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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:PFDN5-CAPN2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PFDN5-CAPN2
	FusionPDB ID: 64410
	FusionGDB2.0 ID: 64410
		Hgene	Tgene
	Gene symbol	PFDN5	CAPN2
	Gene ID	5204	824
	Gene name	prefoldin subunit 5	calpain 2
	Synonyms	MM-1\|MM1\|PFD5	CANP2\|CANPL2\|CANPml\|mCANP
	Cytomap	12q13.13	1q41
	Type of gene	protein-coding	protein-coding
	Description	prefoldin subunit 5c-myc binding proteinmyc modulator-1	calpain-2 catalytic subunitCANP 2M-calpaincalcium-activated neutral proteinase 2calpain 2, (m/II) large subunitcalpain 2, large [catalytic] subunitcalpain 2, large subunitcalpain M-typecalpain, large polypeptide L2millimolar-calpain
	Modification date	20200313	20200313
	UniProtAcc	.	P17655
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000334478, ENST00000351500, ENST00000550846, ENST00000551018,	ENST00000474026, ENST00000295006, ENST00000433674,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 4 X 2=56	11 X 7 X 7=539
	# samples	7	11
	** MAII score	log2(7/56*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(11/539*10)=-2.29278174922785 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PFDN5 [Title/Abstract] AND CAPN2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PFDN5(53689423)-CAPN2(223949887), # samples:1
Anticipated loss of major functional domain due to fusion event.	PFDN5-CAPN2 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. PFDN5-CAPN2 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. PFDN5-CAPN2 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. PFDN5-CAPN2 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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	CAPN2	GO:0051603	proteolysis involved in cellular protein catabolic process	12150984

Fusion gene breakpoints across PFDN5 (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 CAPN2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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	Non-Cancer	131Nd	PFDN5	chr12	53689423	+	CAPN2	chr1	223949887	+

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

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)
ENST00000551018	PFDN5	chr12	53689423	+	ENST00000433674	CAPN2	chr1	223949887	+	2045	349	277	885	202
ENST00000551018	PFDN5	chr12	53689423	+	ENST00000295006	CAPN2	chr1	223949887	+	2047	349	277	885	202
ENST00000351500	PFDN5	chr12	53689423	+	ENST00000433674	CAPN2	chr1	223949887	+	1811	115	43	651	202
ENST00000351500	PFDN5	chr12	53689423	+	ENST00000295006	CAPN2	chr1	223949887	+	1813	115	43	651	202
ENST00000550846	PFDN5	chr12	53689423	+	ENST00000433674	CAPN2	chr1	223949887	+	1800	104	32	640	202
ENST00000550846	PFDN5	chr12	53689423	+	ENST00000295006	CAPN2	chr1	223949887	+	1802	104	32	640	202
ENST00000334478	PFDN5	chr12	53689423	+	ENST00000433674	CAPN2	chr1	223949887	+	1784	88	16	624	202
ENST00000334478	PFDN5	chr12	53689423	+	ENST00000295006	CAPN2	chr1	223949887	+	1786	88	16	624	202

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
ENST00000551018	ENST00000433674	PFDN5	chr12	53689423	+	CAPN2	chr1	223949887	+	0.000623829	0.99937624
ENST00000551018	ENST00000295006	PFDN5	chr12	53689423	+	CAPN2	chr1	223949887	+	0.000621472	0.99937844
ENST00000351500	ENST00000433674	PFDN5	chr12	53689423	+	CAPN2	chr1	223949887	+	0.000443641	0.99955636
ENST00000351500	ENST00000295006	PFDN5	chr12	53689423	+	CAPN2	chr1	223949887	+	0.000443075	0.99955696
ENST00000550846	ENST00000433674	PFDN5	chr12	53689423	+	CAPN2	chr1	223949887	+	0.000491003	0.999509
ENST00000550846	ENST00000295006	PFDN5	chr12	53689423	+	CAPN2	chr1	223949887	+	0.000490533	0.99950945
ENST00000334478	ENST00000433674	PFDN5	chr12	53689423	+	CAPN2	chr1	223949887	+	0.000538597	0.99946135
ENST00000334478	ENST00000295006	PFDN5	chr12	53689423	+	CAPN2	chr1	223949887	+	0.000537055	0.9994629

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>64410_64410_1_PFDN5-CAPN2_PFDN5_chr12_53689423_ENST00000334478_CAPN2_chr1_223949887_ENST00000295006_length(amino acids)=202AA_BP=23
MAQSINITELNLPQLEMLKNQLDQFDISEDDIDDGFRRLFAQLAGEDAEISAFELQTILRRVLAKRQDIKSDGFSIETCKIMVDMLDSDG
SGKLGLKEFYILWTKIQKYQKIYREIDVDRSGTMNSYEMRKALEEAGFKMPCQLHQVIVARFADDQLIIDFDNFVRCLVRLETLFKIFKQ

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

>64410_64410_2_PFDN5-CAPN2_PFDN5_chr12_53689423_ENST00000334478_CAPN2_chr1_223949887_ENST00000433674_length(amino acids)=202AA_BP=23
MAQSINITELNLPQLEMLKNQLDQFDISEDDIDDGFRRLFAQLAGEDAEISAFELQTILRRVLAKRQDIKSDGFSIETCKIMVDMLDSDG
SGKLGLKEFYILWTKIQKYQKIYREIDVDRSGTMNSYEMRKALEEAGFKMPCQLHQVIVARFADDQLIIDFDNFVRCLVRLETLFKIFKQ

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

>64410_64410_3_PFDN5-CAPN2_PFDN5_chr12_53689423_ENST00000351500_CAPN2_chr1_223949887_ENST00000295006_length(amino acids)=202AA_BP=23
MAQSINITELNLPQLEMLKNQLDQFDISEDDIDDGFRRLFAQLAGEDAEISAFELQTILRRVLAKRQDIKSDGFSIETCKIMVDMLDSDG
SGKLGLKEFYILWTKIQKYQKIYREIDVDRSGTMNSYEMRKALEEAGFKMPCQLHQVIVARFADDQLIIDFDNFVRCLVRLETLFKIFKQ

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

>64410_64410_4_PFDN5-CAPN2_PFDN5_chr12_53689423_ENST00000351500_CAPN2_chr1_223949887_ENST00000433674_length(amino acids)=202AA_BP=23
MAQSINITELNLPQLEMLKNQLDQFDISEDDIDDGFRRLFAQLAGEDAEISAFELQTILRRVLAKRQDIKSDGFSIETCKIMVDMLDSDG
SGKLGLKEFYILWTKIQKYQKIYREIDVDRSGTMNSYEMRKALEEAGFKMPCQLHQVIVARFADDQLIIDFDNFVRCLVRLETLFKIFKQ

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

>64410_64410_5_PFDN5-CAPN2_PFDN5_chr12_53689423_ENST00000550846_CAPN2_chr1_223949887_ENST00000295006_length(amino acids)=202AA_BP=23
MAQSINITELNLPQLEMLKNQLDQFDISEDDIDDGFRRLFAQLAGEDAEISAFELQTILRRVLAKRQDIKSDGFSIETCKIMVDMLDSDG
SGKLGLKEFYILWTKIQKYQKIYREIDVDRSGTMNSYEMRKALEEAGFKMPCQLHQVIVARFADDQLIIDFDNFVRCLVRLETLFKIFKQ

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

>64410_64410_6_PFDN5-CAPN2_PFDN5_chr12_53689423_ENST00000550846_CAPN2_chr1_223949887_ENST00000433674_length(amino acids)=202AA_BP=23
MAQSINITELNLPQLEMLKNQLDQFDISEDDIDDGFRRLFAQLAGEDAEISAFELQTILRRVLAKRQDIKSDGFSIETCKIMVDMLDSDG
SGKLGLKEFYILWTKIQKYQKIYREIDVDRSGTMNSYEMRKALEEAGFKMPCQLHQVIVARFADDQLIIDFDNFVRCLVRLETLFKIFKQ

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

>64410_64410_7_PFDN5-CAPN2_PFDN5_chr12_53689423_ENST00000551018_CAPN2_chr1_223949887_ENST00000295006_length(amino acids)=202AA_BP=23
MAQSINITELNLPQLEMLKNQLDQFDISEDDIDDGFRRLFAQLAGEDAEISAFELQTILRRVLAKRQDIKSDGFSIETCKIMVDMLDSDG
SGKLGLKEFYILWTKIQKYQKIYREIDVDRSGTMNSYEMRKALEEAGFKMPCQLHQVIVARFADDQLIIDFDNFVRCLVRLETLFKIFKQ

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

>64410_64410_8_PFDN5-CAPN2_PFDN5_chr12_53689423_ENST00000551018_CAPN2_chr1_223949887_ENST00000433674_length(amino acids)=202AA_BP=23
MAQSINITELNLPQLEMLKNQLDQFDISEDDIDDGFRRLFAQLAGEDAEISAFELQTILRRVLAKRQDIKSDGFSIETCKIMVDMLDSDG
SGKLGLKEFYILWTKIQKYQKIYREIDVDRSGTMNSYEMRKALEEAGFKMPCQLHQVIVARFADDQLIIDFDNFVRCLVRLETLFKIFKQ

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

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:53689423/chr1:223949887)
- 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
.	CAPN2 P17655
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.	FUNCTION: Calcium-regulated non-lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction. Proteolytically cleaves MYOC at 'Arg-226' (PubMed:17650508). Proteolytically cleaves CPEB3 following neuronal stimulation which abolishes CPEB3 translational repressor activity, leading to translation of CPEB3 target mRNAs (By similarity). {ECO:0000250\|UniProtKB:O08529, ECO:0000269\|PubMed:17650508}.

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.

- 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

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000295006

585_596

522.0

701.0

Calcium binding

Note=1

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000295006

615_626

522.0

701.0

Calcium binding

Note=2

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000433674

585_596

444.0

623.0

Calcium binding

Note=1

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000433674

615_626

444.0

623.0

Calcium binding

Note=2

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000295006

572_605

522.0

701.0

Domain

EF-hand 1

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000295006

602_637

522.0

701.0

Domain

EF-hand 2

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000295006

667_700

522.0

701.0

Domain

EF-hand 3

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000433674

572_605

444.0

623.0

Domain

EF-hand 1

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000433674

602_637

444.0

623.0

Domain

EF-hand 2

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000433674

667_700

444.0

623.0

Domain

EF-hand 3

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000295006

530_700

522.0

701.0

Region

Note=Domain IV

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000433674

515_529

444.0

623.0

Region

Note=Linker

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000433674

530_700

444.0

623.0

Region

Note=Domain IV

- 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

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000295006

45_344

522.0

701.0

Domain

Calpain catalytic

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000433674

45_344

444.0

623.0

Domain

Calpain catalytic

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000295006

345_514

522.0

701.0

Region

Note=Domain III

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000295006

515_529

522.0

701.0

Region

Note=Linker

Tgene

CAPN2

chr12:53689423

chr1:223949887

ENST00000433674

345_514

444.0

623.0

Region

Note=Domain III

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Fusion Protein-Protein Interaction

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 from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
PFDN5
CAPN2

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to PFDN5-CAPN2

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to PFDN5-CAPN2

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source