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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:BCR-STAG2 (FusionGDB2 ID:HG613TG10735)

Fusion Gene Summary for BCR-STAG2

check button Fusion gene summary
Fusion gene informationFusion gene name: BCR-STAG2
Fusion gene ID: hg613tg10735
HgeneTgene
Gene symbol

BCR

STAG2

Gene ID

613

10735

Gene nameBCR activator of RhoGEF and GTPasestromal antigen 2
SynonymsALL|BCR1|CML|D22S11|D22S662|PHLMKMS|NEDXCF|SA-2|SA2|SCC3B|bA517O1.1
Cytomap('BCR')('STAG2')

22q11.23

Xq25

Type of geneprotein-codingprotein-coding
Descriptionbreakpoint cluster region proteinBCR, RhoGEF and GTPase activating proteinBCR/FGFR1 chimera proteinFGFR1/BCR chimera proteinbreakpoint cluster regionrenal carcinoma antigen NY-REN-26cohesin subunit SA-2SCC3 homolog 2
Modification date2020031320200327
UniProtAcc

P11274

.
Ensembl transtripts involved in fusion geneENST00000305877, ENST00000359540, 
ENST00000398512, ENST00000436990, 
Fusion gene scores* DoF score22 X 142 X 16=4998415 X 18 X 5=1350
# samples 16319
** MAII scorelog2(163/49984*10)=-4.93852248902354
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(19/1350*10)=-2.82888808360725
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BCR [Title/Abstract] AND STAG2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBCR(23607192)-STAG2(123185455), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneBCR

GO:0090630

activation of GTPase activity

7479768



check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS5.0N/ANR_033408BCRchr22

23607192

+STAG2chrX

123185455

-


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Fusion Gene ORF analysis for BCR-STAG2

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
intron-intronENST00000305877ENST00000218089BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000305877ENST00000354548BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000305877ENST00000371144BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000305877ENST00000371145BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000305877ENST00000371157BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000305877ENST00000371160BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000305877ENST00000469481BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000359540ENST00000218089BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000359540ENST00000354548BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000359540ENST00000371144BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000359540ENST00000371145BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000359540ENST00000371157BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000359540ENST00000371160BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000359540ENST00000469481BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000398512ENST00000218089BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000398512ENST00000354548BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000398512ENST00000371144BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000398512ENST00000371145BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000398512ENST00000371157BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000398512ENST00000371160BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000398512ENST00000469481BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000436990ENST00000218089BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000436990ENST00000354548BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000436990ENST00000371144BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000436990ENST00000371145BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000436990ENST00000371157BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000436990ENST00000371160BCRchr22

23607192

+STAG2chrX

123185455

-
intron-intronENST00000436990ENST00000469481BCRchr22

23607192

+STAG2chrX

123185455

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for BCR-STAG2


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for BCR-STAG2


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:23607192/:123185455)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
BCR

P11274

.
FUNCTION: Protein with a unique structure having two opposing regulatory activities toward small GTP-binding proteins. The C-terminus is a GTPase-activating protein (GAP) domain which stimulates GTP hydrolysis by RAC1, RAC2 and CDC42. Accelerates the intrinsic rate of GTP hydrolysis of RAC1 or CDC42, leading to down-regulation of the active GTP-bound form (PubMed:7479768, PubMed:1903516, PubMed:17116687). The central Dbl homology (DH) domain functions as guanine nucleotide exchange factor (GEF) that modulates the GTPases CDC42, RHOA and RAC1. Promotes the conversion of CDC42, RHOA and RAC1 from the GDP-bound to the GTP-bound form (PubMed:7479768, PubMed:23940119). The amino terminus contains an intrinsic kinase activity (PubMed:1657398). Functions as an important negative regulator of neuronal RAC1 activity (By similarity). Regulates macrophage functions such as CSF1-directed motility and phagocytosis through the modulation of RAC1 activity (PubMed:17116687). Plays a major role as a RHOA GEF in keratinocytes being involved in focal adhesion formation and keratinocyte differentiation (PubMed:23940119). {ECO:0000250|UniProtKB:Q6PAJ1, ECO:0000269|PubMed:1657398, ECO:0000269|PubMed:17116687, ECO:0000269|PubMed:1903516, ECO:0000269|PubMed:23940119, ECO:0000269|PubMed:7479768}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

check buttonRetention 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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for BCR-STAG2


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for BCR-STAG2


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for BCR-STAG2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneBCRP11274DB00619ImatinibInhibitorSmall moleculeApproved
HgeneBCRP11274DB00619ImatinibInhibitorSmall moleculeApproved
HgeneBCRP11274DB00619ImatinibInhibitorSmall moleculeApproved
HgeneBCRP11274DB06616BosutinibInhibitorSmall moleculeApproved
HgeneBCRP11274DB06616BosutinibInhibitorSmall moleculeApproved
HgeneBCRP11274DB06616BosutinibInhibitorSmall moleculeApproved
HgeneBCRP11274DB01254DasatinibSmall moleculeApproved|Investigational
HgeneBCRP11274DB01254DasatinibSmall moleculeApproved|Investigational
HgeneBCRP11274DB01254DasatinibSmall moleculeApproved|Investigational
HgeneBCRP11274DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
HgeneBCRP11274DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
HgeneBCRP11274DB08901PonatinibInhibitorSmall moleculeApproved|Investigational

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Related Diseases for BCR-STAG2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBCRC0005586Bipolar Disorder4PSYGENET
HgeneBCRC0023473Myeloid Leukemia, Chronic3CTD_human;ORPHANET
HgeneBCRC0005699Blast Phase1CTD_human
HgeneBCRC0006413Burkitt Lymphoma1ORPHANET
HgeneBCRC0023893Liver Cirrhosis, Experimental1CTD_human
HgeneBCRC0027022Myeloproliferative disease1CTD_human
HgeneBCRC0027540Necrosis1CTD_human
HgeneBCRC0027659Neoplasms, Experimental1CTD_human
HgeneBCRC0041696Unipolar Depression1PSYGENET
HgeneBCRC1269683Major Depressive Disorder1PSYGENET
HgeneBCRC1292769Precursor B-cell lymphoblastic leukemia1ORPHANET
TgeneC0005684Malignant neoplasm of urinary bladder3CGI;CTD_human
TgeneC0005695Bladder Neoplasm3CGI;CTD_human
TgeneC4310830Xq25 TRIPLICATION SYNDROME2ORPHANET
TgeneC4311049Xq25 DUPLICATION SYNDROME2ORPHANET
TgeneC0007138Carcinoma, Transitional Cell1CTD_human
TgeneC0018798Congenital Heart Defects1GENOMICS_ENGLAND
TgeneC0023466Leukemia, Monocytic, Chronic1CTD_human
TgeneC0023470Myeloid Leukemia1CTD_human
TgeneC0025958Microcephaly1GENOMICS_ENGLAND
TgeneC0456070Growth delay1GENOMICS_ENGLAND
TgeneC0557874Global developmental delay1GENOMICS_ENGLAND
TgeneC1384666hearing impairment1GENOMICS_ENGLAND
TgeneC1860789Leukemia, Megakaryoblastic, of Down Syndrome1CTD_human
TgeneC2713368Hematopoetic Myelodysplasia1CTD_human
TgeneC3463824MYELODYSPLASTIC SYNDROME1CTD_human
TgeneC3714756Intellectual Disability1GENOMICS_ENGLAND
TgeneC4021817Abnormality of head or neck1GENOMICS_ENGLAND