UTHEALTH HOME ABOUT SBMI A-Z WEBMAIL INSIDE THE UNIVERSITY

Home

Download

Statistics

Examples

Help

Contact

level1

	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:PCTP-BRIP1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PCTP-BRIP1
	FusionPDB ID: 63541
	FusionGDB2.0 ID: 63541
		Hgene	Tgene
	Gene symbol	PCTP	BRIP1
	Gene ID	58488	83990
	Gene name	phosphatidylcholine transfer protein	BRCA1 interacting protein C-terminal helicase 1
	Synonyms	PC-TP\|STARD2	BACH1\|FANCJ\|OF
	Cytomap	17q22	17q23.2
	Type of gene	protein-coding	protein-coding
	Description	phosphatidylcholine transfer proteinSTART domain-containing protein 2StAR-related lipid transfer (START) domain containing 2stAR-related lipid transfer protein 2	Fanconi anemia group J proteinATP-dependent RNA helicase BRIP1BRCA1-associated C-terminal helicase 1BRCA1-binding helicase-like protein BACH1BRCA1/BRCA2-associated helicase 1
	Modification date	20200313	20200315
	UniProtAcc	.	Q9BX63
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000268896, ENST00000573500, ENST00000576183, ENST00000325214, ENST00000576221,	ENST00000583837, ENST00000259008, ENST00000577598,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 3 X 5=90	12 X 15 X 7=1260
	# samples	7	13
	** MAII score	log2(7/90*10)=-0.362570079384708 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(13/1260*10)=-3.27684020535882 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PCTP [Title/Abstract] AND BRIP1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PCTP(53828605)-BRIP1(59861785), # samples:1
Anticipated loss of major functional domain due to fusion event.	PCTP-BRIP1 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. PCTP-BRIP1 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. PCTP-BRIP1 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. PCTP-BRIP1 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	PCTP	GO:0015914	phospholipid transport	12055623
Tgene	BRIP1	GO:0006357	regulation of transcription by RNA polymerase II	14504288

Fusion gene breakpoints across PCTP (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 BRIP1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Top

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-IE-A3OV-01A	PCTP	chr17	53828605	+	BRIP1	chr17	59861785	-

Top

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)
ENST00000573500	PCTP	chr17	53828605	+	ENST00000259008	BRIP1	chr17	59861785	-	4458	151	10	2427	805
ENST00000573500	PCTP	chr17	53828605	+	ENST00000577598	BRIP1	chr17	59861785	-	2647	151	10	1662	550
ENST00000268896	PCTP	chr17	53828605	+	ENST00000259008	BRIP1	chr17	59861785	-	4573	266	89	2542	817
ENST00000268896	PCTP	chr17	53828605	+	ENST00000577598	BRIP1	chr17	59861785	-	2762	266	89	1777	562
ENST00000576183	PCTP	chr17	53828605	+	ENST00000259008	BRIP1	chr17	59861785	-	4491	184	7	2460	817
ENST00000576183	PCTP	chr17	53828605	+	ENST00000577598	BRIP1	chr17	59861785	-	2680	184	7	1695	562

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
ENST00000573500	ENST00000259008	PCTP	chr17	53828605	+	BRIP1	chr17	59861785	-	0.000458302	0.99954176
ENST00000573500	ENST00000577598	PCTP	chr17	53828605	+	BRIP1	chr17	59861785	-	0.000565195	0.99943477
ENST00000268896	ENST00000259008	PCTP	chr17	53828605	+	BRIP1	chr17	59861785	-	0.000462182	0.9995378
ENST00000268896	ENST00000577598	PCTP	chr17	53828605	+	BRIP1	chr17	59861785	-	0.000589687	0.9994103
ENST00000576183	ENST00000259008	PCTP	chr17	53828605	+	BRIP1	chr17	59861785	-	0.000466956	0.99953306
ENST00000576183	ENST00000577598	PCTP	chr17	53828605	+	BRIP1	chr17	59861785	-	0.00059627	0.9994037

Top

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

>63541_63541_1_PCTP-BRIP1_PCTP_chr17_53828605_ENST00000268896_BRIP1_chr17_59861785_ENST00000259008_length(amino acids)=817AA_BP=59
MPSRRRSPDCGRMELAAGSFSEEQFWEACAELQQPALAGADWQLLVETSGISIYRLLDKGHFSAVLQKEEKISPIYGKEEAREVPVISAS
TQIMLKGLFMVLDYLFRQNSRFADDYKIAIQQTYSWTNQIDISDKNGLLVLPKNKKRSRQKTAVHVLNFWCLNPAVAFSDINGKVQTIVL
TSGTLSPMKSFSSELGVTFTIQLEANHIIKNSQVWVGTIGSGPKGRNLCATFQNTETFEFQDEVGALLLSVCQTVSQGILCFLPSYKLLE
KLKERWLSTGLWHNLELVKTVIVEPQGGEKTNFDELLQVYYDAIKYKGEKDGALLVAVCRGKVSEGLDFSDDNARAVITIGIPFPNVKDL
QVELKRQYNDHHSKLRGLLPGRQWYEIQAYRALNQALGRCIRHRNDWGALILVDDRFRNNPSRYISGLSKWVRQQIQHHSTFESALESLA
EFSKKHQKVLNVSIKDRTNIQDNESTLEVTSLKYSTSPYLLEAASHLSPENFVEDEAKICVQELQCPKIITKNSPLPSSIISRKEKNDPV
FLEEAGKAEKIVISRSTSPTFNKQTKRVSWSSFNSLGQYFTGKIPKATPELGSSENSASSPPRFKTEKMESKTVLPFTDKCESSNLTVNT
SFGSCPQSETIISSLKIDATLTRKNHSEHPLCSEEALDPDIELSLVSEEDKQSTSNRDFETEAEDESIYFTPELYDPEDTDEEKNDLAET
DRGNRLANNSDCILAKDLFEIRTIKEVDSAREVKAEDCIDTKLNGILHIEESKIDDIDGNVKTTWINELELGKTHEIEIKNFKPSPSKNK

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

>63541_63541_2_PCTP-BRIP1_PCTP_chr17_53828605_ENST00000268896_BRIP1_chr17_59861785_ENST00000577598_length(amino acids)=562AA_BP=59
MPSRRRSPDCGRMELAAGSFSEEQFWEACAELQQPALAGADWQLLVETSGISIYRLLDKGHFSAVLQKEEKISPIYGKEEAREVPVISAS
TQIMLKGLFMVLDYLFRQNSRFADDYKIAIQQTYSWTNQIDISDKNGLLVLPKNKKRSRQKTAVHVLNFWCLNPAVAFSDINGKVQTIVL
TSGTLSPMKSFSSELGVTFTIQLEANHIIKNSQVWVGTIGSGPKGRNLCATFQNTETFEFQDEVGALLLSVCQTVSQGILCFLPSYKLLE
KLKERWLSTGLWHNLELVKTVIVEPQGGEKTNFDELLQVYYDAIKYKGEKDGALLVAVCRGKVSEGLDFSDDNARAVITIGIPFPNVKDL
QVELKRQYNDHHSKLRGLLPGRQWYEIQAYRALNQALGRCIRHRNDWGALILVDDRFRNNPSRYISGLSKWVRQQIQHHSTFESALESLA
EFSKKHQKVLNVSIKDRTNIQDNESTLEVTSLKYSTSPYLLEAASHLSPENFVEDEAKICVQELQCPKIITKNSPLPSSIISRKEKSMKS

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

>63541_63541_3_PCTP-BRIP1_PCTP_chr17_53828605_ENST00000573500_BRIP1_chr17_59861785_ENST00000259008_length(amino acids)=805AA_BP=47
MELAAGSFSEEQFWEACAELQQPALAGADWQLLVETSGISIYRLLDKGHFSAVLQKEEKISPIYGKEEAREVPVISASTQIMLKGLFMVL
DYLFRQNSRFADDYKIAIQQTYSWTNQIDISDKNGLLVLPKNKKRSRQKTAVHVLNFWCLNPAVAFSDINGKVQTIVLTSGTLSPMKSFS
SELGVTFTIQLEANHIIKNSQVWVGTIGSGPKGRNLCATFQNTETFEFQDEVGALLLSVCQTVSQGILCFLPSYKLLEKLKERWLSTGLW
HNLELVKTVIVEPQGGEKTNFDELLQVYYDAIKYKGEKDGALLVAVCRGKVSEGLDFSDDNARAVITIGIPFPNVKDLQVELKRQYNDHH
SKLRGLLPGRQWYEIQAYRALNQALGRCIRHRNDWGALILVDDRFRNNPSRYISGLSKWVRQQIQHHSTFESALESLAEFSKKHQKVLNV
SIKDRTNIQDNESTLEVTSLKYSTSPYLLEAASHLSPENFVEDEAKICVQELQCPKIITKNSPLPSSIISRKEKNDPVFLEEAGKAEKIV
ISRSTSPTFNKQTKRVSWSSFNSLGQYFTGKIPKATPELGSSENSASSPPRFKTEKMESKTVLPFTDKCESSNLTVNTSFGSCPQSETII
SSLKIDATLTRKNHSEHPLCSEEALDPDIELSLVSEEDKQSTSNRDFETEAEDESIYFTPELYDPEDTDEEKNDLAETDRGNRLANNSDC

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

>63541_63541_4_PCTP-BRIP1_PCTP_chr17_53828605_ENST00000573500_BRIP1_chr17_59861785_ENST00000577598_length(amino acids)=550AA_BP=47
MELAAGSFSEEQFWEACAELQQPALAGADWQLLVETSGISIYRLLDKGHFSAVLQKEEKISPIYGKEEAREVPVISASTQIMLKGLFMVL
DYLFRQNSRFADDYKIAIQQTYSWTNQIDISDKNGLLVLPKNKKRSRQKTAVHVLNFWCLNPAVAFSDINGKVQTIVLTSGTLSPMKSFS
SELGVTFTIQLEANHIIKNSQVWVGTIGSGPKGRNLCATFQNTETFEFQDEVGALLLSVCQTVSQGILCFLPSYKLLEKLKERWLSTGLW
HNLELVKTVIVEPQGGEKTNFDELLQVYYDAIKYKGEKDGALLVAVCRGKVSEGLDFSDDNARAVITIGIPFPNVKDLQVELKRQYNDHH
SKLRGLLPGRQWYEIQAYRALNQALGRCIRHRNDWGALILVDDRFRNNPSRYISGLSKWVRQQIQHHSTFESALESLAEFSKKHQKVLNV
SIKDRTNIQDNESTLEVTSLKYSTSPYLLEAASHLSPENFVEDEAKICVQELQCPKIITKNSPLPSSIISRKEKSMKSSSHLPLIEKSFI

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

>63541_63541_5_PCTP-BRIP1_PCTP_chr17_53828605_ENST00000576183_BRIP1_chr17_59861785_ENST00000259008_length(amino acids)=817AA_BP=59
MPSRRRSPDCGRMELAAGSFSEEQFWEACAELQQPALAGADWQLLVETSGISIYRLLDKGHFSAVLQKEEKISPIYGKEEAREVPVISAS
TQIMLKGLFMVLDYLFRQNSRFADDYKIAIQQTYSWTNQIDISDKNGLLVLPKNKKRSRQKTAVHVLNFWCLNPAVAFSDINGKVQTIVL
TSGTLSPMKSFSSELGVTFTIQLEANHIIKNSQVWVGTIGSGPKGRNLCATFQNTETFEFQDEVGALLLSVCQTVSQGILCFLPSYKLLE
KLKERWLSTGLWHNLELVKTVIVEPQGGEKTNFDELLQVYYDAIKYKGEKDGALLVAVCRGKVSEGLDFSDDNARAVITIGIPFPNVKDL
QVELKRQYNDHHSKLRGLLPGRQWYEIQAYRALNQALGRCIRHRNDWGALILVDDRFRNNPSRYISGLSKWVRQQIQHHSTFESALESLA
EFSKKHQKVLNVSIKDRTNIQDNESTLEVTSLKYSTSPYLLEAASHLSPENFVEDEAKICVQELQCPKIITKNSPLPSSIISRKEKNDPV
FLEEAGKAEKIVISRSTSPTFNKQTKRVSWSSFNSLGQYFTGKIPKATPELGSSENSASSPPRFKTEKMESKTVLPFTDKCESSNLTVNT
SFGSCPQSETIISSLKIDATLTRKNHSEHPLCSEEALDPDIELSLVSEEDKQSTSNRDFETEAEDESIYFTPELYDPEDTDEEKNDLAET
DRGNRLANNSDCILAKDLFEIRTIKEVDSAREVKAEDCIDTKLNGILHIEESKIDDIDGNVKTTWINELELGKTHEIEIKNFKPSPSKNK

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

>63541_63541_6_PCTP-BRIP1_PCTP_chr17_53828605_ENST00000576183_BRIP1_chr17_59861785_ENST00000577598_length(amino acids)=562AA_BP=59
MPSRRRSPDCGRMELAAGSFSEEQFWEACAELQQPALAGADWQLLVETSGISIYRLLDKGHFSAVLQKEEKISPIYGKEEAREVPVISAS
TQIMLKGLFMVLDYLFRQNSRFADDYKIAIQQTYSWTNQIDISDKNGLLVLPKNKKRSRQKTAVHVLNFWCLNPAVAFSDINGKVQTIVL
TSGTLSPMKSFSSELGVTFTIQLEANHIIKNSQVWVGTIGSGPKGRNLCATFQNTETFEFQDEVGALLLSVCQTVSQGILCFLPSYKLLE
KLKERWLSTGLWHNLELVKTVIVEPQGGEKTNFDELLQVYYDAIKYKGEKDGALLVAVCRGKVSEGLDFSDDNARAVITIGIPFPNVKDL
QVELKRQYNDHHSKLRGLLPGRQWYEIQAYRALNQALGRCIRHRNDWGALILVDDRFRNNPSRYISGLSKWVRQQIQHHSTFESALESLA
EFSKKHQKVLNVSIKDRTNIQDNESTLEVTSLKYSTSPYLLEAASHLSPENFVEDEAKICVQELQCPKIITKNSPLPSSIISRKEKSMKS

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

Top

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/chr17:53828605/chr17:59861785)
- 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
.	BRIP1 Q9BX63
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: DNA-dependent ATPase and 5' to 3' DNA helicase required for the maintenance of chromosomal stability. Acts late in the Fanconi anemia pathway, after FANCD2 ubiquitination. Involved in the repair of DNA double-strand breaks by homologous recombination in a manner that depends on its association with BRCA1. {ECO:0000269\|PubMed:11301010, ECO:0000269\|PubMed:14983014, ECO:0000269\|PubMed:16116421, ECO:0000269\|PubMed:16153896}.

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

PCTP

chr17:53828605

chr17:59861785

ENST00000268896

1_212

47.0

215.0

Domain

START

Hgene

PCTP

chr17:53828605

chr17:59861785

ENST00000325214

1_212

143.0

Domain

START

Tgene

BRIP1

chr17:53828605

chr17:59861785

ENST00000259008

11_442

491.0

1250.0

Domain

Helicase ATP-binding

Tgene

BRIP1

chr17:53828605

chr17:59861785

ENST00000259008

158_175

491.0

1250.0

Motif

Nuclear localization signal

Tgene

BRIP1

chr17:53828605

chr17:59861785

ENST00000259008

393_396

491.0

1250.0

Motif

Note=DEAH box

Tgene

BRIP1

chr17:53828605

chr17:59861785

ENST00000259008

185_192

491.0

1250.0

Nucleotide binding

ATP

Top

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
PCTP
BRIP1

- 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

Top

Related Drugs to PCTP-BRIP1

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to PCTP-BRIP1

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