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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:NF2-CLTCL1 (FusionGDB2 ID:58719)

Fusion Gene Summary for NF2-CLTCL1

check button Fusion gene summary
Fusion gene informationFusion gene name: NF2-CLTCL1
Fusion gene ID: 58719
HgeneTgene
Gene symbol

NF2

CLTCL1

Gene ID

4771

8218

Gene nameneurofibromin 2clathrin heavy chain like 1
SynonymsACN|BANF|SCHCHC22|CLH22|CLTCL|CLTD
Cytomap

22q12.2

22q11.21

Type of geneprotein-codingprotein-coding
Descriptionmerlinmoesin-ezrin-radixin likemoesin-ezrin-radixin-like proteinmoesin-ezrin-radizin-like proteinneurofibromin 2 (bilateral acoustic neuroma)schwannomerlinschwannominclathrin heavy chain 2CLH-22Clathrin, heavy polypeptide Dclathrin heavy chain on chromosome 22clathrin, heavy polypeptide-like 1
Modification date2020032220200313
UniProtAcc

P35240

P53675

Ensembl transtripts involved in fusion geneENST00000334961, ENST00000347330, 
ENST00000353887, ENST00000361166, 
ENST00000361452, ENST00000361676, 
ENST00000397789, ENST00000403435, 
ENST00000403999, ENST00000338641, 
ENST00000413209, 		ENST00000263200, 
ENST00000353891, ENST00000427926, 
ENST00000442042, 
Fusion gene scores* DoF score15 X 11 X 7=11559 X 7 X 7=441
# samples 1812
** MAII scorelog2(18/1155*10)=-2.68182403997375
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/441*10)=-1.877744249949
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NF2 [Title/Abstract] AND CLTCL1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNF2(30079053)-CLTCL1(19171124), # samples:3
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
HgeneNF2

GO:0008285

negative regulation of cell proliferation

12444102|20178741

HgeneNF2

GO:0022408

negative regulation of cell-cell adhesion

17210637

HgeneNF2

GO:0042532

negative regulation of tyrosine phosphorylation of STAT protein

12444102

HgeneNF2

GO:0046426

negative regulation of JAK-STAT cascade

12444102

TgeneCLTCL1

GO:0000278

mitotic cell cycle

19509056

TgeneCLTCL1

GO:0000278

mitotic cell cycle

20065094

TgeneCLTCL1

GO:0006898

receptor-mediated endocytosis

19509056


check buttonFusion gene breakpoints across NF2 (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 CLTCL1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4BRCATCGA-EW-A1PH-01ANF2chr22

30079053

-CLTCL1chr22

19171124

-
ChimerDB4BRCATCGA-EW-A1PH-01ANF2chr22

30079053

+CLTCL1chr22

19171124

-


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Fusion Gene ORF analysis for NF2-CLTCL1

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
3UTR-3CDSENST00000334961ENST00000263200NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000334961ENST00000353891NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000334961ENST00000427926NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000347330ENST00000263200NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000347330ENST00000353891NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000347330ENST00000427926NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000353887ENST00000263200NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000353887ENST00000353891NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000353887ENST00000427926NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000361166ENST00000263200NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000361166ENST00000353891NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000361166ENST00000427926NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000361452ENST00000263200NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000361452ENST00000353891NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000361452ENST00000427926NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000361676ENST00000263200NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000361676ENST00000353891NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000361676ENST00000427926NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000397789ENST00000263200NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000397789ENST00000353891NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000397789ENST00000427926NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000403435ENST00000263200NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000403435ENST00000353891NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000403435ENST00000427926NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000403999ENST00000263200NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000403999ENST00000353891NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-3CDSENST00000403999ENST00000427926NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-5UTRENST00000334961ENST00000442042NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-5UTRENST00000347330ENST00000442042NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-5UTRENST00000353887ENST00000442042NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-5UTRENST00000361166ENST00000442042NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-5UTRENST00000361452ENST00000442042NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-5UTRENST00000361676ENST00000442042NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-5UTRENST00000397789ENST00000442042NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-5UTRENST00000403435ENST00000442042NF2chr22

30079053

+CLTCL1chr22

19171124

-
3UTR-5UTRENST00000403999ENST00000442042NF2chr22

30079053

+CLTCL1chr22

19171124

-
intron-3CDSENST00000338641ENST00000263200NF2chr22

30079053

+CLTCL1chr22

19171124

-
intron-3CDSENST00000338641ENST00000353891NF2chr22

30079053

+CLTCL1chr22

19171124

-
intron-3CDSENST00000338641ENST00000427926NF2chr22

30079053

+CLTCL1chr22

19171124

-
intron-3CDSENST00000413209ENST00000263200NF2chr22

30079053

+CLTCL1chr22

19171124

-
intron-3CDSENST00000413209ENST00000353891NF2chr22

30079053

+CLTCL1chr22

19171124

-
intron-3CDSENST00000413209ENST00000427926NF2chr22

30079053

+CLTCL1chr22

19171124

-
intron-5UTRENST00000338641ENST00000442042NF2chr22

30079053

+CLTCL1chr22

19171124

-
intron-5UTRENST00000413209ENST00000442042NF2chr22

30079053

+CLTCL1chr22

19171124

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

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 Genomic Features for NF2-CLTCL1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for NF2-CLTCL1


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/:30079053/:19171124)
- 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
NF2

P35240

CLTCL1

P53675

FUNCTION: Probable regulator of the Hippo/SWH (Sav/Wts/Hpo) signaling pathway, a signaling pathway that plays a pivotal role in tumor suppression by restricting proliferation and promoting apoptosis. Along with WWC1 can synergistically induce the phosphorylation of LATS1 and LATS2 and can probably function in the regulation of the Hippo/SWH (Sav/Wts/Hpo) signaling pathway. May act as a membrane stabilizing protein. May inhibit PI3 kinase by binding to AGAP2 and impairing its stimulating activity. Suppresses cell proliferation and tumorigenesis by inhibiting the CUL4A-RBX1-DDB1-VprBP/DCAF1 E3 ubiquitin-protein ligase complex. {ECO:0000269|PubMed:20159598, ECO:0000269|PubMed:20178741, ECO:0000269|PubMed:21167305}.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}.

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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for NF2-CLTCL1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for NF2-CLTCL1


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 (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for NF2-CLTCL1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for NF2-CLTCL1


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