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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:KLHL3-TYMS (FusionGDB2 ID:43015)

Fusion Gene Summary for KLHL3-TYMS

check button Fusion gene summary
Fusion gene informationFusion gene name: KLHL3-TYMS
Fusion gene ID: 43015
HgeneTgene
Gene symbol

KLHL3

TYMS

Gene ID

26249

7298

Gene namekelch like family member 3thymidylate synthetase
SynonymsPHA2DHST422|TMS|TS
Cytomap

5q31.2

18p11.32

Type of geneprotein-codingprotein-coding
Descriptionkelch-like protein 3thymidylate synthaseTSase
Modification date2020031320200322
UniProtAcc

Q9UH77

TYMSOS,C18orf56

Ensembl transtripts involved in fusion geneENST00000309755, ENST00000394937, 
ENST00000506491, ENST00000506873, 
ENST00000508657, ENST00000541417, 
ENST00000323224, ENST00000323250, 
ENST00000323274, ENST00000581920, 
Fusion gene scores* DoF score6 X 6 X 2=722 X 2 X 1=4
# samples 62
** MAII scorelog2(6/72*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/4*10)=2.32192809488736
Context

PubMed: KLHL3 [Title/Abstract] AND TYMS [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKLHL3(136997780)-TYMS(672549), # samples:2
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
HgeneKLHL3

GO:0006511

ubiquitin-dependent protein catabolic process

23453970|23576762

HgeneKLHL3

GO:0016567

protein ubiquitination

23453970

HgeneKLHL3

GO:0070936

protein K48-linked ubiquitination

23576762

TgeneTYMS

GO:0006231

dTMP biosynthetic process

8845352|11278511|15093541

TgeneTYMS

GO:0017148

negative regulation of translation

1924359

TgeneTYMS

GO:0035999

tetrahydrofolate interconversion

15093541


check buttonFusion gene breakpoints across KLHL3 (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 TYMS (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/ABM144222KLHL3chr5

136997780

-TYMSchr18

672549

+
ChiTaRS5.0N/ABM194340KLHL3chr5

136997780

-TYMSchr18

672549

+


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Fusion Gene ORF analysis for KLHL3-TYMS

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-intronENST00000309755ENST00000323224KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000309755ENST00000323250KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000309755ENST00000323274KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000309755ENST00000581920KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000394937ENST00000323224KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000394937ENST00000323250KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000394937ENST00000323274KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000394937ENST00000581920KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000506491ENST00000323224KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000506491ENST00000323250KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000506491ENST00000323274KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000506491ENST00000581920KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000506873ENST00000323224KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000506873ENST00000323250KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000506873ENST00000323274KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000506873ENST00000581920KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000508657ENST00000323224KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000508657ENST00000323250KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000508657ENST00000323274KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000508657ENST00000581920KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000541417ENST00000323224KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000541417ENST00000323250KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000541417ENST00000323274KLHL3chr5

136997780

-TYMSchr18

672549

+
intron-intronENST00000541417ENST00000581920KLHL3chr5

136997780

-TYMSchr18

672549

+

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 KLHL3-TYMS


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 KLHL3-TYMS


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/:136997780/:672549)
- 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
KLHL3

Q9UH77

TYMS

TYMSOS,C18orf56

FUNCTION: Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that acts as a regulator of ion transport in the distal nephron (PubMed:14528312, PubMed:22406640, PubMed:23387299, PubMed:23453970, PubMed:23576762, PubMed:23665031). The BCR(KLHL3) complex acts by mediating ubiquitination of WNK4, an inhibitor of potassium channel KCNJ1, leading to WNK4 degradation (PubMed:23387299, PubMed:23453970, PubMed:23576762, PubMed:23665031). The BCR(KLHL3) complex also mediates ubiquitination and degradation of CLDN8, a tight-junction protein required for paracellular chloride transport in the kidney (By similarity). {ECO:0000250|UniProtKB:E0CZ16, ECO:0000269|PubMed:14528312, ECO:0000269|PubMed:22406640, ECO:0000269|PubMed:23387299, ECO:0000269|PubMed:23453970, ECO:0000269|PubMed:23576762, ECO:0000269|PubMed:23665031}.123

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 KLHL3-TYMS


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 KLHL3-TYMS


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 KLHL3-TYMS


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 KLHL3-TYMS


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