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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:TMEM259-CNN2 (FusionGDB2 ID:92023)

Fusion Gene Summary for TMEM259-CNN2

Fusion gene summary

Fusion gene information	Fusion gene name: TMEM259-CNN2
	Fusion gene ID: 92023
		Hgene	Tgene
	Gene symbol	TMEM259	CNN2
	Gene ID	91304	1265
	Gene name	transmembrane protein 259	calponin 2
	Synonyms	ASBABP1\|C19orf6\|MBRL\|MEMBRALIN\|R32184_3	-
	Cytomap	19p13.3	19p13.3
	Type of gene	protein-coding	protein-coding
	Description	membralinaspecific BCL2 ARE-binding protein 1	calponin-2calponin H2, smooth muscleneutral calponin
	Modification date	20200313	20200313
	UniProtAcc	Q4ZIN3	Q99439
	Ensembl transtripts involved in fusion gene	ENST00000333175, ENST00000356663,	ENST00000348419, ENST00000562958, ENST00000565096, ENST00000606983, ENST00000263097,
Fusion gene scores	* DoF score	11 X 9 X 5=495	12 X 12 X 8=1152
	# samples	11	14
	** MAII score	log2(11/495*10)=-2.16992500144231 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(14/1152*10)=-3.04064198449735 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: TMEM259 [Title/Abstract] AND CNN2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	TMEM259(1014191)-CNN2(1031070), # 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
Tgene	CNN2	GO:0032970	regulation of actin filament-based process	16236705
Tgene	CNN2	GO:0071260	cellular response to mechanical stimulus	16236705

Fusion gene breakpoints across TMEM259 (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 CNN2 (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	PRAD	TCGA-KC-A4BL	TMEM259	chr19	1014191	-	CNN2	chr19	1031070	+

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Fusion Gene ORF analysis for TMEM259-CNN2

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
5CDS-3UTR	ENST00000333175	ENST00000348419	TMEM259	chr19	1014191	-	CNN2	chr19	1031070	+
5CDS-3UTR	ENST00000333175	ENST00000562958	TMEM259	chr19	1014191	-	CNN2	chr19	1031070	+
5CDS-3UTR	ENST00000333175	ENST00000565096	TMEM259	chr19	1014191	-	CNN2	chr19	1031070	+
5CDS-3UTR	ENST00000333175	ENST00000606983	TMEM259	chr19	1014191	-	CNN2	chr19	1031070	+
5CDS-3UTR	ENST00000356663	ENST00000348419	TMEM259	chr19	1014191	-	CNN2	chr19	1031070	+
5CDS-3UTR	ENST00000356663	ENST00000562958	TMEM259	chr19	1014191	-	CNN2	chr19	1031070	+
5CDS-3UTR	ENST00000356663	ENST00000565096	TMEM259	chr19	1014191	-	CNN2	chr19	1031070	+
5CDS-3UTR	ENST00000356663	ENST00000606983	TMEM259	chr19	1014191	-	CNN2	chr19	1031070	+
In-frame	ENST00000333175	ENST00000263097	TMEM259	chr19	1014191	-	CNN2	chr19	1031070	+
In-frame	ENST00000356663	ENST00000263097	TMEM259	chr19	1014191	-	CNN2	chr19	1031070	+

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 TMEM259-CNN2

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)
TMEM259	chr19	1014190	-	CNN2	chr19	1031069	+	0.000124688	0.9998753
TMEM259	chr19	1014190	-	CNN2	chr19	1031069	+	0.000124688	0.9998753

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 TMEM259-CNN2

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:1014191/chr19:1031070)
- 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
TMEM259 Q4ZIN3	CNN2 Q99439
FUNCTION: May have a role in the ERAD pathway required for clearance of misfolded proteins in the endoplasmic reticulum (ER). Promotes survival of motor neurons, probably by protecting against ER stress. {ECO:0000250\|UniProtKB:Q8CIV2}.	FUNCTION: Thin filament-associated protein that is implicated in the regulation and modulation of smooth muscle contraction. It is capable of binding to actin, calmodulin and tropomyosin. The interaction of calponin with actin inhibits the actomyosin Mg-ATPase activity.

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

TMEM259

chr19:1014191

chr19:1031070

ENST00000333175

70_90

169

409.0

Transmembrane

Helical

Hgene

TMEM259

chr19:1014191

chr19:1031070

ENST00000356663

70_90

169

621.0

Transmembrane

Helical

Tgene

CNN2

chr19:1014191

chr19:1031070

ENST00000263097

28_132

310.0

Domain

Calponin-homology (CH)

Tgene

CNN2

chr19:1014191

chr19:1031070

ENST00000348419

28_132

271.0

Domain

Calponin-homology (CH)

Tgene

CNN2

chr19:1014191

chr19:1031070

ENST00000263097

166_191

310.0

Repeat

Note=Calponin-like 1

Tgene

CNN2

chr19:1014191

chr19:1031070

ENST00000263097

206_231

310.0

Repeat

Note=Calponin-like 2

Tgene

CNN2

chr19:1014191

chr19:1031070

ENST00000263097

245_269

310.0

Repeat

Note=Calponin-like 3

Tgene

CNN2

chr19:1014191

chr19:1031070

ENST00000348419

166_191

271.0

Repeat

Note=Calponin-like 1

Tgene

CNN2

chr19:1014191

chr19:1031070

ENST00000348419

206_231

271.0

Repeat

Note=Calponin-like 2

Tgene

CNN2

chr19:1014191

chr19:1031070

ENST00000348419

245_269

271.0

Repeat

Note=Calponin-like 3

- 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

TMEM259

chr19:1014191

chr19:1031070

ENST00000333175

302_322

169

409.0

Transmembrane

Helical

Hgene

TMEM259

chr19:1014191

chr19:1031070

ENST00000333175

346_366

169

409.0

Transmembrane

Helical

Hgene

TMEM259

chr19:1014191

chr19:1031070

ENST00000333175

426_446

169

409.0

Transmembrane

Helical

Hgene

TMEM259

chr19:1014191

chr19:1031070

ENST00000356663

302_322

169

621.0

Transmembrane

Helical

Hgene

TMEM259

chr19:1014191

chr19:1031070

ENST00000356663

346_366

169

621.0

Transmembrane

Helical

Hgene

TMEM259

chr19:1014191

chr19:1031070

ENST00000356663

426_446

169

621.0

Transmembrane

Helical

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Fusion Gene Sequence for TMEM259-CNN2

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 TMEM259-CNN2

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 TMEM259-CNN2

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 TMEM259-CNN2

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source