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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:CLTC-TFE3

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CLTC-TFE3
FusionPDB ID: 17412
FusionGDB2.0 ID: 17412
HgeneTgene
Gene symbol

CLTC

TFE3

Gene ID

1213

7030

Gene nameclathrin heavy chaintranscription factor binding to IGHM enhancer 3
SynonymsCHC|CHC17|CLH-17|CLTCL2|Hc|MRD56RCCP2|RCCX1|TFEA|bHLHe33
Cytomap

17q23.1

Xp11.23

Type of geneprotein-codingprotein-coding
Descriptionclathrin heavy chain 1clathrin heavy chain on chromosome 17clathrin, heavy polypeptide (Hc)clathrin, heavy polypeptide-like 2transcription 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

P53675

P19532

Ensembl transtripts involved in fusion geneENST idsENST00000269122, ENST00000393043, 
ENST00000579456, ENST00000579815, 
ENST00000487451, ENST00000315869, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score27 X 40 X 17=1836014 X 15 X 6=1260
# samples 8415
** MAII scorelog2(84/18360*10)=-4.45003292063505
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: CLTC [Title/Abstract] AND TFE3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)
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
HgeneCLTC

GO:1900126

negative regulation of hyaluronan biosynthetic process

24251095


check buttonFusion gene breakpoints across CLTC (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 TFE3 (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

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
ChimerKB3..CLTCchr17

57754549

+TFE3chrX

48891766

-


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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)
ENST00000393043CLTCchr1757754549+ENST00000315869TFE3chrX48891766-5340307027439121212
ENST00000269122CLTCchr1757754549+ENST00000315869TFE3chrX48891766-5340307027439121212

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 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

>17412_17412_1_CLTC-TFE3_CLTC_chr17_57754549_ENST00000269122_TFE3_chrX_48891766_ENST00000315869_length(amino acids)=1212AA_BP=932
MAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQI
FNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGA
MQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKH
DVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGA
EELFARKFNALFAQGNYSEAAKVAANAPKGILRTPDTIRRFQSVPAQPGQTSPLLQYFGILLDQGQLNKYESLELCRPVLQQGRKQLLEK
WLKEDKLECSEELGDLVKSVDPTLALSVYLRANVPNKVIQCFAETGQVQKIVLYAKKVGYTPDWIFLLRNVMRISPDQGQQFAQMLVQDE
EPLADITQIVDVFMEYNLIQQCTAFLLDALKNNRPSEGPLQTRLLEMNLMHAPQVADAILGNQMFTHYDRAHIAQLCEKAGLLQRALEHF
TDLYDIKRAVVHTHLLNPEWLVNYFGSLSVEDSLECLRAMLSANIRQNLQICVQVASKYHEQLSTQSLIELFESFKSFEGLFYFLGSIVN
FSQDPDVHFKYIQAACKTGQIKEVERICRESNCYDPERVKNFLKEAKLTDQLPLIIVCDRFDFVHDLVLYLYRNNLQKYIEIYVQKVNPS
RLPVVIGGLLDVDCSEDVIKNLILVVRGQFSTDELVAEVEKRNRLKLLLPWLEARIHEGCEEPATHNALAKIYIDSNNNPERFLRENPYY
DSRVVGKYCEKRDPHLACVAYERGQCDLELINLPVSGNLLDVYSSQGVATPAITVSNSCPAELPNIKREISETEAKALLKERQKKDNHNL
IERRRRFNINDRIKELGTLIPKSSDPEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRQRSLEQANRSLQLRIQELELQAQIHGLPVPP
TPGLLSLATTSASDSLKPEQLDIEEEGRPGAATFHVGGGPAQNAPHQQPPAPPSDALLDLHFPSDHLGDLGDPFHLGLEDILMEEEEGVV

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

>17412_17412_2_CLTC-TFE3_CLTC_chr17_57754549_ENST00000393043_TFE3_chrX_48891766_ENST00000315869_length(amino acids)=1212AA_BP=932
MAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQI
FNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGA
MQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKH
DVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGA
EELFARKFNALFAQGNYSEAAKVAANAPKGILRTPDTIRRFQSVPAQPGQTSPLLQYFGILLDQGQLNKYESLELCRPVLQQGRKQLLEK
WLKEDKLECSEELGDLVKSVDPTLALSVYLRANVPNKVIQCFAETGQVQKIVLYAKKVGYTPDWIFLLRNVMRISPDQGQQFAQMLVQDE
EPLADITQIVDVFMEYNLIQQCTAFLLDALKNNRPSEGPLQTRLLEMNLMHAPQVADAILGNQMFTHYDRAHIAQLCEKAGLLQRALEHF
TDLYDIKRAVVHTHLLNPEWLVNYFGSLSVEDSLECLRAMLSANIRQNLQICVQVASKYHEQLSTQSLIELFESFKSFEGLFYFLGSIVN
FSQDPDVHFKYIQAACKTGQIKEVERICRESNCYDPERVKNFLKEAKLTDQLPLIIVCDRFDFVHDLVLYLYRNNLQKYIEIYVQKVNPS
RLPVVIGGLLDVDCSEDVIKNLILVVRGQFSTDELVAEVEKRNRLKLLLPWLEARIHEGCEEPATHNALAKIYIDSNNNPERFLRENPYY
DSRVVGKYCEKRDPHLACVAYERGQCDLELINLPVSGNLLDVYSSQGVATPAITVSNSCPAELPNIKREISETEAKALLKERQKKDNHNL
IERRRRFNINDRIKELGTLIPKSSDPEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRQRSLEQANRSLQLRIQELELQAQIHGLPVPP
TPGLLSLATTSASDSLKPEQLDIEEEGRPGAATFHVGGGPAQNAPHQQPPAPPSDALLDLHFPSDHLGDLGDPFHLGLEDILMEEEEGVV

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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/chr17:/chrX:)
- 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
CLTC

P53675

TFE3

P19532

FUNCTION: Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. Two different adapter protein complexes link the clathrin lattice either to the plasma membrane or to the trans-Golgi network (By similarity). {ECO:0000250}.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

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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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 (859) >>>859.pdbFusion protein BP residue: 932
CIF file (859) >>>859.cif		CLTCchr1757754549+TFE3chrX48891766-
MAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQV
VIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMK
AHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAG
CQIINYRTDAKQKWLLLTGISAQQNRVVGAMQLYSVDRKVSQPIEGHAAS
FAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDV
FFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISG
ETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALR
MAVRNNLAGAEELFARKFNALFAQGNYSEAAKVAANAPKGILRTPDTIRR
FQSVPAQPGQTSPLLQYFGILLDQGQLNKYESLELCRPVLQQGRKQLLEK
WLKEDKLECSEELGDLVKSVDPTLALSVYLRANVPNKVIQCFAETGQVQK
IVLYAKKVGYTPDWIFLLRNVMRISPDQGQQFAQMLVQDEEPLADITQIV
DVFMEYNLIQQCTAFLLDALKNNRPSEGPLQTRLLEMNLMHAPQVADAIL
GNQMFTHYDRAHIAQLCEKAGLLQRALEHFTDLYDIKRAVVHTHLLNPEW
LVNYFGSLSVEDSLECLRAMLSANIRQNLQICVQVASKYHEQLSTQSLIE
LFESFKSFEGLFYFLGSIVNFSQDPDVHFKYIQAACKTGQIKEVERICRE
SNCYDPERVKNFLKEAKLTDQLPLIIVCDRFDFVHDLVLYLYRNNLQKYI
EIYVQKVNPSRLPVVIGGLLDVDCSEDVIKNLILVVRGQFSTDELVAEVE
KRNRLKLLLPWLEARIHEGCEEPATHNALAKIYIDSNNNPERFLRENPYY
DSRVVGKYCEKRDPHLACVAYERGQCDLELINLPVSGNLLDVYSSQGVAT
PAITVSNSCPAELPNIKREISETEAKALLKERQKKDNHNLIERRRRFNIN
DRIKELGTLIPKSSDPEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRQ
RSLEQANRSLQLRIQELELQAQIHGLPVPPTPGLLSLATTSASDSLKPEQ
LDIEEEGRPGAATFHVGGGPAQNAPHQQPPAPPSDALLDLHFPSDHLGDL
GDPFHLGLEDILMEEEEGVVGGLSGGALSPLRAASDPLLSSVSPAVSKAS
1212
3D view using mol* of 859 (AA BP:932)


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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.
CLTC_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.
CLTC_TFE3_859_pLDDT.png (AA BP:932)
all structure
CLTC_TFE3_859_pLDDT_and_active_sites.png (AA BP:932)
all structure
CLTC_TFE3_859_violinplot.png (AA BP:932)
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
CLTC_TFE3_859.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
8591.0443591.062932.2740.5290.7560.9550.5361.0170.5270.704Chain A: 26,27,28,29,30,31,32,33,34,41,69,70,71,72
,75,76,83,108,109,110,111,112,113,114,115,116,124,
144,151,152,153,154,155,156,157,158,159,160,162,16
6,168,170,197,198,199,200,201,202,203,214,260,262,
263,264,265,266,267,268,269,278,302,304,305,306,30
7,308,310,313,320

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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
859ZINC000014210876DB09272Eluxadoline-5.40873-6.13633
859ZINC000000057624DB00368Norepinephrine-6.09449-6.11199
859ZINC000008214483DB00479Amikacin-5.95929-6.03649
859ZINC000000895457DB08847Hydroxyproline-6.01408-6.01408
859ZINC000029416466DB01232Saquinavir-5.98867-6.00187
859ZINC000000034157DB06707Levonordefrin-5.97621-5.99371
859ZINC000000388081DB05381Histamine-4.5534-5.885
859ZINC000000895302DB06770Benzyl alcohol-5.88406-5.88406
859ZINC000029571072DB06636Isavuconazonium-5.424-5.856
859ZINC000000020259DB00852Pseudoephedrine-5.82006-5.82676
859ZINC000019166991DB00780Phenelzine-4.96968-5.75018
859ZINC000000000746DB00871Terbutaline-5.72374-5.73804
859ZINC000003794794DB01204Mitoxantrone-5.71531-5.71531
859ZINC000000896731DB00744Zileuton-5.67916-5.69776
859ZINC000000000469DB00816Orciprenaline-5.65382-5.66822
859ZINC000000004893DB06216Asenapine-5.64894-5.65294
859ZINC000000113355DB00388Phenylephrine-5.64489-5.65159
859ZINC000100007011DB00302Tranexamic acid-5.62982-5.62982
859ZINC000000643055DB01127Econazole-4.89885-5.62185
859ZINC000019168887DB00190Carbidopa-5.55606-5.55606

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check button Drug information from DrugBank of the top 20 interacting small molecules.
ZINC IDDrugBank IDDrug nameDrug typeSMILESDrug group
ZINC000014210876DB09272EluxadolineSmall moleculeCOC1=CC=C(CN([C@@H](C)C2=NC(=CN2)C2=CC=CC=C2)C(=O)[C@@H](N)CC2=C(C)C=C(C=C2C)C(N)=O)C=C1C(O)=OApproved|Investigational
ZINC000000057624DB00368NorepinephrineSmall moleculeNC[C@H](O)C1=CC(O)=C(O)C=C1Approved
ZINC000008214483DB00479AmikacinSmall moleculeNCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](N)[C@H]1OApproved|Investigational|Vet_approved
ZINC000000895457DB08847HydroxyprolineSmall moleculeO[C@H]1CN[C@@H](C1)C(O)=OExperimental
ZINC000000034157DB06707LevonordefrinSmall moleculeC[C@H](N)[C@H](O)C1=CC(O)=C(O)C=C1Approved
ZINC000000388081DB05381HistamineSmall moleculeNCCC1=CNC=N1Approved|Investigational
ZINC000000895302DB06770Benzyl alcoholSmall moleculeOCC1=CC=CC=C1Approved
ZINC000000020259DB00852PseudoephedrineSmall moleculeCN[C@@H](C)[C@@H](O)C1=CC=CC=C1Approved
ZINC000019166991DB00780PhenelzineSmall moleculeNNCCC1=CC=CC=C1Approved
ZINC000003794794DB01204MitoxantroneSmall moleculeOCCNCCNC1=CC=C(NCCNCCO)C2=C1C(=O)C1=C(C(O)=CC=C1O)C2=OApproved|Investigational
ZINC000000896731DB00744ZileutonSmall moleculeCC(N(O)C(N)=O)C1=CC2=CC=CC=C2S1Approved|Investigational|Withdrawn
ZINC000000000469DB00816OrciprenalineSmall moleculeCC(C)NCC(O)C1=CC(O)=CC(O)=C1Approved
ZINC000000113355DB00388PhenylephrineSmall moleculeCNC[C@H](O)C1=CC(O)=CC=C1Approved
ZINC000000643055DB01127EconazoleSmall moleculeClC1=CC=C(COC(CN2C=CN=C2)C2=C(Cl)C=C(Cl)C=C2)C=C1Approved
ZINC000019168887DB00190CarbidopaSmall moleculeC[C@@](CC1=CC(O)=C(O)C=C1)(NN)C(O)=OApproved

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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
ZINC000014210876569.6597.127866.349287.048259.904319.39701681.617610.758.68917.53822
ZINC000014210876569.6593.679901.19287.315271.102342.77301718.172610.758.88816.54622
ZINC000014210876569.6596.683902.919270.324282.937349.65801740.575610.758.9214.83122
ZINC000014210876569.6596.148862.573279.279281.556301.73701689.73610.758.98413.05322
ZINC000014210876569.65914.843858.111275.061269.062313.98801679.1610.759.13316.01322
ZINC000014210876569.65914.363896.983280.954265.963350.06601717.668610.759.0117.35222
ZINC000000057624169.183.43375.22557.715204.72112.790592.16854.28.952246.79100
ZINC000000057624169.182.409366.47858.999201.357106.1220584.36954.28.77247.30600
ZINC000008214483585.6077.114830.321338.822491.499001599.8461726.99.6291032
ZINC000008214483585.6074.555814.872354.051460.821001597.3381726.99.4241032
ZINC000008214483585.60712.3828.375361.409466.966001597.7451726.99.4971032
ZINC000000895457131.1317.237313.333137.57175.76300472.62835.210.259230.29901
ZINC000029416466670.856.1541020.69508.33132.906379.45402024.819513.78.648239.15731
ZINC000029416466670.855.8181108.855506.927192.124409.80302112.978513.78.927226.10132
ZINC000029416466670.854.1071071.641527.824184.088359.72902091.307513.78.879226.78832
ZINC000000034157183.2071.584399.847106.772186.848106.2270646.19954.28.948252.10900
ZINC000000034157183.2072.284398.836105.841186.106106.8890643.15454.28.781252.1900
ZINC000000388081111.1464.788315.23192.229118.535104.4680466.77632.59.295265.25300
ZINC000000388081111.1465.535313.53290.818116.688106.0260465.559339.188264.91700
ZINC000000388081111.1464.794316.56991.628116.549108.3930470.46832.59.292265.82300
ZINC000000895302108.142.044309.51749.93555.235204.3470461.18711.79.646395.53700
ZINC000000020259165.2351.645408.608167.77458.787182.0460662.69723.29.158384.99100
ZINC000000020259165.2351.679405.001165.63758.444180.9210657.17623.29.01384.84600
ZINC000019166991136.1963.232356.42381.76587.193187.4660561.68631.58.991263.33400
ZINC000019166991136.1963.226364.81672.47195.426196.9190568.55331.59.191261.88700
ZINC000019166991136.1961.465367.92174.22696.877196.8180568.8231.59.505261.57500
ZINC000000000746225.2873.599496.174234.367155.26106.5470827.34444.29.067261.8700
ZINC000000000746225.2871.595496.002233.982154.54107.480824.98644.28.979261.98100
ZINC000003794794444.4865.02786.306339.526291.766155.01401393.6349.97.456117.85912
ZINC000000896731236.2883.773444.59884.301131.134195.10534.058746.48133.78.644378.1800
ZINC000000896731236.2885.297450.81685.528135.414201.88127.993746.81233.78.57376.55600
ZINC000000000469211.262.192479.658212.457159.848107.3530782.09444.79.205261.39100
ZINC000000000469211.263.668477.852212.113158.053107.6850779.05944.78.929261.6900
ZINC000000004893285.7722.935505.956170.4748.432255.47371.578892.61102.59.23310000
ZINC000000004893285.7722.515507.857169.7058.429258.1771.553893.3902.59.299310000
ZINC000000113355167.2072.072404.418139.15116.415148.8530642.53233.959.18268.88100
ZINC000000113355167.2072.123400.929135.071117.85148.0080637.05233.959.132268.36900
ZINC000100007011157.2121.799375.783216.456159.32700603.499339.574242.47101
ZINC000000643055381.6883.522625.9465.52430.702344.327185.3871104.8403.79.333310011
ZINC000000643055381.6885.315630.72759.72932.959342.705195.3341112.71903.79.213310011
ZINC000019168887226.2323.09431.11796.823239.53394.7610720.488548.9241011


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Drug Toxicity Information


check button Toxicity information of individual drugs using eToxPred
ZINC IDSmileSurface AccessibilityToxicity
ZINC000014210876COc1ccc(CN(C(=O)[C@@H](N)Cc2c(C)cc(C(N)=O)cc2C)[C@@H](C)c2nc(-c3ccccc3)c[nH]2)cc1C(=O)O0.0678197430.140534867
ZINC000000057624NC[C@H](O)c1ccc(O)c(O)c10.187147430.309816979
ZINC000008214483NCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](N)[C@H]1O0.0137355550.304219313
ZINC000000895457O=C(O)[C@H]1C[C@H](O)CN10.0992782670.470163896
ZINC000029416466CC(C)(C)NC(=O)[C@@H]1C[C@H]2CCCC[C@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(N)=O)NC(=O)c1ccc2ccccc2n10.0392487760.333476835
ZINC000000034157C[C@H](N)[C@H](O)c1ccc(O)c(O)c10.1350791920.302260037
ZINC000000388081NCCc1cnc[nH]10.2129447840.352067312
ZINC000000895302OCc1ccccc10.8687502150.569537247
ZINC000029571072CNCC(=O)OCc1cccnc1N(C)C(=O)O[C@H](C)[n+]1cnn(C[C@](O)(c2cc(F)ccc2F)[C@@H](C)c2nc(-c3ccc(C#N)cc3)cs2)c10.0254160270.235213823
ZINC000000020259CN[C@@H](C)[C@@H](O)c1ccccc10.2085878950.312560893
ZINC000019166991NNCCc1ccccc10.4887226720.493119705
ZINC000000000746CC(C)(C)NC[C@H](O)c1cc(O)cc(O)c10.1598452130.248277396
ZINC000003794794O=C1c2c(O)ccc(O)c2C(=O)c2c(NCCNCCO)ccc(NCCNCCO)c210.1629240550.487926509
ZINC000000896731C[C@H](c1cc2ccccc2s1)N(O)C(N)=O0.1363358820.223511692
ZINC000000000469CC(C)NC[C@@H](O)c1cc(O)cc(O)c10.1702212550.19797014
ZINC000000004893CN1C[C@H]2c3ccccc3Oc3ccc(Cl)cc3[C@@H]2C10.1331176950.325998169
ZINC000000113355CNC[C@H](O)c1cccc(O)c10.2276558640.251523685
ZINC000100007011NC[C@@H]1CC[C@@H](C(=O)O)CC10.343577740.472488357
ZINC000000643055Clc1ccc(CO[C@@H](Cn2ccnc2)c2ccc(Cl)cc2Cl)cc10.1798207540.346527688
ZINC000019168887C[C@@](Cc1ccc(O)c(O)c1)(NN)C(=O)O0.1368359620.241973462


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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
CLTCHGS, MCC, IKBKE, TFE3, SNX5, TOM1, SNX9, DNAJC6, ARMCX3, C10orf88, EPN1, EHD1, GGA1, GGA2, GGA3, KIT, AMPH, CLINT1, TNK2, LDLRAP1, HIP1, AP1B1, AP2A2, AP3B2, MAP3K10, PICALM, EPN2, Epn1, VCL, Arrb2, STAMBP, STAMBPL1, STAM, MAP1LC3A, SNCA, PRKACA, WNK1, Mapk13, HDAC5, SPG20, RICTOR, Erh, Cd2ap, Pttg1, EBNA-LP, PCM1, NDRG1, PPP1CA, ITSN1, ARRB1, SIRT7, SH3KBP1, DYRK1A, SNAP91, AP2B1, BIN1, AP1G1, RAC1, TOM1L1, TOM1L2, ISG15, CUL3, CUL5, CUL2, CDK2, CUL1, COPS5, DCUN1D1, CAND1, NEDD8, XRCC6, HERC1, ATG16L1, SYNJ1, LRRK2, Nfe2l2, AKT1, GRB2, SHC1, AP2M1, MYO6, SRC, FYN, Htt, DNAJA3, RPSA, ESR1, PAXIP1, PPP1CC, SMURF1, ARRB2, ERBB2, FN1, VCAM1, Fcho2, DAB2, UBL4A, ITGA4, MYBL2, SVIL, PAN2, NPM1, PTAFR, ATP4A, EP300, QARS, YWHAQ, FBXO6, RPA1, RPA2, RPA3, ERG, EPHA2, LGR4, Fbxl16, STAU1, TP53, HUWE1, FBXW11, GJB5, NXF1, ADRB2, AVPR2, CUL7, OBSL1, CCDC8, EED, ZFYVE9, OCRL, ATR, SCYL2, HTR6, HNRNPA1, UNK, ATP1A1, ATP1A2, ATP1A3, ATP5C1, CCDC47, CCT3, CCT6A, BLOC1S1, CAD, CANX, CCT6B, CISD1, CLTA, CYC1, DHX38, EHD2, FASTKD2, HSP90B1, IPO5, MTCH2, NDUFB9, NDUFS1, NLRP1, RAB5B, RANBP2, RANBP6, SLC25A3, SSR3, TECR, TOMM22, UQCRC2, VDAC1, VDAC2, VDAC3, ZMPSTE24, DDOST, EIF6, COX2, PHB, PHB2, PPP2R1A, PPP2R1B, RPN1, TMCO1, TUFM, UQCRQ, NTRK1, OFD1, CEP97, CNTRL, FBF1, NPHP1, DCTN1, POC5, POC1B, PPME1, ABCA2, PARP4, AP2A1, ATP6V1B2, ATP6V0A1, CAV1, CLTB, CAPZA2, DBN1, FLNA, GAK, MYH9, DNAJC7, IQGAP1, PDLIM7, SEC16A, SYNPO, MAPRE1, LIMA1, GTSE1, ANLN, MYO19, ARX, MYO18A, CSNK1A1, CSNK1E, STOM, EPS15, HSPA1A, HSPA4, NDUFA9, CHMP1A, PIK3C2A, PRKAR2A, SEC13, SOAT1, CLTCL1, SORBS2, PKP4, USO1, NUMB, TNK1, RAB11A, HIP1R, ATP6V0D1, XPR1, SEC24C, KIAA0430, IST1, HELZ, MVP, TROAP, SEC24B, RBM14, SEC23A, VTI1B, TRAFD1, PKP3, AAK1, BTBD3, TNRC6B, EDC4, DSTYK, PTPN23, NECAP1, TNRC6A, EHD4, EGFL7, ATP6V1D, PTRH2, PLEKHA5, CPVL, BMP2K, DCP1A, ERBB2IP, CHMP1B, KIDINS220, MTUS1, DENND1A, CRTC3, CPSF7, EDC3, CCDC115, FAM83A, REPS1, STON2, FCHO2, CHMP4B, MITD1, CRTC2, FAM83B, FAM83H, SLC35B2, Actb, Myh9, Myo1c, Ppp1cb, Tpm1, Coro1c, Cul3, Spast, Tmod3, Dctn3, Uso1, Lima1, Samm50, Calml3, Myh10, Strn3, Smap1, Ptpn23, Nhsl1, Sec24c, Flnb, IKBKB, MAP3K7, MCM2, AP3D1, U2AF2, CDC73, ZNF746, ARF6, CYLD, LASP1, BRCA1, TES, MTF1, BRD1, CFTR, ZNF598, PDGFRB, FBXO7, TMPO, PTCH1, HSPA8, MAP2K1, PIK3CA, APOE, BMPR1A, JUP, UQCRB, UBE2M, RAD18, PRPF8, EFTUD2, AAR2, PIH1D1, TNIP2, LARP7, RNF4, TNF, SPDL1, RIOK1, PRKCZ, HEXIM1, MEPCE, RUNX1, RNF123, PPT1, HERC2, UBE3A, AGR2, RECQL4, SMAP1, MYC, CDK9, Prkaa1, Prkab1, CDK5RAP2, GRWD1, KRT17, KIAA1429, PLEKHA2, RC3H2, ACTC1, TET2, NR2C2, UCHL3, PRDM16, MECOM, AGRN, BMH1, BMH2, ATXN3, TCF7L2, STX2, GSK3B, ABCC6, BIRC3, LMBR1L, WWP2, Hsp22, TRIM28, GJA1, TEX101, ARIH2, PLEKHA4, PINK1, YAP1, TFCP2, FANCD2, Clta, PXN, RALBP1, PTCHD3, C18orf54, ANKRD55, E, M, nsp13, nsp14, nsp4, nsp5, nsp6, ORF14, ORF3a, ORF6, ORF7a, ORF7b, ABCC2, CDCA5, ACO1, OPTN, NEK4, LRRC31, DUX4, CIT, AURKB, ECT2, KIF14, KIF20A, MAD2L2, KIF23, PRC1, PRNP, CHCHD1, HAX1, MFN2, SLC25A46, LDLR, SUMO2, PRKCB, Rnf183, AIMP2, BRD4, NINL, AFTPH, NUPR1, EPHA3, CIC, Apc2, RBM39, LGALS9, RIN3, EIF3H, DNAJA1, HSPA1L, HSPA2, HSPA6, BAG5, AR, UFL1, DDRGK1, CD3EAP, LAMTOR1, POLR2C, TRIM37, HTRA4, DRD2, ADRBK1, WDR5, PAGE4, NUDCD2, BGLT3, EDEM1, BAG2, DTX3, BTF3, IGF1R, NEDD4, FBXW7, TFRC, IFITM1, BSG, IFITM3, TMPRSS11B, CLEC4E, nsp15, ORF10, FGD5, MAP1LC3B, NBR1, CALCOCO2, SQSTM1, TOLLIP, Chrna4, SIRT6, PER2,
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
CLTCall 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 CLTC-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 CLTC-TFE3


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
HgeneCLTCC4518356MiT family translocation renal cell carcinoma2ORPHANET
HgeneCLTCC4693389MENTAL RETARDATION, AUTOSOMAL DOMINANT 562GENOMICS_ENGLAND;UNIPROT
HgeneCLTCC0079744Diffuse Large B-Cell Lymphoma1CTD_human
HgeneCLTCC0334121Inflammatory Myofibroblastic Tumor1ORPHANET
TgeneTFE3C4518356MiT family translocation renal cell carcinoma2ORPHANET
TgeneTFE3C0206657Alveolar Soft Part Sarcoma1ORPHANET
TgeneTFE3C0206732Epithelioid hemangioendothelioma1ORPHANET