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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:KANSL3-KCNIP3 (FusionGDB2 ID:41163)

Fusion Gene Summary for KANSL3-KCNIP3

check button Fusion gene summary
Fusion gene informationFusion gene name: KANSL3-KCNIP3
Fusion gene ID: 41163
HgeneTgene
Gene symbol

KANSL3

KCNIP3

Gene ID

55683

30818

Gene nameKAT8 regulatory NSL complex subunit 3potassium voltage-gated channel interacting protein 3
SynonymsKIAA1310|NSL3|Rcd1CSEN|DREAM|KCHIP3
Cytomap

2q11.2

2q11.1

Type of geneprotein-codingprotein-coding
DescriptionKAT8 regulatory NSL complex subunit 3NSL complex protein NSL3non-specific lethal 3 homologserum inhibited-related proteintestis development protein PRTDcalsenilinA-type potassium channel modulatory protein 3DRE-antagonist modulatorKv channel interacting protein 3, calsenilincalsenilin, presenilin-binding protein, EF hand transcription factorkv channel-interacting protein 3potassium channel interact
Modification date2020031320200320
UniProtAcc

Q9P2N6

Q9Y2W7

Ensembl transtripts involved in fusion geneENST00000431828, ENST00000435669, 
ENST00000440133, ENST00000441706, 
ENST00000599854, ENST00000487070, 
ENST00000295225, ENST00000360990, 
ENST00000377181, ENST00000468529, 
Fusion gene scores* DoF score9 X 8 X 5=3604 X 5 X 3=60
# samples 116
** MAII scorelog2(11/360*10)=-1.71049338280502
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/60*10)=0
Context

PubMed: KANSL3 [Title/Abstract] AND KCNIP3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKANSL3(97285096)-KCNIP3(95964431), # 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
HgeneKANSL3

GO:0043981

histone H4-K5 acetylation

20018852

HgeneKANSL3

GO:0043982

histone H4-K8 acetylation

20018852

HgeneKANSL3

GO:0043984

histone H4-K16 acetylation

20018852


check buttonFusion gene breakpoints across KANSL3 (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 KCNIP3 (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-BH-A1FH-01AKANSL3chr2

97285096

-KCNIP3chr2

95964431

+


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Fusion Gene ORF analysis for KANSL3-KCNIP3

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
5CDS-intronENST00000431828ENST00000295225KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000431828ENST00000360990KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000431828ENST00000377181KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000431828ENST00000468529KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000435669ENST00000295225KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000435669ENST00000360990KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000435669ENST00000377181KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000435669ENST00000468529KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000440133ENST00000295225KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000440133ENST00000360990KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000440133ENST00000377181KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000440133ENST00000468529KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000441706ENST00000295225KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000441706ENST00000360990KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000441706ENST00000377181KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000441706ENST00000468529KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000599854ENST00000295225KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000599854ENST00000360990KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000599854ENST00000377181KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5CDS-intronENST00000599854ENST00000468529KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5UTR-intronENST00000487070ENST00000295225KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5UTR-intronENST00000487070ENST00000360990KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5UTR-intronENST00000487070ENST00000377181KANSL3chr2

97285096

-KCNIP3chr2

95964431

+
5UTR-intronENST00000487070ENST00000468529KANSL3chr2

97285096

-KCNIP3chr2

95964431

+

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 KANSL3-KCNIP3


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 KANSL3-KCNIP3


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/:97285096/:95964431)
- 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
KANSL3

Q9P2N6

KCNIP3

Q9Y2W7

FUNCTION: As part of the NSL complex it is involved in acetylation of nucleosomal histone H4 on several lysine residues and therefore may be involved in the regulation of transcription. {ECO:0000269|PubMed:20018852}.FUNCTION: Calcium-dependent transcriptional repressor that binds to the DRE element of genes including PDYN and FOS. Affinity for DNA is reduced upon binding to calcium and enhanced by binding to magnesium. Seems to be involved in nociception (By similarity). {ECO:0000250|UniProtKB:Q9QXT8}.; FUNCTION: Regulatory subunit of Kv4/D (Shal)-type voltage-gated rapidly inactivating A-type potassium channels, such as KCND2/Kv4.2 and KCND3/Kv4.3. Modulates channel expression at the cell membrane, gating characteristics, inactivation kinetics and rate of recovery from inactivation in a calcium-dependent and isoform-specific manner. {ECO:0000269|PubMed:10676964, ECO:0000269|PubMed:12829703, ECO:0000269|PubMed:15485870, ECO:0000269|PubMed:16123112, ECO:0000269|PubMed:18957440}.; FUNCTION: May play a role in the regulation of PSEN2 proteolytic processing and apoptosis. Together with PSEN2 involved in modulation of amyloid-beta formation. {ECO:0000269|PubMed:11259376, ECO:0000269|PubMed:11988022, ECO:0000269|PubMed:9771752}.

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 KANSL3-KCNIP3


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 KANSL3-KCNIP3


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 KANSL3-KCNIP3


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 KANSL3-KCNIP3


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