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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-C16orf45 (FusionGDB2 ID:42817)

Fusion Gene Summary for KLHL3-C16orf45

check button Fusion gene summary
Fusion gene informationFusion gene name: KLHL3-C16orf45
Fusion gene ID: 42817
HgeneTgene
Gene symbol

KLHL3

C16orf45

Gene ID

26249

89927

Gene namekelch like family member 3bMERB domain containing 1
SynonymsPHA2DC16orf45|MINP
Cytomap

5q31.2

16p13.11

Type of geneprotein-codingprotein-coding
Descriptionkelch-like protein 3bMERB domain-containing protein 1migration inhibitory proteinuncharacterized protein C16orf45
Modification date2020031320200313
UniProtAcc

Q9UH77

.
Ensembl transtripts involved in fusion geneENST00000506491, ENST00000508657, 
ENST00000309755, ENST00000506873, 
ENST00000541417, ENST00000394937, 
ENST00000300006, ENST00000566490, 
ENST00000452191, ENST00000561692, 
ENST00000565913, 
Fusion gene scores* DoF score6 X 6 X 2=7214 X 11 X 8=1232
# samples 616
** MAII scorelog2(6/72*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1232*10)=-2.94485844580754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KLHL3 [Title/Abstract] AND C16orf45 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKLHL3(137071322)-C16orf45(15609162), # samples:2
Anticipated loss of major functional domain due to fusion event.KLHL3-C16orf45 seems lost the major protein functional domain in Hgene partner, which is a essential gene 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
HgeneKLHL3

GO:0006511

ubiquitin-dependent protein catabolic process

23453970|23576762

HgeneKLHL3

GO:0016567

protein ubiquitination

23453970

HgeneKLHL3

GO:0070936

protein K48-linked ubiquitination

23576762


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 C16orf45 (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
ChimerDB4OVTCGA-13-0924-01AKLHL3chr5

137071322

-C16orf45chr16

15609162

+
ChimerDB4OVTCGA-13-0924-01AKLHL3chr5

137071322

-C16orf45chr16

15609162

+


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Fusion Gene ORF analysis for KLHL3-C16orf45

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-3CDSENST00000506491ENST00000300006KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-3CDSENST00000506491ENST00000566490KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-3CDSENST00000506491ENST00000452191KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-intronENST00000506491ENST00000561692KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-intronENST00000506491ENST00000565913KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-3CDSENST00000508657ENST00000300006KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-3CDSENST00000508657ENST00000566490KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-3CDSENST00000508657ENST00000452191KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-intronENST00000508657ENST00000561692KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-intronENST00000508657ENST00000565913KLHL3chr5

137071322

-C16orf45chr16

15609162

+
Frame-shiftENST00000309755ENST00000300006KLHL3chr5

137071322

-C16orf45chr16

15609162

+
Frame-shiftENST00000309755ENST00000566490KLHL3chr5

137071322

-C16orf45chr16

15609162

+
Frame-shiftENST00000309755ENST00000452191KLHL3chr5

137071322

-C16orf45chr16

15609162

+
5CDS-intronENST00000309755ENST00000561692KLHL3chr5

137071322

-C16orf45chr16

15609162

+
5CDS-intronENST00000309755ENST00000565913KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-3CDSENST00000506873ENST00000300006KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-3CDSENST00000506873ENST00000566490KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-3CDSENST00000506873ENST00000452191KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-intronENST00000506873ENST00000561692KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-intronENST00000506873ENST00000565913KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-3CDSENST00000541417ENST00000300006KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-3CDSENST00000541417ENST00000566490KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-3CDSENST00000541417ENST00000452191KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-intronENST00000541417ENST00000561692KLHL3chr5

137071322

-C16orf45chr16

15609162

+
intron-intronENST00000541417ENST00000565913KLHL3chr5

137071322

-C16orf45chr16

15609162

+
Frame-shiftENST00000394937ENST00000300006KLHL3chr5

137071322

-C16orf45chr16

15609162

+
Frame-shiftENST00000394937ENST00000566490KLHL3chr5

137071322

-C16orf45chr16

15609162

+
Frame-shiftENST00000394937ENST00000452191KLHL3chr5

137071322

-C16orf45chr16

15609162

+
5CDS-intronENST00000394937ENST00000561692KLHL3chr5

137071322

-C16orf45chr16

15609162

+
5CDS-intronENST00000394937ENST00000565913KLHL3chr5

137071322

-C16orf45chr16

15609162

+

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-C16orf45


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)
KLHL3chr5137071321-C16orf45chr1615609161+0.0019765080.9980235
KLHL3chr5137071321-C16orf45chr1615609161+0.0019765080.9980235

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-C16orf45


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
KLHL3

Q9UH77

.
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}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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-C16orf45


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-C16orf45


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-C16orf45


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-C16orf45


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKLHL3C3469605PSEUDOHYPOALDOSTERONISM, TYPE IID11CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneKLHL3C0033805Pseudohypoaldosteronism1CTD_human
HgeneKLHL3C0268436Pseudohypoaldosteronism, Type I1CTD_human
HgeneKLHL3C1449842Pseudohypoaldosteronism, Type I, Autosomal Dominant1CTD_human
HgeneKLHL3C1449843Pseudohypoaldosteronism, Type I, Autosomal Recessive1CTD_human
HgeneKLHL3C1449844Pseudohypoaldosteronism, Type II1CTD_human
HgeneKLHL3C2713447Hyperpotassemia and Hypertension, Familial1CTD_human