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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:CADPS2-XRCC6BP1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CADPS2-XRCC6BP1
	FusionPDB ID: 12480
	FusionGDB2.0 ID: 12480
		Hgene	Tgene
	Gene symbol	CADPS2	XRCC6BP1
	Gene ID	93664	91419
	Gene name	calcium dependent secretion activator 2	ATP23 metallopeptidase and ATP synthase assembly factor homolog
	Synonyms	CAPS2	KUB3\|XRCC6BP1
	Cytomap	7q31.32	12q14.1
	Type of gene	protein-coding	protein-coding
	Description	calcium-dependent secretion activator 2CAPS-2Ca++-dependent secretion activator 2Ca2+ dependent secretion activator 2Ca2+-dependent activator protein for secretion 2calcium-dependent activator protein for secretion 2	mitochondrial inner membrane protease ATP23 homologKu70-binding protein 3XRCC6-binding protein 1
	Modification date	20200313	20200320
	UniProtAcc	Q86UW7	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000313070, ENST00000334010, ENST00000412584, ENST00000449022, ENST00000476131,	ENST00000546709, ENST00000300145,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	12 X 11 X 7=924	18 X 7 X 5=630
	# samples	14	21
	** MAII score	log2(14/924*10)=-2.72246602447109 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(21/630*10)=-1.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: CADPS2 [Title/Abstract] AND XRCC6BP1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CADPS2(122526052)-XRCC6BP1(58345540), # samples:2
Anticipated loss of major functional domain due to fusion event.	CADPS2-XRCC6BP1 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. CADPS2-XRCC6BP1 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. CADPS2-XRCC6BP1 seems lost the major protein functional domain in Hgene partner, which is a essential gene 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

Fusion gene breakpoints across CADPS2 (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 XRCC6BP1 (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	SARC	TCGA-DX-A6BH-01A	CADPS2	chr7	122525447	-	XRCC6BP1	chr12	58339410	+
ChimerDB4	SARC	TCGA-DX-A6BH-01A	CADPS2	chr7	122526052	-	XRCC6BP1	chr12	58339410	+
ChimerDB4	SARC	TCGA-DX-A6BH-01A	CADPS2	chr7	122526052	-	XRCC6BP1	chr12	58345540	+
ChimerDB4	SARC	TCGA-DX-A6BH-01A	CADPS2	chr7	122526053	-	XRCC6BP1	chr12	58345541	+
ChimerDB4	SARC	TCGA-DX-A6BH	CADPS2	chr7	122526052	-	XRCC6BP1	chr12	58345540	+

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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)
ENST00000313070	CADPS2	chr7	122526052	-	ENST00000300145	XRCC6BP1	chr12	58345540	+	1566	761	422	1186	254
ENST00000334010	CADPS2	chr7	122526052	-	ENST00000300145	XRCC6BP1	chr12	58345540	+	1566	761	422	1186	254
ENST00000412584	CADPS2	chr7	122526052	-	ENST00000300145	XRCC6BP1	chr12	58345540	+	1265	460	121	885	254
ENST00000449022	CADPS2	chr7	122526052	-	ENST00000300145	XRCC6BP1	chr12	58345540	+	1164	359	20	784	254
ENST00000313070	CADPS2	chr7	122526053	-	ENST00000300145	XRCC6BP1	chr12	58345541	+	1566	761	422	1186	254
ENST00000334010	CADPS2	chr7	122526053	-	ENST00000300145	XRCC6BP1	chr12	58345541	+	1566	761	422	1186	254
ENST00000412584	CADPS2	chr7	122526053	-	ENST00000300145	XRCC6BP1	chr12	58345541	+	1265	460	121	885	254
ENST00000449022	CADPS2	chr7	122526053	-	ENST00000300145	XRCC6BP1	chr12	58345541	+	1164	359	20	784	254

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
ENST00000313070	ENST00000300145	CADPS2	chr7	122526052	-	XRCC6BP1	chr12	58345540	+	0.00388871	0.99611133
ENST00000334010	ENST00000300145	CADPS2	chr7	122526052	-	XRCC6BP1	chr12	58345540	+	0.00388871	0.99611133
ENST00000412584	ENST00000300145	CADPS2	chr7	122526052	-	XRCC6BP1	chr12	58345540	+	0.002682812	0.99731714
ENST00000449022	ENST00000300145	CADPS2	chr7	122526052	-	XRCC6BP1	chr12	58345540	+	0.002063593	0.9979365
ENST00000313070	ENST00000300145	CADPS2	chr7	122526053	-	XRCC6BP1	chr12	58345541	+	0.00388871	0.99611133
ENST00000334010	ENST00000300145	CADPS2	chr7	122526053	-	XRCC6BP1	chr12	58345541	+	0.00388871	0.99611133
ENST00000412584	ENST00000300145	CADPS2	chr7	122526053	-	XRCC6BP1	chr12	58345541	+	0.002682812	0.99731714
ENST00000449022	ENST00000300145	CADPS2	chr7	122526053	-	XRCC6BP1	chr12	58345541	+	0.002063593	0.9979365

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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

>12480_12480_1_CADPS2-XRCC6BP1_CADPS2_chr7_122526052_ENST00000313070_XRCC6BP1_chr12_58345540_ENST00000300145_length(amino acids)=254AA_BP=113
MLDPSSSEEESDEGLEEESRDVLVAAGSSQRAPPAPTREGRRDAPGRAGGGGAARSVSPSPSVLSEGRDEPQRQLDDEQERRIRLQLYVF
VVRCIAYPFNAKQPTDMARRQQKIVLCQNNIHNQAHMNRVVTHELIHAFDHCRAHVDWFTNIRHLACSEVRAANLSGDCSLVNEIFRLHF

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

>12480_12480_2_CADPS2-XRCC6BP1_CADPS2_chr7_122526052_ENST00000334010_XRCC6BP1_chr12_58345540_ENST00000300145_length(amino acids)=254AA_BP=113
MLDPSSSEEESDEGLEEESRDVLVAAGSSQRAPPAPTREGRRDAPGRAGGGGAARSVSPSPSVLSEGRDEPQRQLDDEQERRIRLQLYVF
VVRCIAYPFNAKQPTDMARRQQKIVLCQNNIHNQAHMNRVVTHELIHAFDHCRAHVDWFTNIRHLACSEVRAANLSGDCSLVNEIFRLHF

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

>12480_12480_3_CADPS2-XRCC6BP1_CADPS2_chr7_122526052_ENST00000412584_XRCC6BP1_chr12_58345540_ENST00000300145_length(amino acids)=254AA_BP=113
MLDPSSSEEESDEGLEEESRDVLVAAGSSQRAPPAPTREGRRDAPGRAGGGGAARSVSPSPSVLSEGRDEPQRQLDDEQERRIRLQLYVF
VVRCIAYPFNAKQPTDMARRQQKIVLCQNNIHNQAHMNRVVTHELIHAFDHCRAHVDWFTNIRHLACSEVRAANLSGDCSLVNEIFRLHF

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

>12480_12480_4_CADPS2-XRCC6BP1_CADPS2_chr7_122526052_ENST00000449022_XRCC6BP1_chr12_58345540_ENST00000300145_length(amino acids)=254AA_BP=113
MLDPSSSEEESDEGLEEESRDVLVAAGSSQRAPPAPTREGRRDAPGRAGGGGAARSVSPSPSVLSEGRDEPQRQLDDEQERRIRLQLYVF
VVRCIAYPFNAKQPTDMARRQQKIVLCQNNIHNQAHMNRVVTHELIHAFDHCRAHVDWFTNIRHLACSEVRAANLSGDCSLVNEIFRLHF

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

>12480_12480_5_CADPS2-XRCC6BP1_CADPS2_chr7_122526053_ENST00000313070_XRCC6BP1_chr12_58345541_ENST00000300145_length(amino acids)=254AA_BP=113
MLDPSSSEEESDEGLEEESRDVLVAAGSSQRAPPAPTREGRRDAPGRAGGGGAARSVSPSPSVLSEGRDEPQRQLDDEQERRIRLQLYVF
VVRCIAYPFNAKQPTDMARRQQKIVLCQNNIHNQAHMNRVVTHELIHAFDHCRAHVDWFTNIRHLACSEVRAANLSGDCSLVNEIFRLHF

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

>12480_12480_6_CADPS2-XRCC6BP1_CADPS2_chr7_122526053_ENST00000334010_XRCC6BP1_chr12_58345541_ENST00000300145_length(amino acids)=254AA_BP=113
MLDPSSSEEESDEGLEEESRDVLVAAGSSQRAPPAPTREGRRDAPGRAGGGGAARSVSPSPSVLSEGRDEPQRQLDDEQERRIRLQLYVF
VVRCIAYPFNAKQPTDMARRQQKIVLCQNNIHNQAHMNRVVTHELIHAFDHCRAHVDWFTNIRHLACSEVRAANLSGDCSLVNEIFRLHF

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

>12480_12480_7_CADPS2-XRCC6BP1_CADPS2_chr7_122526053_ENST00000412584_XRCC6BP1_chr12_58345541_ENST00000300145_length(amino acids)=254AA_BP=113
MLDPSSSEEESDEGLEEESRDVLVAAGSSQRAPPAPTREGRRDAPGRAGGGGAARSVSPSPSVLSEGRDEPQRQLDDEQERRIRLQLYVF
VVRCIAYPFNAKQPTDMARRQQKIVLCQNNIHNQAHMNRVVTHELIHAFDHCRAHVDWFTNIRHLACSEVRAANLSGDCSLVNEIFRLHF

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

>12480_12480_8_CADPS2-XRCC6BP1_CADPS2_chr7_122526053_ENST00000449022_XRCC6BP1_chr12_58345541_ENST00000300145_length(amino acids)=254AA_BP=113
MLDPSSSEEESDEGLEEESRDVLVAAGSSQRAPPAPTREGRRDAPGRAGGGGAARSVSPSPSVLSEGRDEPQRQLDDEQERRIRLQLYVF
VVRCIAYPFNAKQPTDMARRQQKIVLCQNNIHNQAHMNRVVTHELIHAFDHCRAHVDWFTNIRHLACSEVRAANLSGDCSLVNEIFRLHF

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

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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/chr7:122526052/chr12:58345540)
- 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
CADPS2 Q86UW7	.
FUNCTION: Calcium-binding protein involved in exocytosis of vesicles filled with neurotransmitters and neuropeptides. Probably acts upstream of fusion in the biogenesis or maintenance of mature secretory vesicles. Regulates neurotrophin release from granule cells leading to regulate cell differentiation and survival during cerebellar development. May specifically mediate the Ca(2+)-dependent exocytosis of large dense-core vesicles (DCVs) and other dense-core vesicles (By similarity). {ECO:0000250}.	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.

- 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

- 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

CADPS2

chr7:122526052

chr12:58345540

ENST00000412584

350_464

113.0

1256.0

Domain

Hgene

CADPS2

chr7:122526052

chr12:58345540

ENST00000412584

487_590

113.0

1256.0

Domain

Hgene

CADPS2

chr7:122526052

chr12:58345540

ENST00000412584

885_1056

113.0

1256.0

Domain

MHD1

Hgene

CADPS2

chr7:122526052

chr12:58345540

ENST00000449022

350_464

113.0

1297.0

Domain

Hgene

CADPS2

chr7:122526052

chr12:58345540

ENST00000449022

487_590

113.0

1297.0

Domain

Hgene

CADPS2

chr7:122526052

chr12:58345540

ENST00000449022

885_1056

113.0

1297.0

Domain

MHD1

Hgene

CADPS2

chr7:122526053

chr12:58345541

ENST00000412584

350_464

113.0

1256.0

Domain

Hgene

CADPS2

chr7:122526053

chr12:58345541

ENST00000412584

487_590

113.0

1256.0

Domain

Hgene

CADPS2

chr7:122526053

chr12:58345541

ENST00000412584

885_1056

113.0

1256.0

Domain

MHD1

Hgene

CADPS2

chr7:122526053

chr12:58345541

ENST00000449022

350_464

113.0

1297.0

Domain

Hgene

CADPS2

chr7:122526053

chr12:58345541

ENST00000449022

487_590

113.0

1297.0

Domain

Hgene

CADPS2

chr7:122526053

chr12:58345541

ENST00000449022

885_1056

113.0

1297.0

Domain

MHD1

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>425_CADPS2_122526052_XRCC6BP1_58345540_ranked_0.pdb	CADPS2	122526053	122526052	ENST00000300145	XRCC6BP1	chr12	58345540	+	MLDPSSSEEESDEGLEEESRDVLVAAGSSQRAPPAPTREGRRDAPGRAGGGGAARSVSPSPSVLSEGRDEPQRQLDDEQERRIRLQLYVF VVRCIAYPFNAKQPTDMARRQQKIVLCQNNIHNQAHMNRVVTHELIHAFDHCRAHVDWFTNIRHLACSEVRAANLSGDCSLVNEIFRLHF	254

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

CADPS2_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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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
CADPS2
XRCC6BP1

- 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
Hgene	CADPS2	chr7:122526052	chr12:58345540	ENST00000412584	-	1	28	755_1074	113.0	1256.0	DRD2
Hgene	CADPS2	chr7:122526052	chr12:58345540	ENST00000449022	-	1	30	755_1074	113.0	1297.0	DRD2
Hgene	CADPS2	chr7:122526053	chr12:58345541	ENST00000412584	-	1	28	755_1074	113.0	1256.0	DRD2
Hgene	CADPS2	chr7:122526053	chr12:58345541	ENST00000449022	-	1	30	755_1074	113.0	1297.0	DRD2

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Related Drugs to CADPS2-XRCC6BP1

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 CADPS2-XRCC6BP1

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