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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:KCNT2-ZC3H14 (FusionGDB2 ID:41402)

Fusion Gene Summary for KCNT2-ZC3H14

Fusion gene summary

Fusion gene information	Fusion gene name: KCNT2-ZC3H14
	Fusion gene ID: 41402
		Hgene	Tgene
	Gene symbol	KCNT2	ZC3H14
	Gene ID	343450	79882
	Gene name	potassium sodium-activated channel subfamily T member 2	zinc finger CCCH-type containing 14
	Synonyms	EIEE57\|KCa4.2\|SLICK\|SLO2.1	MRT56\|MSUT-2\|NY-REN-37\|SUT2\|UKp68
	Cytomap	1q31.3	14q31.3
	Type of gene	protein-coding	protein-coding
	Description	potassium channel subfamily T member 2potassium channel, subfamily T, member 2sequence like an intermediate conductance potassium channel subunitsodium and chloride-activated ATP-sensitive potassium channel Slo2.1sodium-and chloride-activated ATP-sens	zinc finger CCCH domain-containing protein 14mammalian suppressor of tau pathology-2nuclear protein UKp68renal carcinoma antigen NY-REN-37
	Modification date	20200322	20200313
	UniProtAcc	Q6UVM3	.
	Ensembl transtripts involved in fusion gene	ENST00000367433, ENST00000498426, ENST00000367431, ENST00000609185, ENST00000451324, ENST00000294725,	ENST00000359301, ENST00000251038, ENST00000302216, ENST00000556945, ENST00000557607, ENST00000555755, ENST00000393514, ENST00000336693, ENST00000557605, ENST00000318308, ENST00000555900, ENST00000406216,
Fusion gene scores	* DoF score	6 X 6 X 1=36	7 X 7 X 4=196
	# samples	6	7
	** MAII score	log2(6/36*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(7/196*10)=-1.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: KCNT2 [Title/Abstract] AND ZC3H14 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	KCNT2(196506781)-ZC3H14(89078094), # 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner

Gene

GO ID

GO term

PubMed ID

Fusion gene breakpoints across KCNT2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across ZC3H14 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChiTaRS5.0	N/A	FN148469	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+

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Fusion Gene ORF analysis for KCNT2-ZC3H14

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
intron-3CDS	ENST00000367433	ENST00000359301	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367433	ENST00000251038	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367433	ENST00000302216	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367433	ENST00000556945	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367433	ENST00000557607	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367433	ENST00000555755	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367433	ENST00000393514	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367433	ENST00000336693	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000367433	ENST00000557605	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000367433	ENST00000318308	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000367433	ENST00000555900	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000367433	ENST00000406216	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000498426	ENST00000359301	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000498426	ENST00000251038	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000498426	ENST00000302216	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000498426	ENST00000556945	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000498426	ENST00000557607	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000498426	ENST00000555755	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000498426	ENST00000393514	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000498426	ENST00000336693	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000498426	ENST00000557605	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000498426	ENST00000318308	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000498426	ENST00000555900	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000498426	ENST00000406216	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367431	ENST00000359301	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367431	ENST00000251038	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367431	ENST00000302216	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367431	ENST00000556945	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367431	ENST00000557607	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367431	ENST00000555755	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367431	ENST00000393514	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000367431	ENST00000336693	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000367431	ENST00000557605	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000367431	ENST00000318308	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000367431	ENST00000555900	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000367431	ENST00000406216	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000609185	ENST00000359301	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000609185	ENST00000251038	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000609185	ENST00000302216	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000609185	ENST00000556945	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000609185	ENST00000557607	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000609185	ENST00000555755	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000609185	ENST00000393514	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000609185	ENST00000336693	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000609185	ENST00000557605	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000609185	ENST00000318308	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000609185	ENST00000555900	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000609185	ENST00000406216	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000451324	ENST00000359301	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000451324	ENST00000251038	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000451324	ENST00000302216	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000451324	ENST00000556945	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000451324	ENST00000557607	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000451324	ENST00000555755	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000451324	ENST00000393514	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000451324	ENST00000336693	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000451324	ENST00000557605	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000451324	ENST00000318308	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000451324	ENST00000555900	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000451324	ENST00000406216	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000294725	ENST00000359301	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000294725	ENST00000251038	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000294725	ENST00000302216	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000294725	ENST00000556945	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000294725	ENST00000557607	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000294725	ENST00000555755	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000294725	ENST00000393514	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-3CDS	ENST00000294725	ENST00000336693	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000294725	ENST00000557605	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000294725	ENST00000318308	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000294725	ENST00000555900	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+
intron-intron	ENST00000294725	ENST00000406216	KCNT2	chr1	196506781	-	ZC3H14	chr14	89078094	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

DeepORF 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.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

No-coding score

Coding score

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Fusion Genomic Features for KCNT2-ZC3H14

FusionAI 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.

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution 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.

Distribution 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 KCNT2-ZC3H14

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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
KCNT2 Q6UVM3	.
FUNCTION: Outward rectifying potassium channel. Produces rapidly activating outward rectifier K(+) currents. Activated by high intracellular sodium and chloride levels (PubMed:14684870, PubMed:16687497, PubMed:29069600). Channel activity is inhibited by ATP and by inhalation anesthetics, such as isoflurane (PubMed:16687497) (By similarity). Inhibited upon stimulation of G-protein coupled receptors, such as CHRM1 and GRM1 (PubMed:16687497). {ECO:0000250\|UniProtKB:Q6UVM4, ECO:0000269\|PubMed:14684870, ECO:0000269\|PubMed:16687497, ECO:0000269\|PubMed:29069600}.	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.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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Fusion Gene Sequence for KCNT2-ZC3H14

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 KCNT2-ZC3H14

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for KCNT2-ZC3H14

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for KCNT2-ZC3H14

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	KCNT2	C4540411	EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 57	2	GENOMICS_ENGLAND;UNIPROT
Hgene	KCNT2	C0014544	Epilepsy	1	GENOMICS_ENGLAND
Tgene	ZC3H14	C3714756	Intellectual Disability	1	GENOMICS_ENGLAND
Tgene	ZC3H14	C4310703	MENTAL RETARDATION, AUTOSOMAL RECESSIVE 56	1	CTD_human;GENOMICS_ENGLAND