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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:BAP1-IGHG3 (FusionGDB2 ID:HG8314TG3502)

Fusion Gene Summary for BAP1-IGHG3

check button Fusion gene summary
Fusion gene informationFusion gene name: BAP1-IGHG3
Fusion gene ID: hg8314tg3502
HgeneTgene
Gene symbol

BAP1

IGHG3

Gene ID

8314

3502

Gene nameBRCA1 associated protein 1
SynonymsHUCEP-13|UCHL2|hucep-6
Cytomap('BAP1')('IGHG3')

3p21.1

Type of geneprotein-coding
Descriptionubiquitin carboxyl-terminal hydrolase BAP1BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)cerebral protein 6cerebral protein-13
Modification date20200315
UniProtAcc.

P01860

Ensembl transtripts involved in fusion geneENST00000296288, ENST00000460680, 
Fusion gene scores* DoF score12 X 13 X 7=1092138 X 68 X 15=140760
# samples 13115
** MAII scorelog2(13/1092*10)=-3.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(115/140760*10)=-6.93545974780529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BAP1 [Title/Abstract] AND IGHG3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBAP1(52443953)-IGHG3(106330840), # 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
HgeneBAP1

GO:0016579

protein deubiquitination

18757409|19815555

HgeneBAP1

GO:0035520

monoubiquitinated protein deubiquitination

24703950

HgeneBAP1

GO:0035522

monoubiquitinated histone H2A deubiquitination

20436459|25451922

HgeneBAP1

GO:0045892

negative regulation of transcription, DNA-templated

25451922



check button Fusion gene information
* 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
ChimerDB4LUSCTCGA-66-2788BAP1chr3

52443953

-IGHG3chr14

106330840

-


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Fusion Gene ORF analysis for BAP1-IGHG3

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-intronENST00000296288ENST00000390551BAP1chr3

52443953

-IGHG3chr14

106330840

-
intron-intronENST00000460680ENST00000390551BAP1chr3

52443953

-IGHG3chr14

106330840

-

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 BAP1-IGHG3


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 BAP1-IGHG3


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/:52443953/:106330840)
- 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
.IGHG3

P01860

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}.FUNCTION: Constant region of immunoglobulin heavy chains. Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:22158414, PubMed:20176268). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:17576170, PubMed:20176268). {ECO:0000303|PubMed:17576170, ECO:0000303|PubMed:20176268, ECO:0000303|PubMed:22158414}.

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 BAP1-IGHG3


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 BAP1-IGHG3


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 BAP1-IGHG3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for BAP1-IGHG3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBAP1C3280492TUMOR PREDISPOSITION SYNDROME7CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneBAP1C0220633Uveal melanoma5CGI;CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneBAP1C0345967Malignant mesothelioma5CTD_human
HgeneBAP1C0007134Renal Cell Carcinoma4CTD_human
HgeneBAP1C0025500Mesothelioma4CGI;CTD_human
HgeneBAP1C0279702Conventional (Clear Cell) Renal Cell Carcinoma4CGI;CTD_human
HgeneBAP1C1266042Chromophobe Renal Cell Carcinoma4CTD_human
HgeneBAP1C1266043Sarcomatoid Renal Cell Carcinoma4CTD_human
HgeneBAP1C1266044Collecting Duct Carcinoma of the Kidney4CTD_human
HgeneBAP1C1306837Papillary Renal Cell Carcinoma4CTD_human
HgeneBAP1C0006142Malignant neoplasm of breast2CGI;CTD_human
HgeneBAP1C0024623Malignant neoplasm of stomach2CTD_human
HgeneBAP1C0038356Stomach Neoplasms2CTD_human
HgeneBAP1C0151779Cutaneous Melanoma2CGI;CTD_human;GENOMICS_ENGLAND
HgeneBAP1C0206698Cholangiocarcinoma2CTD_human
HgeneBAP1C0345905Intrahepatic Cholangiocarcinoma2CTD_human
HgeneBAP1C0346373Malignant melanoma of iris2ORPHANET
HgeneBAP1C0346388Malignant melanoma of choroid2ORPHANET
HgeneBAP1C0678222Breast Carcinoma2CGI;CTD_human
HgeneBAP1C1257931Mammary Neoplasms, Human2CTD_human
HgeneBAP1C1458155Mammary Neoplasms2CTD_human
HgeneBAP1C1708349Hereditary Diffuse Gastric Cancer2CTD_human
HgeneBAP1C3805278Extrahepatic Cholangiocarcinoma2CTD_human
HgeneBAP1C4704874Mammary Carcinoma, Human2CTD_human
HgeneBAP1C0005684Malignant neoplasm of urinary bladder1CTD_human
HgeneBAP1C0005695Bladder Neoplasm1CTD_human
HgeneBAP1C0005967Bone neoplasms1CTD_human
HgeneBAP1C0007102Malignant tumor of colon1CTD_human
HgeneBAP1C0009375Colonic Neoplasms1CTD_human
HgeneBAP1C0018671Head and Neck Neoplasms1CTD_human
HgeneBAP1C0018675Head Neoplasms1CTD_human
HgeneBAP1C0022665Kidney Neoplasm1CGI;CTD_human
HgeneBAP1C0023418leukemia1CTD_human
HgeneBAP1C0023798Lipoma1CTD_human
HgeneBAP1C0023903Liver neoplasms1CTD_human
HgeneBAP1C0024121Lung Neoplasms1CTD_human
HgeneBAP1C0025286Meningioma1CTD_human;GENOMICS_ENGLAND
HgeneBAP1C0027533Neck Neoplasms1CTD_human
HgeneBAP1C0030297Pancreatic Neoplasm1CTD_human
HgeneBAP1C0030421Paraganglioma1CTD_human
HgeneBAP1C0033578Prostatic Neoplasms1CTD_human
HgeneBAP1C0039590Testicular Neoplasms1CTD_human
HgeneBAP1C0040100Thymoma1CTD_human
HgeneBAP1C0042138Uterine Neoplasms1CTD_human
HgeneBAP1C0085136Central Nervous System Neoplasms1CTD_human
HgeneBAP1C0152013Adenocarcinoma of lung (disorder)1CTD_human
HgeneBAP1C0153567Uterine Cancer1CTD_human
HgeneBAP1C0153594Malignant neoplasm of testis1CTD_human
HgeneBAP1C0205822Hibernoma1CTD_human
HgeneBAP1C0205823Pleomorphic Lipoma1CTD_human
HgeneBAP1C0205834Meningiomas, Multiple1CTD_human
HgeneBAP1C0205969Thymic Carcinoma1CTD_human
HgeneBAP1C0206686Adrenocortical carcinoma1CTD_human
HgeneBAP1C0206694Mucoepidermoid Carcinoma1CTD_human
HgeneBAP1C0206739Epithelioid and spindle cell nevus1CTD_human
HgeneBAP1C0206754Neuroendocrine Tumors1CTD_human
HgeneBAP1C0206769Nevi and Melanomas1CTD_human
HgeneBAP1C0242379Malignant neoplasm of lung1CTD_human;UNIPROT
HgeneBAP1C0259785Malignant Meningioma1CTD_human
HgeneBAP1C0278996Malignant Head and Neck Neoplasm1CTD_human
HgeneBAP1C0279530Malignant Bone Neoplasm1CTD_human
HgeneBAP1C0281784Benign Meningioma1CTD_human
HgeneBAP1C0334605Meningothelial meningioma1CTD_human
HgeneBAP1C0334606Fibrous Meningioma1CTD_human
HgeneBAP1C0334607Psammomatous Meningioma1CTD_human
HgeneBAP1C0334608Angiomatous Meningioma1CTD_human
HgeneBAP1C0334609Hemangioblastic Meningioma1CTD_human
HgeneBAP1C0334610Hemangiopericytic Meningioma1CTD_human
HgeneBAP1C0334611Transitional Meningioma1CTD_human
HgeneBAP1C0345904Malignant neoplasm of liver1CTD_human
HgeneBAP1C0346647Malignant neoplasm of pancreas1CTD_human
HgeneBAP1C0347515Spinal Meningioma1CTD_human
HgeneBAP1C0349604Intracranial Meningioma1CTD_human
HgeneBAP1C0376358Malignant neoplasm of prostate1CTD_human
HgeneBAP1C0431121Clear Cell Meningioma1CTD_human
HgeneBAP1C0457190Xanthomatous Meningioma1CTD_human
HgeneBAP1C0740457Malignant neoplasm of kidney1CGI;CTD_human
HgeneBAP1C0746787Cancer of Neck1CTD_human
HgeneBAP1C0751177Cancer of Head1CTD_human
HgeneBAP1C0751303Cerebral Convexity Meningioma1CTD_human
HgeneBAP1C0751304Parasagittal Meningioma1CTD_human
HgeneBAP1C0751620Central Nervous System Neoplasms, Primary1CTD_human
HgeneBAP1C0887900Upper Aerodigestive Tract Neoplasms1CTD_human
HgeneBAP1C0919267ovarian neoplasm1CTD_human
HgeneBAP1C1140680Malignant neoplasm of ovary1CTD_human
HgeneBAP1C1334261Intraorbital Meningioma1CTD_human
HgeneBAP1C1334271Intraventricular Meningioma1CTD_human
HgeneBAP1C1335107Olfactory Groove Meningioma1CTD_human
HgeneBAP1C1368275Pigmented Basal Cell Carcinoma1CTD_human
HgeneBAP1C1384406Secretory meningioma1CTD_human
HgeneBAP1C1384408Microcystic meningioma1CTD_human
HgeneBAP1C1527197Angioblastic Meningioma1CTD_human
HgeneBAP1C1565950Posterior Fossa Meningioma1CTD_human
HgeneBAP1C1565951Sphenoid Wing Meningioma1CTD_human
HgeneBAP1C1708353Hereditary Paraganglioma-Pheochromocytoma Syndrome1CLINGEN
HgeneBAP1C1720811Tumor of Rete Testis1CTD_human
HgeneBAP1C2314896Familial Atypical Mole Melanoma Syndrome1ORPHANET
HgeneBAP1C2931822Nasopharyngeal carcinoma1CTD_human
HgeneBAP1C3163622Papillary Meningioma1CTD_human
HgeneBAP1C3489413Lipomatosis, Multiple1CTD_human
HgeneBAP1C4721806Carcinoma, Basal Cell1CTD_human