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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:VCPIP1-CDH17

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: VCPIP1-CDH17
	FusionPDB ID: 97995
	FusionGDB2.0 ID: 97995
		Hgene	Tgene
	Gene symbol	VCPIP1	CDH17
	Gene ID	80124	1015
	Gene name	valosin containing protein interacting protein 1	cadherin 17
	Synonyms	DUBA3\|VCIP135	CDH16\|HPT-1\|HPT1
	Cytomap	8q13.1	8q22.1
	Type of gene	protein-coding	protein-coding
	Description	deubiquitinating protein VCIP135VCP/p47 complex-interacting 135-kDa proteinvalosin-containing protein p97/p47 complex-interacting protein 1valosin-containing protein p97/p47 complex-interacting protein p135	cadherin-17HPT-1 cadherinLI cadherincadherin 17, LI cadherin (liver-intestine)cadherin-16human intestinal peptide-associated transporter HPT-1human peptide transporter 1intestinal peptide-associated transporter HPT-1liver-intestine cadherin
	Modification date	20200313	20200313
	UniProtAcc	.	Q12864
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000310421,	ENST00000027335, ENST00000441892, ENST00000450165,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	2 X 2 X 2=8	6 X 6 X 3=108
	# samples	2	6
	** MAII score	log2(2/8*10)=1.32192809488736	log2(6/108*10)=-0.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: VCPIP1 [Title/Abstract] AND CDH17 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	VCPIP1(67563693)-CDH17(95178204), # samples:1
Anticipated loss of major functional domain due to fusion event.	VCPIP1-CDH17 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. VCPIP1-CDH17 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. VCPIP1-CDH17 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. VCPIP1-CDH17 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
Hgene	VCPIP1	GO:0035871	protein K11-linked deubiquitination	23827681
Hgene	VCPIP1	GO:0071108	protein K48-linked deubiquitination	23827681

Fusion gene breakpoints across VCPIP1 (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 CDH17 (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	BRCA	TCGA-AN-A0XV-01A	VCPIP1	chr8	67563693	-	CDH17	chr8	95178204	-

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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)
ENST00000310421	VCPIP1	chr8	67563693	-	ENST00000027335	CDH17	chr8	95178204	-	5558	3056	259	4488	1409
ENST00000310421	VCPIP1	chr8	67563693	-	ENST00000441892	CDH17	chr8	95178204	-	4743	3056	259	4374	1371
ENST00000310421	VCPIP1	chr8	67563693	-	ENST00000450165	CDH17	chr8	95178204	-	4489	3056	259	4488	1410

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
ENST00000310421	ENST00000027335	VCPIP1	chr8	67563693	-	CDH17	chr8	95178204	-	0.000208547	0.99979144
ENST00000310421	ENST00000441892	VCPIP1	chr8	67563693	-	CDH17	chr8	95178204	-	0.000151433	0.9998485
ENST00000310421	ENST00000450165	VCPIP1	chr8	67563693	-	CDH17	chr8	95178204	-	0.00025811	0.99974185

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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

>97995_97995_1_VCPIP1-CDH17_VCPIP1_chr8_67563693_ENST00000310421_CDH17_chr8_95178204_ENST00000027335_length(amino acids)=1409AA_BP=932
MSQPPPPPPPLPPPPPPPEAPQTPSSLASAAASGGLLKRRDRRILSGSCPDPKCQARLFFPASGSVSIECTECGQRHEQQQLLGVEEVTD
PDVVLHNLLRNALLGVTGAPKKNTELVKVMGLSNYHCKLLSPILARYGMDKQTGRAKLLRDMNQGELFDCALLGDRAFLIEPEHVNTVGY
GKDRSGSLLYLHDTLEDIKRANKSQECLIPVHVDGDGHCLVHAVSRALVGRELFWHALRENLKQHFQQHLARYQALFHDFIDAAEWEDII
NECDPLFVPPEGVPLGLRNIHIFGLANVLHRPIILLDSLSGMRSSGDYSATFLPGLIPAEKCTGKDGHLNKPICIAWSSSGRNHYIPLVG
IKGAALPKLPMNLLPKAWGVPQDLIKKYIKLEEDGGCVIGGDRSLQDKYLLRLVAAMEEVFMDKHGIHPSLVADVHQYFYRRTGVIGVQP
EEVTAAAKKAVMDNRLHKCLLCGALSELHVPPEWLAPGGKLYNLAKSTHGQLRTDKNYSFPLNNLVCSYDSVKDVLVPDYGMSNLTACNW
CHGTSVRKVRGDGSIVYLDGDRTNSRSTGGKCGCGFKHFWDGKEYDNLPEAFPITLEWGGRVVRETVYWFQYESDSSLNSNVYDVAMKLV
TKHFPGEFGSEILVQKVVHTILHQTAKKNPDDYTPVNIDGAHAQRVGDVQGQESESQLPTKIILTGQKTKTLHKEELNMSKTERTIQQNI
TEQASVMQKRKTEKLKQEQKGQPRTVSPSTIRDGPSSAPATPTKAPYSPTTSKEKKIRITTNDGRQSMVTLKSSTTFFELQESIAREFNI
PPYLQCIRYGFPPKELMPPQAGMEKEPVPLQHGDRITIEILKSKAEGGQSAAAHSAHTVKQEDIAVTGKLSSKELQEQAEKEMYSLCLLA
TLMGEDVWSYAKGLPHMFQQGGVFYSIMKKTMGNSIGTLTAHDRDEENTANSFLNYRIVEQTPKLPMDGLFLIQTYAGMLQLAKQSLKKQ
DTPQYNLTIEVSDKDFKTLCFVQINVIDINDQIPIFEKSDYGNLTLAEDTNIGSTILTIQATDADEPFTGSSKILYHIIKGDSEGRLGVD
TDPHTNTGYVIIKKPLDFETAAVSNIVFKAENPEPLVFGVKYNASSFAKFTLIVTDVNEAPQFSQHVFQAKVSEDVAIGTKVGNVTAKDP
EGLDISYSLRGDTRGWLKIDHVTGEIFSVAPLDREAGSPYRVQVVATEVGGSSLSSVSEFHLILMDVNDNPPRLAKDYTGLFFCHPLSAP
GSLIFEATDDDQHLFRGPHFTFSLGSGSLQNDWEVSKINGTHARLSTRHTEFEEREYVVLIRINDGGRPPLEGIVSLPVTFCSCVEGSCF

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

>97995_97995_2_VCPIP1-CDH17_VCPIP1_chr8_67563693_ENST00000310421_CDH17_chr8_95178204_ENST00000441892_length(amino acids)=1371AA_BP=932
MSQPPPPPPPLPPPPPPPEAPQTPSSLASAAASGGLLKRRDRRILSGSCPDPKCQARLFFPASGSVSIECTECGQRHEQQQLLGVEEVTD
PDVVLHNLLRNALLGVTGAPKKNTELVKVMGLSNYHCKLLSPILARYGMDKQTGRAKLLRDMNQGELFDCALLGDRAFLIEPEHVNTVGY
GKDRSGSLLYLHDTLEDIKRANKSQECLIPVHVDGDGHCLVHAVSRALVGRELFWHALRENLKQHFQQHLARYQALFHDFIDAAEWEDII
NECDPLFVPPEGVPLGLRNIHIFGLANVLHRPIILLDSLSGMRSSGDYSATFLPGLIPAEKCTGKDGHLNKPICIAWSSSGRNHYIPLVG
IKGAALPKLPMNLLPKAWGVPQDLIKKYIKLEEDGGCVIGGDRSLQDKYLLRLVAAMEEVFMDKHGIHPSLVADVHQYFYRRTGVIGVQP
EEVTAAAKKAVMDNRLHKCLLCGALSELHVPPEWLAPGGKLYNLAKSTHGQLRTDKNYSFPLNNLVCSYDSVKDVLVPDYGMSNLTACNW
CHGTSVRKVRGDGSIVYLDGDRTNSRSTGGKCGCGFKHFWDGKEYDNLPEAFPITLEWGGRVVRETVYWFQYESDSSLNSNVYDVAMKLV
TKHFPGEFGSEILVQKVVHTILHQTAKKNPDDYTPVNIDGAHAQRVGDVQGQESESQLPTKIILTGQKTKTLHKEELNMSKTERTIQQNI
TEQASVMQKRKTEKLKQEQKGQPRTVSPSTIRDGPSSAPATPTKAPYSPTTSKEKKIRITTNDGRQSMVTLKSSTTFFELQESIAREFNI
PPYLQCIRYGFPPKELMPPQAGMEKEPVPLQHGDRITIEILKSKAEGGQSAAAHSAHTVKQEDIAVTGKLSSKELQEQAEKEMYSLCLLA
TLMGEDVWSYAKGLPHMFQQGGVFYSIMKKTMGNSIGTLTAHDRDEENTANSFLNYRIVEQTPKLPMDGLFLIQTYAGMLQLAKQSLKKQ
DTPQYNLTIEVSDKDFKTLCFVQINVIDINDQIPIFEKSDYGNLTLAEDTNIGSTILTIQATDADEPFTGSSKILYHIIKGDSEGRLGVD
TDPHTNTGYVIIKKPLDFETAAVSNIVFKAENPEPLVFGVKYNASSFAKFTLIVTDVNEAPQFSQHVFQAKVSEDVAIGTKVGNVTAKDP
EGLDISYSLRGDTRGWLKIDHVTGEIFSVAPLDREAGSPYRVQVVATEVGGSSLSSVSEFHLILMDVNDNPPRLAKDYTGLFFCHPLSAP
GSLIFEATDDDQHLFRGPHFTFSLGSGSLQNDWEVSKINGTHARLSTRHTEFEEREYVVLIRINDGGRPPLEGIVSLPGIILAVVFIRIK

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

>97995_97995_3_VCPIP1-CDH17_VCPIP1_chr8_67563693_ENST00000310421_CDH17_chr8_95178204_ENST00000450165_length(amino acids)=1410AA_BP=932
MSQPPPPPPPLPPPPPPPEAPQTPSSLASAAASGGLLKRRDRRILSGSCPDPKCQARLFFPASGSVSIECTECGQRHEQQQLLGVEEVTD
PDVVLHNLLRNALLGVTGAPKKNTELVKVMGLSNYHCKLLSPILARYGMDKQTGRAKLLRDMNQGELFDCALLGDRAFLIEPEHVNTVGY
GKDRSGSLLYLHDTLEDIKRANKSQECLIPVHVDGDGHCLVHAVSRALVGRELFWHALRENLKQHFQQHLARYQALFHDFIDAAEWEDII
NECDPLFVPPEGVPLGLRNIHIFGLANVLHRPIILLDSLSGMRSSGDYSATFLPGLIPAEKCTGKDGHLNKPICIAWSSSGRNHYIPLVG
IKGAALPKLPMNLLPKAWGVPQDLIKKYIKLEEDGGCVIGGDRSLQDKYLLRLVAAMEEVFMDKHGIHPSLVADVHQYFYRRTGVIGVQP
EEVTAAAKKAVMDNRLHKCLLCGALSELHVPPEWLAPGGKLYNLAKSTHGQLRTDKNYSFPLNNLVCSYDSVKDVLVPDYGMSNLTACNW
CHGTSVRKVRGDGSIVYLDGDRTNSRSTGGKCGCGFKHFWDGKEYDNLPEAFPITLEWGGRVVRETVYWFQYESDSSLNSNVYDVAMKLV
TKHFPGEFGSEILVQKVVHTILHQTAKKNPDDYTPVNIDGAHAQRVGDVQGQESESQLPTKIILTGQKTKTLHKEELNMSKTERTIQQNI
TEQASVMQKRKTEKLKQEQKGQPRTVSPSTIRDGPSSAPATPTKAPYSPTTSKEKKIRITTNDGRQSMVTLKSSTTFFELQESIAREFNI
PPYLQCIRYGFPPKELMPPQAGMEKEPVPLQHGDRITIEILKSKAEGGQSAAAHSAHTVKQEDIAVTGKLSSKELQEQAEKEMYSLCLLA
TLMGEDVWSYAKGLPHMFQQGGVFYSIMKKTMGNSIGTLTAHDRDEENTANSFLNYRIVEQTPKLPMDGLFLIQTYAGMLQLAKQSLKKQ
DTPQYNLTIEVSDKDFKTLCFVQINVIDINDQIPIFEKSDYGNLTLAEDTNIGSTILTIQATDADEPFTGSSKILYHIIKGDSEGRLGVD
TDPHTNTGYVIIKKPLDFETAAVSNIVFKAENPEPLVFGVKYNASSFAKFTLIVTDVNEAPQFSQHVFQAKVSEDVAIGTKVGNVTAKDP
EGLDISYSLRGDTRGWLKIDHVTGEIFSVAPLDREAGSPYRVQVVATEVGGSSLSSVSEFHLILMDVNDNPPRLAKDYTGLFFCHPLSAP
GSLIFEATDDDQHLFRGPHFTFSLGSGSLQNDWEVSKINGTHARLSTRHTEFEEREYVVLIRINDGGRPPLEGIVSLPVTFCSCVEGSCF

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

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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/chr8:67563693/chr8:95178204)
- 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
.	CDH17 Q12864
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: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. LI-cadherin may have a role in the morphological organization of liver and intestine. Involved in intestinal peptide transport. {ECO:0000269\|PubMed:8153632}.

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

Hgene

VCPIP1

chr8:67563693

chr8:95178204

ENST00000310421

4_24

932.3333333333334

1223.0

Compositional bias

Note=Pro-rich

Hgene

VCPIP1

chr8:67563693

chr8:95178204

ENST00000310421

208_361

932.3333333333334

1223.0

Domain

OTU

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000027335

450_566

355.3333333333333

833.0

Domain

Cadherin 5

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000027335

567_667

355.3333333333333

833.0

Domain

Cadherin 6

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000027335

668_777

355.3333333333333

833.0

Domain

Cadherin 7

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000450165

450_566

355.3333333333333

833.0

Domain

Cadherin 5

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000450165

567_667

355.3333333333333

833.0

Domain

Cadherin 6

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000450165

668_777

355.3333333333333

833.0

Domain

Cadherin 7

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000027335

809_832

355.3333333333333

833.0

Topological domain

Cytoplasmic

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000450165

809_832

355.3333333333333

833.0

Topological domain

Cytoplasmic

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000027335

788_808

355.3333333333333

833.0

Transmembrane

Helical

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000450165

788_808

355.3333333333333

833.0

Transmembrane

Helical

- 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

CDH17

chr8:67563693

chr8:95178204

ENST00000027335

129_244

355.3333333333333

833.0

Domain

Cadherin 2

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000027335

245_340

355.3333333333333

833.0

Domain

Cadherin 3

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000027335

30_128

355.3333333333333

833.0

Domain

Cadherin 1

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000027335

341_449

355.3333333333333

833.0

Domain

Cadherin 4

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000450165

129_244

355.3333333333333

833.0

Domain

Cadherin 2

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000450165

245_340

355.3333333333333

833.0

Domain

Cadherin 3

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000450165

30_128

355.3333333333333

833.0

Domain

Cadherin 1

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000450165

341_449

355.3333333333333

833.0

Domain

Cadherin 4

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000027335

23_787

355.3333333333333

833.0

Topological domain

Extracellular

Tgene

CDH17

chr8:67563693

chr8:95178204

ENST00000450165

23_787

355.3333333333333

833.0

Topological domain

Extracellular

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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
VCPIP1
CDH17

- 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 VCPIP1-CDH17

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 VCPIP1-CDH17

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