeOC(=O)C1=C(O)C=CC(=C1)C1=C(F)C=C(F)C=C1Approved|Investigational
ZINC000000008492DB11145OxyquinolineSmall moleculeOC1=CC=CC2=C1N=CC=C2Approved|Vet_approved
ZINC000000896546DB01099FlucytosineSmall moleculeNC1=C(F)C=NC(=O)N1Approved|Investigational
ZINC000084843283DB00356ChlorzoxazoneSmall moleculeClC1=CC2=C(OC(=O)N2)C=C1Approved
ZINC000000000922DB00233Aminosalicylic acidSmall moleculeNC1=CC(O)=C(C=C1)C(O)=OApproved
ZINC000018203737DB12243EdaravoneSmall moleculeCC1=NN(C(=O)C1)C1=CC=CC=C1Approved|Investigational
ZINC000001482184DB00853TemozolomideSmall moleculeCN1N=NC2=C(N=CN2C1=O)C(N)=OApproved|Investigational
ZINC000016929327DB01262DecitabineSmall moleculeNC1=NC(=O)N(C=N1)[C@H]1C[C@H](O)[C@@H](CO)O1Approved|Investigational
ZINC000006382803DB00352TioguanineSmall moleculeNC1=NC(=S)C2=C(N1)N=CN2Approved
ZINC000000000882DB00173AdenineSmall moleculeNC1=C2NC=NC2=NC=N1Approved|Nutraceutical

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Biochemical Features of Small Molecules


check button ADME (Absorption, Distribution, Metabolism, and Excretion) of drugs using QikProp(v3.9)
ZINC IDmol_MWdipoleSASAFOSAFISAPISAWPSAvolumedonorHBaccptHBIPHuman Oral AbsorptionPercent Human Oral AbsorptionRule Of FiveRule Of Three
ZINC000019632917299.7594.645553.04137.02264.707279.78871.524941.819138.565310000
ZINC000019632917299.7595.502549.003118.96574.766283.8271.453935.577138.408310000
ZINC000000018635243.3087.2492.762217.467154.534120.7610833.223448.296366.4100
ZINC000000083315204.2283.132419.18346.221166.648206.3140687.589438.088242.50601
ZINC000002015035213.195.76408.68526.39279.826102.4690664.78655.28.9081011
ZINC000000105216230.2632.528470.733180.42192.826197.4860787.83512.758.546390.65400
ZINC000003842753296.2038.671452.2125.183206.5539.446111.018773.03338.610.189361.74800
ZINC000003842753296.2036.973450.843125.482197.47913.613114.268769.6938.610.058363.65500
ZINC000003813010246.1958.241414.89124.921222.5322.14345.296694.04638.69.724254.7600
ZINC000003813010246.1957.122409.023126.439210.1227.64744.817690.71338.69.573257.40300
ZINC000000001735209.255.141437.436217.593169.97449.8690711.86443.57.733376.87300
ZINC000004099200383.3698.318623.128213.24477.412222.302110.171084.47189.124376.69200
ZINC000004099200383.3698.299620.121215.6578.983216.916108.5731082.558189.183376.22100
ZINC000004099200383.3698.355619.5212.86177.163219.295110.1821080.981189.019376.60300
ZINC000004099200383.3698.428625.396215.33578.49221.055110.5161084.724189.007376.45900
ZINC000000020243250.2018.261459.0810144.436231.00583.64751.87911.759.879386.60100
ZINC000000008492145.162.589340.545068.394272.150527.27511.758.638310000
ZINC000000008492145.162.225339.564068.018271.5460525.50411.758.457310000
ZINC000001530948258.2336.265444.71583.913189.185171.6180765.6241610.446368.30100
ZINC000000896546129.0945.933283.8030174.82165.19643.787412.204349.417259.95700
ZINC000084843283169.5674.063322.7980106.536144.74471.517497.554139.228386.76600
ZINC000084843283169.5674.554322.4890105.966144.97771.546495.802139.258386.85700
ZINC000000000922153.1376.332333.640206.343127.2970510.5472.52.758.479254.82800
ZINC000018203737174.2022.325404.43194.12858.961251.3410640.161119.04310000
ZINC000018203737174.2023.578409.548143.4264.553201.5750650.24603.59.401395.30700
ZINC000018203737174.2022.598402.42994.1656.932251.3370637.516118.913310000
ZINC000018203737174.2026.978408.8194.82570.219243.7660645.326148.853391.84400
ZINC000001482184194.1523.411379.12887.887235.05156.190597.216279.649251.42500
ZINC000016929327228.2076.404419.717123.692262.10133.9250692.11549.19.544243.04300
ZINC000016929327228.2077.988419.927123.411262.44334.0720692.27949.19.468242.98200
ZINC000016929327228.2075.889424.346123.621268.44332.2820698.619410.19.722241.31900
ZINC000006382803167.1882.913334.0990174.67282.56276.865508.157458.609368.38600
ZINC000006382803167.18810.353334.2370175.32682.48776.423508.122458.464368.2800
ZINC000006382803167.1883.972333.7640164.06191.94377.76507.0323.848.378369.61600
ZINC000000000882135.1282.734303.1530170.481132.6720451.892348.538368.3800
ZINC000000000882135.1289.438304.2780171.466132.8120454.287348.639368.21400


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Drug Toxicity Information


check button Toxicity information of individual drugs using eToxPred
ZINC IDSmileSurface AccessibilityToxicity
ZINC000019632917CNC1=Nc2ccc(Cl)cc2C(c2ccccc2)=[N+]([O-])C10.1473206730.447326601
ZINC000000018635CN[C@@H]1CCc2[nH]c3ccc(C(N)=O)cc3c2C10.156787310.476568578
ZINC000000083315N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O0.2723590650.412747788
ZINC000002015035N[C@@H](C(=O)O)[C@@H](O)c1ccc(O)c(O)c10.1333451210.276427601
ZINC000000105216COc1ccc2cc([C@H](C)C(=O)O)ccc2c10.2978003420.311406087
ZINC000003842753O=c1[nH]c(=O)n([C@H]2C[C@H](O)[C@@H](CO)O2)cc1C(F)(F)F0.0733993370.470521911
ZINC000003813010O=c1[nH]c(=O)n([C@H]2C[C@H](O)[C@@H](CO)O2)cc1F0.0842996920.452167919
ZINC000000001735Nc1cc(N2CCCCC2)nc(N)[n+]1[O-]0.1297409460.395964399
ZINC000004099200COc1ccnc(C[S@](=O)c2nc3ccc(OC(F)F)cc3[nH]2)c1OC0.1146673540.321842622
ZINC000000020243O=C(O)c1cc(-c2ccc(F)cc2F)ccc1O0.4404093730.371648269
ZINC000000008492Oc1cccc2cccnc120.4696341470.557043533
ZINC000001530948O=C1CC[C@@H](N2C(=O)c3ccccc3C2=O)C(=O)N10.2024022320.556220101
ZINC000000896546Nc1nc(=O)[nH]cc1F0.1160196950.475808288
ZINC000084843283O=c1[nH]c2cc(Cl)ccc2o10.3045104230.412888168
ZINC000000000922Nc1ccc(C(=O)O)c(O)c10.4164916230.463983011
ZINC000018203737CC1=NN(c2ccccc2)C(=O)C10.3275623840.370968878
ZINC000001482184Cn1nnc2c(C(N)=O)ncn2c1=O0.1608864090.261932701
ZINC000016929327Nc1ncn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)n10.0711317810.402029462
ZINC000006382803Nc1nc2nc[nH]c2c(=S)[nH]10.100054570.571375233
ZINC000000000882Nc1ncnc2[nH]cnc120.1746372290.465480638


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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
PRCCEGFR, 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,
TFE3AKR1B1, 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,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
PRCCall structure
TFE3all structure


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 PRCC-TFE3


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 PRCC-TFE3


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID
PRCCTFE3Translocation-Associated Renal Cell CarcinomaMyCancerGenome
PRCCTFE3Renal Cell CarcinomaMyCancerGenome
PRCCTFE3Large Cell Neuroendocrine CarcinomaMyCancerGenome

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePRCCC4518356MiT family translocation renal cell carcinoma3ORPHANET
TgeneTFE3C4518356MiT family translocation renal cell carcinoma2ORPHANET
TgeneTFE3C0206657Alveolar Soft Part Sarcoma1ORPHANET
TgeneTFE3C0206732Epithelioid hemangioendothelioma1ORPHANET