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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:KCNN1-GATA6 (FusionGDB2 ID:41519)

Fusion Gene Summary for KCNN1-GATA6

Fusion gene summary

Fusion gene information	Fusion gene name: KCNN1-GATA6
	Fusion gene ID: 41519
		Hgene	Tgene
	Gene symbol	KCNN1	GATA6
	Gene ID	3780	2627
	Gene name	potassium calcium-activated channel subfamily N member 1	GATA binding protein 6
	Synonyms	KCa2.1\|SK1\|SKCA1\|hSK1	-
	Cytomap	19p13.11	18q11.2
	Type of gene	protein-coding	protein-coding
	Description	small conductance calcium-activated potassium channel protein 1potassium channel, calcium activated intermediate/small conductance subfamily N alpha, member 1potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1small	transcription factor GATA-6GATA-binding factor 6
	Modification date	20200313	20200313
	UniProtAcc	Q92952	Q92908
	Ensembl transtripts involved in fusion gene	ENST00000222249, ENST00000594192,	ENST00000269216, ENST00000581694,
Fusion gene scores	* DoF score	5 X 6 X 3=90	7 X 5 X 5=175
	# samples	5	7
	** MAII score	log2(5/90*10)=-0.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/175*10)=-1.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: KCNN1 [Title/Abstract] AND GATA6 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	KCNN1(18085996)-GATA6(19780619), # samples:3
Anticipated loss of major functional domain due to fusion event.	KCNN1-GATA6 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. KCNN1-GATA6 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. KCNN1-GATA6 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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)

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
Tgene	GATA6	GO:0000122	negative regulation of transcription by RNA polymerase II	18177748
Tgene	GATA6	GO:0006366	transcription by RNA polymerase II	19666519
Tgene	GATA6	GO:0045766	positive regulation of angiogenesis	21127043
Tgene	GATA6	GO:0045892	negative regulation of transcription, DNA-templated	18177748
Tgene	GATA6	GO:0060575	intestinal epithelial cell differentiation	9566909
Tgene	GATA6	GO:0070848	response to growth factor	21127043
Tgene	GATA6	GO:0071158	positive regulation of cell cycle arrest	9593712
Tgene	GATA6	GO:0071456	cellular response to hypoxia	21127043
Tgene	GATA6	GO:0110024	positive regulation of cardiac muscle myoblast proliferation	25068583

Fusion gene breakpoints across KCNN1 (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 GATA6 (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
ChimerDB4	UCEC	TCGA-AJ-A2QM-01A	KCNN1	chr19	18085996	-	GATA6	chr18	19780619	+
ChimerDB4	UCEC	TCGA-AJ-A2QM-01A	KCNN1	chr19	18085996	+	GATA6	chr18	19780619	+

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Fusion Gene ORF analysis for KCNN1-GATA6

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
Frame-shift	ENST00000222249	ENST00000269216	KCNN1	chr19	18085996	+	GATA6	chr18	19780619	+
In-frame	ENST00000222249	ENST00000581694	KCNN1	chr19	18085996	+	GATA6	chr18	19780619	+
intron-3CDS	ENST00000594192	ENST00000269216	KCNN1	chr19	18085996	+	GATA6	chr18	19780619	+
intron-3CDS	ENST00000594192	ENST00000581694	KCNN1	chr19	18085996	+	GATA6	chr18	19780619	+

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)

ENST00000222249

KCNN1

chr19

18085996

ENST00000581694

GATA6

chr18

19780619

1042

817

226

984

252

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
ENST00000222249	ENST00000581694	KCNN1	chr19	18085996	+	GATA6	chr18	19780619	+	0.008692923	0.9913071

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Fusion Genomic Features for KCNN1-GATA6

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)
KCNN1	chr19	18085996	+	GATA6	chr18	19780618	+	3.93E-09	1
KCNN1	chr19	18085996	+	GATA6	chr18	19780618	+	3.93E-09	1

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 KCNN1-GATA6

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:18085996/chr18:19780619)
- 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.

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

Hgene	Tgene
KCNN1 Q92952	GATA6 Q92908
FUNCTION: Forms a voltage-independent potassium channel activated by intracellular calcium. Activation is followed by membrane hyperpolarization. Thought to regulate neuronal excitability by contributing to the slow component of synaptic afterhyperpolarization. The channel is blocked by apamin (By similarity). {ECO:0000250}.	FUNCTION: Transcriptional activator (PubMed:19666519, PubMed:27756709, PubMed:22750565, PubMed:22824924). Regulates SEMA3C and PLXNA2 (PubMed:19666519). Involved in gene regulation specifically in the gastric epithelium (PubMed:9315713). May regulate genes that protect epithelial cells from bacterial infection (PubMed:16968778). Involved in bone morphogenetic protein (BMP)-mediated cardiac-specific gene expression (By similarity). Binds to BMP response element (BMPRE) DNA sequences within cardiac activating regions (By similarity). In human skin, controls several physiological processes contributing to homeostasis of the upper pilosebaceous unit. Triggers ductal and sebaceous differentiation as well as limits cell proliferation and lipid production to prevent hyperseborrhoea. Mediates the effects of retinoic acid on sebocyte proliferation, differentiation and lipid production. Also contributes to immune regulation of sebocytes and antimicrobial responses by modulating the expression of anti-inflammatory genes such as IL10 and pro-inflammatory genes such as IL6, TLR2, TLR4, and IFNG. Activates TGFB1 signaling which controls the interfollicular epidermis fate (PubMed:33082341). {ECO:0000250\|UniProtKB:Q61169, ECO:0000269\|PubMed:16968778, ECO:0000269\|PubMed:19666519, ECO:0000269\|PubMed:22750565, ECO:0000269\|PubMed:22824924, ECO:0000269\|PubMed:27756709, ECO:0000269\|PubMed:33082341, ECO:0000269\|PubMed:9315713}.

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

Hgene

KCNN1

chr19:18085996

chr18:19780619

ENST00000222249

111_131

166

544.0

Transmembrane

Helical%3B Name%3DSegment S1

Hgene

KCNN1

chr19:18085996

chr18:19780619

ENST00000222249

140_160

166

544.0

Transmembrane

Helical%3B Name%3DSegment S2

- 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

Hgene

KCNN1

chr19:18085996

chr18:19780619

ENST00000222249

509_518

166

544.0

Compositional bias

Note=Poly-Pro

Hgene

KCNN1

chr19:18085996

chr18:19780619

ENST00000222249

317_337

166

544.0

Intramembrane

Pore-forming%3B Name%3DSegment H5

Hgene

KCNN1

chr19:18085996

chr18:19780619

ENST00000222249

384_463

166

544.0

Region

Calmodulin-binding

Hgene

KCNN1

chr19:18085996

chr18:19780619

ENST00000222249

179_199

166

544.0

Transmembrane

Helical%3B Name%3DSegment S3

Hgene

KCNN1

chr19:18085996

chr18:19780619

ENST00000222249

228_248

166

544.0

Transmembrane

Helical%3B Name%3DSegment S4

Hgene

KCNN1

chr19:18085996

chr18:19780619

ENST00000222249

277_297

166

544.0

Transmembrane

Helical%3B Name%3DSegment S5

Hgene

KCNN1

chr19:18085996

chr18:19780619

ENST00000222249

346_366

166

544.0

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

GATA6

chr19:18085996

chr18:19780619

ENST00000269216

173_183

540

596.0

Compositional bias

Note=Poly-Ala

Tgene

GATA6

chr19:18085996

chr18:19780619

ENST00000269216

324_333

540

596.0

Compositional bias

Note=Poly-His

Tgene

GATA6

chr19:18085996

chr18:19780619

ENST00000269216

449_453

540

596.0

Compositional bias

Note=Poly-Thr

Tgene

GATA6

chr19:18085996

chr18:19780619

ENST00000581694

173_183

540

596.0

Compositional bias

Note=Poly-Ala

Tgene

GATA6

chr19:18085996

chr18:19780619

ENST00000581694

324_333

540

596.0

Compositional bias

Note=Poly-His

Tgene

GATA6

chr19:18085996

chr18:19780619

ENST00000581694

449_453

540

596.0

Compositional bias

Note=Poly-Thr

Tgene

GATA6

chr19:18085996

chr18:19780619

ENST00000269216

390_414

540

596.0

Zinc finger

GATA-type 1

Tgene

GATA6

chr19:18085996

chr18:19780619

ENST00000269216

444_468

540

596.0

Zinc finger

GATA-type 2

Tgene

GATA6

chr19:18085996

chr18:19780619

ENST00000581694

390_414

540

596.0

Zinc finger

GATA-type 1

Tgene

GATA6

chr19:18085996

chr18:19780619

ENST00000581694

444_468

540

596.0

Zinc finger

GATA-type 2

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Fusion Gene Sequence for KCNN1-GATA6

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.

>41519_41519_1_KCNN1-GATA6_KCNN1_chr19_18085996_ENST00000222249_GATA6_chr18_19780619_ENST00000581694_length(transcript)=1042nt_BP=817nt
GAGGAACACGGTGGTCTGAGCTGGAGCCACGCTTTCTGTTGGAGGGGGCAGCTGAAGGAGAACAGCAAGACATATCCGGCGGCCCTACGG
ACTCGGAGAGCTGGAGGGACCCCGGAGATCTCAAAGGGACAGGAAAGGCAGCAGCAGCCACCCTCTCTCCCAGTCAAGTGGTCACCAGCA
GGACTGAAGGGGACAGCCCCTTTGCAGTGGCTCGGCGAGGAGACCCCTGCACCCTAGGGTCAGTGCAGGAGCCCAGCCGCTGAGCCATGC
CGGGCCCCGGGCGGCCTGCAGCGAGCCCAACCCCTGCACCCAGGTAGTCATGAACAGCCACAGCTACAATGGCAGCGTGGGGCGGCCGCT
GGGCAGCGGGCCGGGCGCCCTGGGACGAGACCCTCCGGACCCTGAGGCCGGCCACCCCCCACAACCCCCGCACAGCCCGGGCCTCCAGGT
GGTAGTGGCCAAGAGTGAGCCAGCCCGGCCCTCACCCGGCAGCCCCCGGGGGCAGCCCCAGGACCAGGACGATGACGAGGATGATGAGGA
AGATGAGGCCGGCAGGCAGAGAGCCTCGGGGAAACCCTCAAATGTGGGCCACCGCCTGGGCCACCGGCGGGCGCTCTTCGAGAAGCGGAA
GCGCCTCAGCGACTATGCCCTCATTTTCGGCATGTTTGGCATCGTCGTCATGGTGACGGAGACCGAGCTGTCCTGGGGGGTGTACACCAA
GGAGTCTCTGTACTCATTCGCACTCAAATGCCTCATCAGCCTCTCCACGGCCATCCTGCTGGGTCTCGTTGTCCTCTACCATGCCCGGGA
GATCCAGGCGGGTGCCCCGGTGATGACTGGTGCGGGAGAGAGCACCAATCCCGAGAACAGCGAGCTCAAGTATTCGGGTCAAGATGGGCT
CTACATAGGCGTCAGTCTCGCCTCGCCGGCCGAAGTCACGTCCTCCGTGCGACCGGATTCCTGGTGCGCCCTGGCCCTGGCCTGAGCCCA

>41519_41519_1_KCNN1-GATA6_KCNN1_chr19_18085996_ENST00000222249_GATA6_chr18_19780619_ENST00000581694_length(amino acids)=252AA_BP=196
MHPRVSAGAQPLSHAGPRAACSEPNPCTQVVMNSHSYNGSVGRPLGSGPGALGRDPPDPEAGHPPQPPHSPGLQVVVAKSEPARPSPGSP
RGQPQDQDDDEDDEEDEAGRQRASGKPSNVGHRLGHRRALFEKRKRLSDYALIFGMFGIVVMVTETELSWGVYTKESLYSFALKCLISLS

--------------------------------------------------------------

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Fusion Gene PPI Analysis for KCNN1-GATA6

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 KCNN1-GATA6

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 KCNN1-GATA6

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source