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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:PTPRC-BCAS3

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PTPRC-BCAS3
	FusionPDB ID: 70328
	FusionGDB2.0 ID: 70328
		Hgene	Tgene
	Gene symbol	PTPRC	BCAS3
	Gene ID	5788	54828
	Gene name	protein tyrosine phosphatase receptor type C	BCAS3 microtubule associated cell migration factor
	Synonyms	B220\|CD45\|CD45R\|GP180\|L-CA\|LCA\|LY5\|T200	GAOB1\|MAAB
	Cytomap	1q31.3-q32.1	17q23.2
	Type of gene	protein-coding	protein-coding
	Description	receptor-type tyrosine-protein phosphatase CCD45 antigenT200 glycoproteinT200 leukocyte common antigenprotein tyrosine phosphatase, receptor type, c polypeptide	breast carcinoma-amplified sequence 3BCAS4/BCAS3 fusionRudhirabreast carcinoma amplified sequence 4/3 fusion proteinmetastasis associated antigen of breast cancerprotein Maab1
	Modification date	20200327	20200313
	UniProtAcc	.	Q9H6U6
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000348564, ENST00000352140, ENST00000367364, ENST00000367376, ENST00000413409, ENST00000442510, ENST00000594404, ENST00000598951, ENST00000391970,	ENST00000585812, ENST00000407086, ENST00000408905, ENST00000585744, ENST00000588462, ENST00000588874, ENST00000390652, ENST00000589222,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 6 X 3=108	45 X 32 X 19=27360
	# samples	6	53
	** MAII score	log2(6/108*10)=-0.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(53/27360*10)=-5.6899320603227 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PTPRC [Title/Abstract] AND BCAS3 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PTPRC(198608471)-BCAS3(59469337), # samples:1
Anticipated loss of major functional domain due to fusion event.	PTPRC-BCAS3 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. PTPRC-BCAS3 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. PTPRC-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. PTPRC-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. PTPRC-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. PTPRC-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF. PTPRC-BCAS3 seems lost the major protein functional domain in Tgene 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
Hgene	PTPRC	GO:0006469	negative regulation of protein kinase activity	9197241
Hgene	PTPRC	GO:0032677	regulation of interleukin-8 production	12100025
Hgene	PTPRC	GO:0050764	regulation of phagocytosis	12100025
Hgene	PTPRC	GO:0050852	T cell receptor signaling pathway	10358156
Hgene	PTPRC	GO:0061097	regulation of protein tyrosine kinase activity	12100025
Tgene	BCAS3	GO:0043085	positive regulation of catalytic activity	17505058
Tgene	BCAS3	GO:0045944	positive regulation of transcription by RNA polymerase II	17505058
Tgene	BCAS3	GO:0071391	cellular response to estrogen stimulus	17505058

Fusion gene breakpoints across PTPRC (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 BCAS3 (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	145N	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+

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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)
ENST00000352140	PTPRC	chr1	198608471	+	ENST00000589222	BCAS3	chr17	59469337	+	1093	238	313	687	124
ENST00000352140	PTPRC	chr1	198608471	+	ENST00000390652	BCAS3	chr17	59469337	+	1100	238	313	687	124
ENST00000594404	PTPRC	chr1	198608471	+	ENST00000589222	BCAS3	chr17	59469337	+	1093	238	313	687	124
ENST00000594404	PTPRC	chr1	198608471	+	ENST00000390652	BCAS3	chr17	59469337	+	1100	238	313	687	124
ENST00000367376	PTPRC	chr1	198608471	+	ENST00000589222	BCAS3	chr17	59469337	+	1093	238	313	687	124
ENST00000367376	PTPRC	chr1	198608471	+	ENST00000390652	BCAS3	chr17	59469337	+	1100	238	313	687	124
ENST00000442510	PTPRC	chr1	198608471	+	ENST00000589222	BCAS3	chr17	59469337	+	1069	214	289	663	124
ENST00000442510	PTPRC	chr1	198608471	+	ENST00000390652	BCAS3	chr17	59469337	+	1076	214	289	663	124
ENST00000348564	PTPRC	chr1	198608471	+	ENST00000589222	BCAS3	chr17	59469337	+	1014	159	234	608	124
ENST00000348564	PTPRC	chr1	198608471	+	ENST00000390652	BCAS3	chr17	59469337	+	1021	159	234	608	124
ENST00000598951	PTPRC	chr1	198608471	+	ENST00000589222	BCAS3	chr17	59469337	+	1093	238	313	687	124
ENST00000598951	PTPRC	chr1	198608471	+	ENST00000390652	BCAS3	chr17	59469337	+	1100	238	313	687	124
ENST00000367364	PTPRC	chr1	198608471	+	ENST00000589222	BCAS3	chr17	59469337	+	1012	157	232	606	124
ENST00000367364	PTPRC	chr1	198608471	+	ENST00000390652	BCAS3	chr17	59469337	+	1019	157	232	606	124
ENST00000413409	PTPRC	chr1	198608471	+	ENST00000589222	BCAS3	chr17	59469337	+	1012	157	232	606	124
ENST00000413409	PTPRC	chr1	198608471	+	ENST00000390652	BCAS3	chr17	59469337	+	1019	157	232	606	124

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
ENST00000352140	ENST00000589222	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.8688953	0.13110468
ENST00000352140	ENST00000390652	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.8703832	0.12961678
ENST00000594404	ENST00000589222	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.8688953	0.13110468
ENST00000594404	ENST00000390652	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.8703832	0.12961678
ENST00000367376	ENST00000589222	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.8688953	0.13110468
ENST00000367376	ENST00000390652	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.8703832	0.12961678
ENST00000442510	ENST00000589222	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.85825866	0.1417413
ENST00000442510	ENST00000390652	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.8656656	0.1343344
ENST00000348564	ENST00000589222	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.92773175	0.072268225
ENST00000348564	ENST00000390652	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.92593783	0.074062094
ENST00000598951	ENST00000589222	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.8688953	0.13110468
ENST00000598951	ENST00000390652	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.8703832	0.12961678
ENST00000367364	ENST00000589222	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.9219759	0.07802412
ENST00000367364	ENST00000390652	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.92119867	0.078801356
ENST00000413409	ENST00000589222	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.9219759	0.07802412
ENST00000413409	ENST00000390652	PTPRC	chr1	198608471	+	BCAS3	chr17	59469337	+	0.92119867	0.078801356

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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

>70328_70328_1_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000348564_BCAS3_chr17_59469337_ENST00000390652_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_2_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000348564_BCAS3_chr17_59469337_ENST00000589222_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_3_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000352140_BCAS3_chr17_59469337_ENST00000390652_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_4_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000352140_BCAS3_chr17_59469337_ENST00000589222_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_5_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000367364_BCAS3_chr17_59469337_ENST00000390652_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_6_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000367364_BCAS3_chr17_59469337_ENST00000589222_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_7_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000367376_BCAS3_chr17_59469337_ENST00000390652_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_8_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000367376_BCAS3_chr17_59469337_ENST00000589222_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_9_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000413409_BCAS3_chr17_59469337_ENST00000390652_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_10_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000413409_BCAS3_chr17_59469337_ENST00000589222_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_11_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000442510_BCAS3_chr17_59469337_ENST00000390652_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_12_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000442510_BCAS3_chr17_59469337_ENST00000589222_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_13_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000594404_BCAS3_chr17_59469337_ENST00000390652_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_14_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000594404_BCAS3_chr17_59469337_ENST00000589222_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_15_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000598951_BCAS3_chr17_59469337_ENST00000390652_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

>70328_70328_16_PTPRC-BCAS3_PTPRC_chr1_198608471_ENST00000598951_BCAS3_chr17_59469337_ENST00000589222_length(amino acids)=124AA_BP=
MMATDLRCPPMRASPSASSRLASRRYQQPASDWPAPSPAGGGEKPRSGPTLQSLLFLHQPPSPSLVTAAAHPTWMEKRPFSKHLSALALC

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

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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/chr1:198608471/chr17:59469337)
- 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
.	BCAS3 Q9H6U6
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: Plays a role in angiogenesis. Participates in the regulation of cell polarity and directional endothelial cell migration by mediating both the activation and recruitment of CDC42 and the reorganization of the actin cytoskeleton at the cell leading edge. Promotes filipodia formation (By similarity). Functions synergistically with PELP1 as a transcriptional coactivator of estrogen receptor-responsive genes. Stimulates histone acetyltransferase activity. Binds to chromatin. {ECO:0000250\|UniProtKB:Q8CCN5, ECO:0000269\|PubMed:17505058}.

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

PTPRC

chr1:198608471

chr17:59469337

ENST00000367376

391_483

22.333333333333332

1305.0

Domain

Fibronectin type-III 1

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000367376

484_576

22.333333333333332

1305.0

Domain

Fibronectin type-III 2

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000367376

653_912

22.333333333333332

1305.0

Domain

Tyrosine-protein phosphatase 1

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000367376

944_1228

22.333333333333332

1305.0

Domain

Tyrosine-protein phosphatase 2

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000594404

391_483

22.333333333333332

1144.0

Domain

Fibronectin type-III 1

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000594404

484_576

22.333333333333332

1144.0

Domain

Fibronectin type-III 2

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000594404

653_912

22.333333333333332

1144.0

Domain

Tyrosine-protein phosphatase 1

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000594404

944_1228

22.333333333333332

1144.0

Domain

Tyrosine-protein phosphatase 2

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000367376

853_859

22.333333333333332

1305.0

Region

Substrate binding

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000594404

853_859

22.333333333333332

1144.0

Region

Substrate binding

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000367376

26_577

22.333333333333332

1305.0

Topological domain

Extracellular

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000367376

599_1306

22.333333333333332

1305.0

Topological domain

Cytoplasmic

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000594404

26_577

22.333333333333332

1144.0

Topological domain

Extracellular

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000594404

599_1306

22.333333333333332

1144.0

Topological domain

Cytoplasmic

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000367376

578_598

22.333333333333332

1305.0

Transmembrane

Helical

Hgene

PTPRC

chr1:198608471

chr17:59469337

ENST00000594404

578_598

22.333333333333332

1144.0

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
PTPRC
BCAS3

- 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 PTPRC-BCAS3

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 PTPRC-BCAS3

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