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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:TFEB-CADM2

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: TFEB-CADM2
FusionPDB ID: 90322
FusionGDB2.0 ID: 90322
HgeneTgene
Gene symbol

TFEB

CADM2

Gene ID

7942

253559

Gene nametranscription factor EBcell adhesion molecule 2
SynonymsALPHATFEB|BHLHE35|TCFEBIGSF4D|NECL3|Necl-3|SynCAM 2|synCAM2
Cytomap

6p21.1

3p12.1

Type of geneprotein-codingprotein-coding
Descriptiontranscription factor EBT-cell transcription factor EBclass E basic helix-loop-helix protein 35cell adhesion molecule 2immunoglobulin superfamily member 4Dnectin-like 3nectin-like protein 3synaptic cell adhesion molecule 2
Modification date2020032920200322
UniProtAcc

P19484

Q8N3J6

Ensembl transtripts involved in fusion geneENST idsENST00000230323, ENST00000358871, 
ENST00000373033, ENST00000403298, 
ENST00000420312, ENST00000394283, 
ENST00000485126, ENST00000383699, 
ENST00000405615, ENST00000407528, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score12 X 11 X 8=105615 X 13 X 8=1560
# samples 1417
** MAII scorelog2(14/1056*10)=-2.91511110241349
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/1560*10)=-3.19793937761191
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: TFEB [Title/Abstract] AND CADM2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)TFEB(41653828)-CADM2(85851197), # samples:1
Anticipated loss of major functional domain due to fusion event.TFEB-CADM2 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.
TFEB-CADM2 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.
TFEB-CADM2 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.
TFEB-CADM2 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.
TFEB-CADM2 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
TFEB-CADM2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
TFEB-CADM2 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
TFEB-CADM2 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
TFEB-CADM2 seems lost the major protein functional domain in Tgene 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
HgeneTFEB

GO:0010468

regulation of gene expression

27278822

HgeneTFEB

GO:0045893

positive regulation of transcription, DNA-templated

27278822|29146937

HgeneTFEB

GO:0045944

positive regulation of transcription by RNA polymerase II

19556463


check buttonFusion gene breakpoints across TFEB (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 CADM2 (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-B9-A69E-01ATFEBchr6

41653828

-CADM2chr3

85851197

+


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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)
ENST00000373033TFEBchr641653828-ENST00000383699CADM2chr385851197+10005123210932358421
ENST00000373033TFEBchr641653828-ENST00000407528CADM2chr385851197+2531123210932478461
ENST00000373033TFEBchr641653828-ENST00000405615CADM2chr385851197+2479123210932478462

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
ENST00000373033ENST00000383699TFEBchr641653828-CADM2chr385851197+0.0001477020.9998523
ENST00000373033ENST00000407528TFEBchr641653828-CADM2chr385851197+0.0033376190.9966624
ENST00000373033ENST00000405615TFEBchr641653828-CADM2chr385851197+0.0032463410.99675363

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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

>90322_90322_1_TFEB-CADM2_TFEB_chr6_41653828_ENST00000373033_CADM2_chr3_85851197_ENST00000383699_length(amino acids)=421AA_BP=46
MEQGHHPQGLCGLHPEDAEGPAKVQGAGEPLSPPGDDQQAALAPYPGSQGQFPLTQNVTVVEGGTAILTCRVDQNDNTSLQWSNPAQQTL
YFDDKKALRDNRIELVRASWHELSISVSDVSLSDEGQYTCSLFTMPVKTSKAYLTVLGVPEKPQISGFSSPVMEGDLMQLTCKTSGSKPA
ADIRWFKNDKEIKDVKYLKEEDANRKTFTVSSTLDFRVDRSDDGVAVICRVDHESLNATPQVAMQVLEIHYTPSVKIIPSTPFPQEGQPL
ILTCESKGKPLPEPVLWTKDGGELPDPDRMVVSGRELNILFLNKTDNGTYRCEATNTIGQSSAEYVLIVHDPNALAGQNGPDHALIGGIV

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

>90322_90322_2_TFEB-CADM2_TFEB_chr6_41653828_ENST00000373033_CADM2_chr3_85851197_ENST00000405615_length(amino acids)=462AA_BP=46
MEQGHHPQGLCGLHPEDAEGPAKVQGAGEPLSPPGDDQQAALAPYPGSQGQFPLTQNVTVVEGGTAILTCRVDQNDNTSLQWSNPAQQTL
YFDDKKALRDNRIELVRASWHELSISVSDVSLSDEGQYTCSLFTMPVKTSKAYLTVLGVPEKPQISGFSSPVMEGDLMQLTCKTSGSKPA
ADIRWFKNDKEIKDVKYLKEEDANRKTFTVSSTLDFRVDRSDDGVAVICRVDHESLNATPQVAMQVLEIHYTPSVKIIPSTPFPQEGQPL
ILTCESKGKPLPEPVLWTKDGGELPDPDRMVVSGRELNILFLNKTDNGTYRCEATNTIGQSSAEYVLIVHDVPNTLLPTTIIPSLTTATV
TTTVAITTSPTTSATTSSIRDPNALAGQNGPDHALIGGIVAVVVFVTLCSIFLLGRYLARHKGTYLTNEAKGAEDAPDADTAIINAEGSQ

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

>90322_90322_3_TFEB-CADM2_TFEB_chr6_41653828_ENST00000373033_CADM2_chr3_85851197_ENST00000407528_length(amino acids)=461AA_BP=46
MEQGHHPQGLCGLHPEDAEGPAKVQGAGEPLSPPGDDQQAALAPYPGSQGQFPLTQNVTVVEGGTAILTCRVDQNDNTSLQWSNPAQQTL
YFDDKKALRDNRIELVRASWHELSISVSDVSLSDEGQYTCSLFTMPVKTSKAYLTVLGVPEKPQISGFSSPVMEGDLMQLTCKTSGSKPA
ADIRWFKNDKEIKDVKYLKEEDANRKTFTVSSTLDFRVDRSDDGVAVICRVDHESLNATPQVAMQVLEIHYTPSVKIIPSTPFPQEGQPL
ILTCESKGKPLPEPVLWTKDGGELPDPDRMVVSGRELNILFLNKTDNGTYRCEATNTIGQSSAEYVLIVHDVPNTLLPTTIIPSLTTATV
TTTVAITTSPTTSATTSSIRDPNALAGQNGPDHALIGGIVAVVVFVTLCSIFLLGRYLARHKGTYLTNEAKGAEDAPDADTAIINAEGSQ

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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/chr6:41653828/chr3:85851197)
- 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
TFEB

P19484

CADM2

Q8N3J6

FUNCTION: Transcription factor that acts as a master regulator of lysosomal biogenesis, autophagy, lysosomal exocytosis, lipid catabolism, energy metabolism and immune response (PubMed:21617040, PubMed:22576015, PubMed:22343943, PubMed:22692423, PubMed:30120233, 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 TFE3 or MITF (PubMed:1748288, PubMed:19556463, PubMed:29146937). Involved in the cellular response to amino acid availability by acting downstream of MTOR: in the presence of nutrients, TFEB phosphorylation by MTOR promotes its cytosolic retention and subsequent inactivation (PubMed:21617040, PubMed:22576015, PubMed:22343943, PubMed:22692423). Upon starvation or lysosomal stress, inhibition of MTOR induces TFEB dephosphorylation, resulting in nuclear localization and transcription factor activity (PubMed:22576015, PubMed:22343943, PubMed:22692423). Specifically recognizes and binds the CLEAR-box sequence (5'-GTCACGTGAC-3') present in the regulatory region of many lysosomal genes, leading to activate their expression, thereby playing a central role in expression of lysosomal genes (PubMed:19556463, PubMed:22692423). Regulates lysosomal positioning in response to nutrient deprivation by promoting the expression of PIP4P1 (PubMed:29146937). Acts as a positive regulator of autophagy by promoting expression of genes involved in autophagy (PubMed:21617040, PubMed:22576015, PubMed:23434374, PubMed:27278822). In association with TFE3, 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 gamma-E3 box, a subset of E-boxes, present in the heavy-chain immunoglobulin enhancer (PubMed:2115126). Plays a role in the signal transduction processes required for normal vascularization of the placenta (By similarity). Involved in the immune response to infection by the bacteria S.aureus or S.enterica, acting downstream of protein kinase D (PKD), probably by regulating cytokine and chemokine expression (By similarity). {ECO:0000250|UniProtKB:Q9R210, ECO:0000269|PubMed:1748288, ECO:0000269|PubMed:19556463, ECO:0000269|PubMed:2115126, ECO:0000269|PubMed:21617040, ECO:0000269|PubMed:22343943, ECO:0000269|PubMed:22576015, ECO:0000269|PubMed:22692423, ECO:0000269|PubMed:23434374, ECO:0000269|PubMed:27278822, ECO:0000269|PubMed:29146937, ECO:0000269|PubMed:30120233, ECO:0000269|PubMed:31672913}.FUNCTION: Adhesion molecule that engages in homo- and heterophilic interactions with the other nectin-like family members, leading to cell aggregation. Important for synapse organization, providing regulated trans-synaptic adhesion. Preferentially binds to oligodendrocytes. {ECO:0000269|PubMed:17967169}.

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
HgeneTFEBchr6:41653828chr3:85851197ENST00000230323-91010_44317.0477.0Compositional biasNote=Gln-rich
HgeneTFEBchr6:41653828chr3:85851197ENST00000230323-91035_44317.0477.0Compositional biasNote=Poly-Gln
HgeneTFEBchr6:41653828chr3:85851197ENST00000373033-8910_44317.0477.0Compositional biasNote=Gln-rich
HgeneTFEBchr6:41653828chr3:85851197ENST00000373033-8935_44317.0477.0Compositional biasNote=Poly-Gln
HgeneTFEBchr6:41653828chr3:85851197ENST00000403298-8910_44317.0477.0Compositional biasNote=Gln-rich
HgeneTFEBchr6:41653828chr3:85851197ENST00000403298-8935_44317.0477.0Compositional biasNote=Poly-Gln
HgeneTFEBchr6:41653828chr3:85851197ENST00000420312-8910_44232.0392.0Compositional biasNote=Gln-rich
HgeneTFEBchr6:41653828chr3:85851197ENST00000420312-8935_44232.0392.0Compositional biasNote=Poly-Gln
HgeneTFEBchr6:41653828chr3:85851197ENST00000230323-910235_288317.0477.0DomainbHLH
HgeneTFEBchr6:41653828chr3:85851197ENST00000373033-89235_288317.0477.0DomainbHLH
HgeneTFEBchr6:41653828chr3:85851197ENST00000403298-89235_288317.0477.0DomainbHLH
HgeneTFEBchr6:41653828chr3:85851197ENST00000230323-910136_153317.0477.0MotifNuclear export signal
HgeneTFEBchr6:41653828chr3:85851197ENST00000373033-89136_153317.0477.0MotifNuclear export signal
HgeneTFEBchr6:41653828chr3:85851197ENST00000403298-89136_153317.0477.0MotifNuclear export signal
HgeneTFEBchr6:41653828chr3:85851197ENST00000420312-89136_153232.0392.0MotifNuclear export signal
HgeneTFEBchr6:41653828chr3:85851197ENST00000230323-910156_165317.0477.0RegionStrong transcription activation domain
HgeneTFEBchr6:41653828chr3:85851197ENST00000230323-910298_319317.0477.0RegionNote=Leucine-zipper
HgeneTFEBchr6:41653828chr3:85851197ENST00000373033-89156_165317.0477.0RegionStrong transcription activation domain
HgeneTFEBchr6:41653828chr3:85851197ENST00000373033-89298_319317.0477.0RegionNote=Leucine-zipper
HgeneTFEBchr6:41653828chr3:85851197ENST00000403298-89156_165317.0477.0RegionStrong transcription activation domain
HgeneTFEBchr6:41653828chr3:85851197ENST00000403298-89298_319317.0477.0RegionNote=Leucine-zipper
HgeneTFEBchr6:41653828chr3:85851197ENST00000420312-89156_165232.0392.0RegionStrong transcription activation domain
TgeneCADM2chr6:41653828chr3:85851197ENST00000383699110319_35029.333333333333332405.0Compositional biasNote=Thr-rich
TgeneCADM2chr6:41653828chr3:85851197ENST00000405615010319_35022.333333333333332438.0Compositional biasNote=Thr-rich
TgeneCADM2chr6:41653828chr3:85851197ENST00000407528010319_35020.333333333333332436.0Compositional biasNote=Thr-rich
TgeneCADM2chr6:41653828chr3:85851197ENST00000383699110127_21929.333333333333332405.0DomainNote=Ig-like C2-type 1
TgeneCADM2chr6:41653828chr3:85851197ENST00000383699110227_31229.333333333333332405.0DomainNote=Ig-like C2-type 2
TgeneCADM2chr6:41653828chr3:85851197ENST0000038369911027_11929.333333333333332405.0DomainNote=Ig-like V-type
TgeneCADM2chr6:41653828chr3:85851197ENST00000405615010127_21922.333333333333332438.0DomainNote=Ig-like C2-type 1
TgeneCADM2chr6:41653828chr3:85851197ENST00000405615010227_31222.333333333333332438.0DomainNote=Ig-like C2-type 2
TgeneCADM2chr6:41653828chr3:85851197ENST0000040561501027_11922.333333333333332438.0DomainNote=Ig-like V-type
TgeneCADM2chr6:41653828chr3:85851197ENST00000407528010127_21920.333333333333332436.0DomainNote=Ig-like C2-type 1
TgeneCADM2chr6:41653828chr3:85851197ENST00000407528010227_31220.333333333333332436.0DomainNote=Ig-like C2-type 2
TgeneCADM2chr6:41653828chr3:85851197ENST0000040752801027_11920.333333333333332436.0DomainNote=Ig-like V-type
TgeneCADM2chr6:41653828chr3:85851197ENST00000383699110389_43529.333333333333332405.0Topological domainCytoplasmic
TgeneCADM2chr6:41653828chr3:85851197ENST0000040561501025_36722.333333333333332438.0Topological domainExtracellular
TgeneCADM2chr6:41653828chr3:85851197ENST00000405615010389_43522.333333333333332438.0Topological domainCytoplasmic
TgeneCADM2chr6:41653828chr3:85851197ENST0000040752801025_36720.333333333333332436.0Topological domainExtracellular
TgeneCADM2chr6:41653828chr3:85851197ENST00000407528010389_43520.333333333333332436.0Topological domainCytoplasmic
TgeneCADM2chr6:41653828chr3:85851197ENST00000383699110368_38829.333333333333332405.0TransmembraneHelical
TgeneCADM2chr6:41653828chr3:85851197ENST00000405615010368_38822.333333333333332438.0TransmembraneHelical
TgeneCADM2chr6:41653828chr3:85851197ENST00000407528010368_38820.333333333333332436.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTFEBchr6:41653828chr3:85851197ENST00000230323-910366_414317.0477.0Compositional biasNote=Pro-rich
HgeneTFEBchr6:41653828chr3:85851197ENST00000373033-89366_414317.0477.0Compositional biasNote=Pro-rich
HgeneTFEBchr6:41653828chr3:85851197ENST00000403298-89366_414317.0477.0Compositional biasNote=Pro-rich
HgeneTFEBchr6:41653828chr3:85851197ENST00000420312-89366_414232.0392.0Compositional biasNote=Pro-rich
HgeneTFEBchr6:41653828chr3:85851197ENST00000420312-89235_288232.0392.0DomainbHLH
HgeneTFEBchr6:41653828chr3:85851197ENST00000420312-89298_319232.0392.0RegionNote=Leucine-zipper
TgeneCADM2chr6:41653828chr3:85851197ENST0000038369911025_36729.333333333333332405.0Topological domainExtracellular


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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
TFEBall structure
CADM2


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 TFEB-CADM2


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 TFEB-CADM2


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
HgeneTFEBC4518356MiT family translocation renal cell carcinoma2ORPHANET