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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:PCDH7-RAP1A

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PCDH7-RAP1A
	FusionPDB ID: 63234
	FusionGDB2.0 ID: 63234
		Hgene	Tgene
	Gene symbol	PCDH7	RAP1A
	Gene ID	5099	5906
	Gene name	protocadherin 7	RAP1A, member of RAS oncogene family
	Synonyms	BH-Pcdh\|BHPCDH\|PPP1R120	C21KG\|G-22K\|KREV-1\|KREV1\|RAP1\|SMGP21
	Cytomap	4p15.1	1p13.2
	Type of gene	protein-coding	protein-coding
	Description	protocadherin-7BH-protocadherin (brain-heart)brain-heart protocadherinprotein phosphatase 1, regulatory subunit 120	ras-related protein Rap-1AGTP-binding protein smg p21ARas-related protein Krev-1
	Modification date	20200313	20200329
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000543491, ENST00000361762, ENST00000509925,	ENST00000494982, ENST00000356415, ENST00000369709, ENST00000436150, ENST00000545460,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 8 X 2=128	10 X 9 X 4=360
	# samples	9	10
	** MAII score	log2(9/128*10)=-0.508146903670325 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/360*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PCDH7 [Title/Abstract] AND RAP1A [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PCDH7(31144315)-RAP1A(112237972), # samples:1
Anticipated loss of major functional domain due to fusion event.	PCDH7-RAP1A 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. PCDH7-RAP1A 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. PCDH7-RAP1A 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. PCDH7-RAP1A 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	RAP1A	GO:0071320	cellular response to cAMP	21840392
Tgene	RAP1A	GO:0072659	protein localization to plasma membrane	17916086
Tgene	RAP1A	GO:0098696	regulation of neurotransmitter receptor localization to postsynaptic specialization membrane	12202034

Fusion gene breakpoints across PCDH7 (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 RAP1A (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
ChiTaRS5.0	N/A	BF948052	PCDH7	chr4	31144315	-	RAP1A	chr1	112237972	+

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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)
ENST00000543491	PCDH7	chr4	31144315	-	ENST00000356415	RAP1A	chr1	112237972	+	4747	3547	0	3419	1139
ENST00000543491	PCDH7	chr4	31144315	-	ENST00000436150	RAP1A	chr1	112237972	+	5113	3547	0	3419	1139
ENST00000543491	PCDH7	chr4	31144315	-	ENST00000369709	RAP1A	chr1	112237972	+	8325	3547	0	3419	1139
ENST00000543491	PCDH7	chr4	31144315	-	ENST00000545460	RAP1A	chr1	112237972	+	4121	3547	0	3419	1139

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
ENST00000543491	ENST00000356415	PCDH7	chr4	31144315	-	RAP1A	chr1	112237972	+	0.000594001	0.999406
ENST00000543491	ENST00000436150	PCDH7	chr4	31144315	-	RAP1A	chr1	112237972	+	0.000375682	0.99962425
ENST00000543491	ENST00000369709	PCDH7	chr4	31144315	-	RAP1A	chr1	112237972	+	0.000105076	0.99989486
ENST00000543491	ENST00000545460	PCDH7	chr4	31144315	-	RAP1A	chr1	112237972	+	0.001103518	0.9988965

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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

>63234_63234_1_PCDH7-RAP1A_PCDH7_chr4_31144315_ENST00000543491_RAP1A_chr1_112237972_ENST00000356415_length(amino acids)=1139AA_BP=
MLRMRTAGWARGWCLGCCLLLPLSLSLAAAKQLLRYRLAEEGPADVRIGNVASDLGIVTGSGEVTFSLESGSEYLKIDNLTGELSTSERR
IDREKLPQCQMIFDENECFLDFEVSVIGPSQSWVDLFEGQVIVLDINDNTPTFPSPVLTLTVEENRPVGTLYLLPTATDRDFGRNGIERY
ELLQEPGGGGSGGESRRAGAADSAPYPGGGGNGASGGGSGGSKRRLDASEGGGGTNPGGRSSVFELQVADTPDGEKQPQLIVKGALDREQ
RDSYELTLRVRDGGDPPRSSQAILRVLITDVNDNSPRFEKSVYEADLAENSAPGTPILQLRAADLDVGVNGQIEYVFGAATESVRRLLRL
DETSGWLSVLHRIDREEVNQLRFTVMARDRGQPPKTDKATVVLNIKDENDNVPSIEIRKIGRIPLKDGVANVAEDVLVDTPIALVQVSDR
DQGENGVVTCTVVGDVPFQLKPASDTEGDQNKKKYFLHTSTPLDYEATREFNVVIVAVDSGSPSLSSNNSLIVKVGDTNDNPPMFGQSVV
EVYFPENNIPGERVATVLATDADSGKNAEIAYSLDSSVMGIFAIDPDSGDILVNTVLDREQTDRYEFKVNAKDKGIPVLQGSTTVIVQVA
DKNDNDPKFMQDVFTFYVKENLQPNSPVGMVTVMDADKGRNAEMSLYIEENNNIFSIENDTGTIYSTMSFDREHQTTYTFRVKAVDGGDP
PRSATATVSLFVMDENDNAPTVTLPKNISYTLLPPSSNVRTVVATVLATDSDDGINADLNYSIVGGNPFKLFEIDPTSGVVSLVGKLTQK
HYGLHRLVVQVNDSGQPSQSTTTLVHVFVNESVSNATAIDSQIARSLHIPLTQDIAGDPSYEISKQRLSIVIGVVAGIMTVILIILIVVM
ARYCRSKNKNGYEAGKKDHEDFFTPQQHDKSKKPKKDKKNKKSKQPLYSSIVTVEASKPNGQRYDSVNEKLSDSPSMGRYRSVNGGPGSP
DLARHYKSSSPLPTVQLHPQSPTAGKKHQAVQDLPPANTFVGAGDNISIGSDHCSEYSCQTNNKYSKQPFRRVTFSVVSQPQDPHQGSLQ

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

>63234_63234_2_PCDH7-RAP1A_PCDH7_chr4_31144315_ENST00000543491_RAP1A_chr1_112237972_ENST00000369709_length(amino acids)=1139AA_BP=
MLRMRTAGWARGWCLGCCLLLPLSLSLAAAKQLLRYRLAEEGPADVRIGNVASDLGIVTGSGEVTFSLESGSEYLKIDNLTGELSTSERR
IDREKLPQCQMIFDENECFLDFEVSVIGPSQSWVDLFEGQVIVLDINDNTPTFPSPVLTLTVEENRPVGTLYLLPTATDRDFGRNGIERY
ELLQEPGGGGSGGESRRAGAADSAPYPGGGGNGASGGGSGGSKRRLDASEGGGGTNPGGRSSVFELQVADTPDGEKQPQLIVKGALDREQ
RDSYELTLRVRDGGDPPRSSQAILRVLITDVNDNSPRFEKSVYEADLAENSAPGTPILQLRAADLDVGVNGQIEYVFGAATESVRRLLRL
DETSGWLSVLHRIDREEVNQLRFTVMARDRGQPPKTDKATVVLNIKDENDNVPSIEIRKIGRIPLKDGVANVAEDVLVDTPIALVQVSDR
DQGENGVVTCTVVGDVPFQLKPASDTEGDQNKKKYFLHTSTPLDYEATREFNVVIVAVDSGSPSLSSNNSLIVKVGDTNDNPPMFGQSVV
EVYFPENNIPGERVATVLATDADSGKNAEIAYSLDSSVMGIFAIDPDSGDILVNTVLDREQTDRYEFKVNAKDKGIPVLQGSTTVIVQVA
DKNDNDPKFMQDVFTFYVKENLQPNSPVGMVTVMDADKGRNAEMSLYIEENNNIFSIENDTGTIYSTMSFDREHQTTYTFRVKAVDGGDP
PRSATATVSLFVMDENDNAPTVTLPKNISYTLLPPSSNVRTVVATVLATDSDDGINADLNYSIVGGNPFKLFEIDPTSGVVSLVGKLTQK
HYGLHRLVVQVNDSGQPSQSTTTLVHVFVNESVSNATAIDSQIARSLHIPLTQDIAGDPSYEISKQRLSIVIGVVAGIMTVILIILIVVM
ARYCRSKNKNGYEAGKKDHEDFFTPQQHDKSKKPKKDKKNKKSKQPLYSSIVTVEASKPNGQRYDSVNEKLSDSPSMGRYRSVNGGPGSP
DLARHYKSSSPLPTVQLHPQSPTAGKKHQAVQDLPPANTFVGAGDNISIGSDHCSEYSCQTNNKYSKQPFRRVTFSVVSQPQDPHQGSLQ

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

>63234_63234_3_PCDH7-RAP1A_PCDH7_chr4_31144315_ENST00000543491_RAP1A_chr1_112237972_ENST00000436150_length(amino acids)=1139AA_BP=
MLRMRTAGWARGWCLGCCLLLPLSLSLAAAKQLLRYRLAEEGPADVRIGNVASDLGIVTGSGEVTFSLESGSEYLKIDNLTGELSTSERR
IDREKLPQCQMIFDENECFLDFEVSVIGPSQSWVDLFEGQVIVLDINDNTPTFPSPVLTLTVEENRPVGTLYLLPTATDRDFGRNGIERY
ELLQEPGGGGSGGESRRAGAADSAPYPGGGGNGASGGGSGGSKRRLDASEGGGGTNPGGRSSVFELQVADTPDGEKQPQLIVKGALDREQ
RDSYELTLRVRDGGDPPRSSQAILRVLITDVNDNSPRFEKSVYEADLAENSAPGTPILQLRAADLDVGVNGQIEYVFGAATESVRRLLRL
DETSGWLSVLHRIDREEVNQLRFTVMARDRGQPPKTDKATVVLNIKDENDNVPSIEIRKIGRIPLKDGVANVAEDVLVDTPIALVQVSDR
DQGENGVVTCTVVGDVPFQLKPASDTEGDQNKKKYFLHTSTPLDYEATREFNVVIVAVDSGSPSLSSNNSLIVKVGDTNDNPPMFGQSVV
EVYFPENNIPGERVATVLATDADSGKNAEIAYSLDSSVMGIFAIDPDSGDILVNTVLDREQTDRYEFKVNAKDKGIPVLQGSTTVIVQVA
DKNDNDPKFMQDVFTFYVKENLQPNSPVGMVTVMDADKGRNAEMSLYIEENNNIFSIENDTGTIYSTMSFDREHQTTYTFRVKAVDGGDP
PRSATATVSLFVMDENDNAPTVTLPKNISYTLLPPSSNVRTVVATVLATDSDDGINADLNYSIVGGNPFKLFEIDPTSGVVSLVGKLTQK
HYGLHRLVVQVNDSGQPSQSTTTLVHVFVNESVSNATAIDSQIARSLHIPLTQDIAGDPSYEISKQRLSIVIGVVAGIMTVILIILIVVM
ARYCRSKNKNGYEAGKKDHEDFFTPQQHDKSKKPKKDKKNKKSKQPLYSSIVTVEASKPNGQRYDSVNEKLSDSPSMGRYRSVNGGPGSP
DLARHYKSSSPLPTVQLHPQSPTAGKKHQAVQDLPPANTFVGAGDNISIGSDHCSEYSCQTNNKYSKQPFRRVTFSVVSQPQDPHQGSLQ

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

>63234_63234_4_PCDH7-RAP1A_PCDH7_chr4_31144315_ENST00000543491_RAP1A_chr1_112237972_ENST00000545460_length(amino acids)=1139AA_BP=
MLRMRTAGWARGWCLGCCLLLPLSLSLAAAKQLLRYRLAEEGPADVRIGNVASDLGIVTGSGEVTFSLESGSEYLKIDNLTGELSTSERR
IDREKLPQCQMIFDENECFLDFEVSVIGPSQSWVDLFEGQVIVLDINDNTPTFPSPVLTLTVEENRPVGTLYLLPTATDRDFGRNGIERY
ELLQEPGGGGSGGESRRAGAADSAPYPGGGGNGASGGGSGGSKRRLDASEGGGGTNPGGRSSVFELQVADTPDGEKQPQLIVKGALDREQ
RDSYELTLRVRDGGDPPRSSQAILRVLITDVNDNSPRFEKSVYEADLAENSAPGTPILQLRAADLDVGVNGQIEYVFGAATESVRRLLRL
DETSGWLSVLHRIDREEVNQLRFTVMARDRGQPPKTDKATVVLNIKDENDNVPSIEIRKIGRIPLKDGVANVAEDVLVDTPIALVQVSDR
DQGENGVVTCTVVGDVPFQLKPASDTEGDQNKKKYFLHTSTPLDYEATREFNVVIVAVDSGSPSLSSNNSLIVKVGDTNDNPPMFGQSVV
EVYFPENNIPGERVATVLATDADSGKNAEIAYSLDSSVMGIFAIDPDSGDILVNTVLDREQTDRYEFKVNAKDKGIPVLQGSTTVIVQVA
DKNDNDPKFMQDVFTFYVKENLQPNSPVGMVTVMDADKGRNAEMSLYIEENNNIFSIENDTGTIYSTMSFDREHQTTYTFRVKAVDGGDP
PRSATATVSLFVMDENDNAPTVTLPKNISYTLLPPSSNVRTVVATVLATDSDDGINADLNYSIVGGNPFKLFEIDPTSGVVSLVGKLTQK
HYGLHRLVVQVNDSGQPSQSTTTLVHVFVNESVSNATAIDSQIARSLHIPLTQDIAGDPSYEISKQRLSIVIGVVAGIMTVILIILIVVM
ARYCRSKNKNGYEAGKKDHEDFFTPQQHDKSKKPKKDKKNKKSKQPLYSSIVTVEASKPNGQRYDSVNEKLSDSPSMGRYRSVNGGPGSP
DLARHYKSSSPLPTVQLHPQSPTAGKKHQAVQDLPPANTFVGAGDNISIGSDHCSEYSCQTNNKYSKQPFRRVTFSVVSQPQDPHQGSLQ

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

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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/chr4:31144315/chr1:112237972)
- 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
.	.
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: 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

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000356415

32_40

315.3333333333333

Motif

Effector region

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000369709

32_40

1554.6666666666667

Motif

Effector region

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000436150

32_40

484.0

Motif

Effector region

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000545460

32_40

137.0

Motif

Effector region

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000356415

10_18

315.3333333333333

Nucleotide binding

GTP

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000356415

116_119

315.3333333333333

Nucleotide binding

GTP

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000356415

29_35

315.3333333333333

Nucleotide binding

GTP

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000369709

10_18

1554.6666666666667

Nucleotide binding

GTP

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000369709

116_119

1554.6666666666667

Nucleotide binding

GTP

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000369709

29_35

1554.6666666666667

Nucleotide binding

GTP

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000436150

10_18

484.0

Nucleotide binding

GTP

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000436150

116_119

484.0

Nucleotide binding

GTP

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000436150

29_35

484.0

Nucleotide binding

GTP

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000545460

10_18

137.0

Nucleotide binding

GTP

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000545460

116_119

137.0

Nucleotide binding

GTP

Tgene

RAP1A

chr4:31144315

chr1:112237972

ENST00000545460

29_35

137.0

Nucleotide binding

GTP

- 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

PCDH7

chr4:31144315

chr1:112237972

ENST00000361762

144_308

1070.0

Domain

Cadherin 2

Hgene

PCDH7

chr4:31144315

chr1:112237972

ENST00000361762

29_143

1070.0

Domain

Cadherin 1

Hgene

PCDH7

chr4:31144315

chr1:112237972

ENST00000361762

309_415

1070.0

Domain

Cadherin 3

Hgene

PCDH7

chr4:31144315

chr1:112237972

ENST00000361762

424_535

1070.0

Domain

Cadherin 4

Hgene

PCDH7

chr4:31144315

chr1:112237972

ENST00000361762

536_639

1070.0

Domain

Cadherin 5

Hgene

PCDH7

chr4:31144315

chr1:112237972

ENST00000361762

640_742

1070.0

Domain

Cadherin 6

Hgene

PCDH7

chr4:31144315

chr1:112237972

ENST00000361762

745_862

1070.0

Domain

Cadherin 7

Hgene

PCDH7

chr4:31144315

chr1:112237972

ENST00000361762

29_879

1070.0

Topological domain

Extracellular

Hgene

PCDH7

chr4:31144315

chr1:112237972

ENST00000361762

901_1069

1070.0

Topological domain

Cytoplasmic

Hgene

PCDH7

chr4:31144315

chr1:112237972

ENST00000361762

880_900

1070.0

Transmembrane

Helical

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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
PCDH7
RAP1A

- 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 PCDH7-RAP1A

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 PCDH7-RAP1A

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