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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:CLTCL1-NAT1 (FusionGDB2 ID:17399)

Fusion Gene Summary for CLTCL1-NAT1

check button Fusion gene summary
Fusion gene informationFusion gene name: CLTCL1-NAT1
Fusion gene ID: 17399
HgeneTgene
Gene symbol

CLTCL1

NAT1

Gene ID

8218

10991

Gene nameclathrin heavy chain like 1solute carrier family 38 member 3
SynonymsCHC22|CLH22|CLTCL|CLTDG17|NAT1|SN1|SNAT3
Cytomap

22q11.21

3p21.31

Type of geneprotein-codingprotein-coding
Descriptionclathrin heavy chain 2CLH-22Clathrin, heavy polypeptide Dclathrin heavy chain on chromosome 22clathrin, heavy polypeptide-like 1sodium-coupled neutral amino acid transporter 3N-system amino acid transporter 1Na(+)-coupled neutral amino acid transporter 3system N amino acid transporter 1system N1 Na+ and H+-coupled glutamine transporter
Modification date2020031320200313
UniProtAcc

P53675

Q8WUY8

Ensembl transtripts involved in fusion geneENST00000263200, ENST00000353891, 
ENST00000427926, ENST00000442042, 
ENST00000307719, ENST00000517492, 
ENST00000518029, ENST00000535084, 
ENST00000539092, ENST00000541942, 
ENST00000545197, ENST00000517441, 
ENST00000520546, 
Fusion gene scores* DoF score5 X 5 X 3=754 X 4 X 2=32
# samples 54
** MAII scorelog2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CLTCL1 [Title/Abstract] AND NAT1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLTCL1(19176830)-NAT1(18080747), # samples:1
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
HgeneCLTCL1

GO:0000278

mitotic cell cycle

19509056

HgeneCLTCL1

GO:0000278

mitotic cell cycle

20065094

HgeneCLTCL1

GO:0006898

receptor-mediated endocytosis

19509056

TgeneNAT1

GO:0006867

asparagine transport

10823827

TgeneNAT1

GO:0006868

glutamine transport

10823827

TgeneNAT1

GO:0015808

L-alanine transport

10823827

TgeneNAT1

GO:0015817

histidine transport

10823827


check buttonFusion gene breakpoints across CLTCL1 (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 NAT1 (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
ChiTaRS5.0N/AEC580463CLTCL1chr22

19176830

+NAT1chr8

18080747

-


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Fusion Gene ORF analysis for CLTCL1-NAT1

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
intron-3UTRENST00000263200ENST00000307719CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000263200ENST00000517492CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000263200ENST00000518029CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000263200ENST00000535084CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000263200ENST00000539092CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000263200ENST00000541942CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000263200ENST00000545197CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000353891ENST00000307719CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000353891ENST00000517492CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000353891ENST00000518029CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000353891ENST00000535084CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000353891ENST00000539092CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000353891ENST00000541942CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000353891ENST00000545197CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000427926ENST00000307719CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000427926ENST00000517492CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000427926ENST00000518029CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000427926ENST00000535084CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000427926ENST00000539092CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000427926ENST00000541942CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000427926ENST00000545197CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000442042ENST00000307719CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000442042ENST00000517492CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000442042ENST00000518029CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000442042ENST00000535084CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000442042ENST00000539092CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000442042ENST00000541942CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-3UTRENST00000442042ENST00000545197CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-intronENST00000263200ENST00000517441CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-intronENST00000263200ENST00000520546CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-intronENST00000353891ENST00000517441CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-intronENST00000353891ENST00000520546CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-intronENST00000427926ENST00000517441CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-intronENST00000427926ENST00000520546CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-intronENST00000442042ENST00000517441CLTCL1chr22

19176830

+NAT1chr8

18080747

-
intron-intronENST00000442042ENST00000520546CLTCL1chr22

19176830

+NAT1chr8

18080747

-

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 CLTCL1-NAT1


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 CLTCL1-NAT1


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/:19176830/:18080747)
- 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
CLTCL1

P53675

NAT1

Q8WUY8

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: Probable acetyltransferase that binds the 5'-GGACTACAG-3' sequence of coproporphyrinogen oxidase promoter. Able to activate transcription of a reporter construct in vitro.

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 CLTCL1-NAT1


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 CLTCL1-NAT1


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 CLTCL1-NAT1


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 CLTCL1-NAT1


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