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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:B2M-CXCR4 (FusionGDB2 ID:HG567TG7852)

Fusion Gene Summary for B2M-CXCR4

check button Fusion gene summary
Fusion gene informationFusion gene name: B2M-CXCR4
Fusion gene ID: hg567tg7852
HgeneTgene
Gene symbol

B2M

CXCR4

Gene ID

567

7852

Gene namebeta-2-microglobulinC-X-C motif chemokine receptor 4
SynonymsIMD43CD184|D2S201E|FB22|HM89|HSY3RR|LAP-3|LAP3|LCR1|LESTR|NPY3R|NPYR|NPYRL|NPYY3R|WHIM|WHIMS
Cytomap('B2M')('CXCR4')

15q21.1

2q22.1

Type of geneprotein-codingprotein-coding
Descriptionbeta-2-microglobulinbeta chain of MHC class I moleculesbeta-2-microglobinC-X-C chemokine receptor type 4CD184 antigenLPS-associated protein 3SDF-1 receptorchemokine (C-X-C motif) receptor 4chemokine receptorfusinleukocyte-derived seven transmembrane domain receptorlipopolysaccharide-associated protein 3neuropeptide Y
Modification date2020032920200313
UniProtAcc.

P61073

Ensembl transtripts involved in fusion geneENST00000544417, ENST00000558401, 
ENST00000559916, ENST00000559220, 
Fusion gene scores* DoF score32 X 24 X 12=92166 X 3 X 4=72
# samples 436
** MAII scorelog2(43/9216*10)=-4.42173215185285
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/72*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: B2M [Title/Abstract] AND CXCR4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointB2M(45003811)-CXCR4(136873482), # samples:1
Anticipated loss of major functional domain due to fusion event.B2M-CXCR4 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
B2M-CXCR4 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
B2M-CXCR4 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneB2M

GO:0002726

positive regulation of T cell cytokine production

24643698

HgeneB2M

GO:0007611

learning or memory

26147761

HgeneB2M

GO:0050680

negative regulation of epithelial cell proliferation

28213472

HgeneB2M

GO:0050768

negative regulation of neurogenesis

26147761

HgeneB2M

GO:0090647

modulation of age-related behavioral decline

26147761

HgeneB2M

GO:1900121

negative regulation of receptor binding

9465039

HgeneB2M

GO:1990000

amyloid fibril formation

28468825

HgeneB2M

GO:2000774

positive regulation of cellular senescence

28213472

HgeneB2M

GO:2000978

negative regulation of forebrain neuron differentiation

26147761

TgeneCXCR4

GO:0007186

G protein-coupled receptor signaling pathway

10644702

TgeneCXCR4

GO:0030155

regulation of cell adhesion

19703720

TgeneCXCR4

GO:0038160

CXCL12-activated CXCR4 signaling pathway

28978524

TgeneCXCR4

GO:0071345

cellular response to cytokine stimulus

21540189



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
ChimerDB4Non-CancerERR315333B2Mchr15

45003811

+CXCR4chr2

136873482

-


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Fusion Gene ORF analysis for B2M-CXCR4

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
5CDS-5UTRENST00000544417ENST00000466288B2Mchr15

45003811

+CXCR4chr2

136873482

-
5CDS-5UTRENST00000558401ENST00000466288B2Mchr15

45003811

+CXCR4chr2

136873482

-
5CDS-5UTRENST00000559916ENST00000466288B2Mchr15

45003811

+CXCR4chr2

136873482

-
Frame-shiftENST00000544417ENST00000241393B2Mchr15

45003811

+CXCR4chr2

136873482

-
Frame-shiftENST00000544417ENST00000409817B2Mchr15

45003811

+CXCR4chr2

136873482

-
Frame-shiftENST00000558401ENST00000241393B2Mchr15

45003811

+CXCR4chr2

136873482

-
Frame-shiftENST00000558401ENST00000409817B2Mchr15

45003811

+CXCR4chr2

136873482

-
Frame-shiftENST00000559916ENST00000241393B2Mchr15

45003811

+CXCR4chr2

136873482

-
Frame-shiftENST00000559916ENST00000409817B2Mchr15

45003811

+CXCR4chr2

136873482

-
intron-3CDSENST00000559220ENST00000241393B2Mchr15

45003811

+CXCR4chr2

136873482

-
intron-3CDSENST00000559220ENST00000409817B2Mchr15

45003811

+CXCR4chr2

136873482

-
intron-5UTRENST00000559220ENST00000466288B2Mchr15

45003811

+CXCR4chr2

136873482

-

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 B2M-CXCR4


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 B2M-CXCR4


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/:45003811/:136873482)
- 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
.CXCR4

P61073

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: Receptor for the C-X-C chemokine CXCL12/SDF-1 that transduces a signal by increasing intracellular calcium ion levels and enhancing MAPK1/MAPK3 activation (PubMed:10452968, PubMed:28978524, PubMed:18799424, PubMed:24912431). Involved in the AKT signaling cascade (PubMed:24912431). Plays a role in regulation of cell migration, e.g. during wound healing (PubMed:28978524). Acts as a receptor for extracellular ubiquitin; leading to enhanced intracellular calcium ions and reduced cellular cAMP levels (PubMed:20228059). Binds bacterial lipopolysaccharide (LPS) et mediates LPS-induced inflammatory response, including TNF secretion by monocytes (PubMed:11276205). Involved in hematopoiesis and in cardiac ventricular septum formation. Also plays an essential role in vascularization of the gastrointestinal tract, probably by regulating vascular branching and/or remodeling processes in endothelial cells. Involved in cerebellar development. In the CNS, could mediate hippocampal-neuron survival (By similarity). {ECO:0000250|UniProtKB:P70658, ECO:0000269|PubMed:10074102, ECO:0000269|PubMed:10452968, ECO:0000269|PubMed:10644702, ECO:0000269|PubMed:10825158, ECO:0000269|PubMed:11276205, ECO:0000269|PubMed:17197449, ECO:0000269|PubMed:18799424, ECO:0000269|PubMed:20048153, ECO:0000269|PubMed:20228059, ECO:0000269|PubMed:20505072, ECO:0000269|PubMed:24912431, ECO:0000269|PubMed:28978524, ECO:0000269|PubMed:8752280, ECO:0000269|PubMed:8752281}.; FUNCTION: (Microbial infection) Acts as a coreceptor (CD4 being the primary receptor) for human immunodeficiency virus-1/HIV-1 X4 isolates and as a primary receptor for some HIV-2 isolates. Promotes Env-mediated fusion of the virus (PubMed:8849450, PubMed:8929542, PubMed:9427609, PubMed:10074122, PubMed:10756055). {ECO:0000269|PubMed:10074122, ECO:0000269|PubMed:10756055, ECO:0000269|PubMed:8849450, ECO:0000269|PubMed:8929542, ECO:0000269|PubMed:9427609}.

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 B2M-CXCR4


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 B2M-CXCR4


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 B2M-CXCR4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneCXCR4P61073DB00452FramycetinAntagonistSmall moleculeApproved
TgeneCXCR4P61073DB06809PlerixaforAntagonistSmall moleculeApproved
TgeneCXCR4P61073DB12698IbalizumabAntagonistBiotechApproved|Investigational

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Related Diseases for B2M-CXCR4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneB2MC0022658Kidney Diseases3CTD_human
HgeneB2MC0022660Kidney Failure, Acute3CTD_human
HgeneB2MC1565662Acute Kidney Insufficiency3CTD_human
HgeneB2MC2609414Acute kidney injury3CTD_human
HgeneB2MC1855796Hypoproteinemia, Hypercatabolic2CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneB2MC0004364Autoimmune Diseases1CTD_human
HgeneB2MC0013221Drug toxicity1CTD_human
HgeneB2MC0018799Heart Diseases1CTD_human
HgeneB2MC0020455Hypergammaglobulinemia1CTD_human
HgeneB2MC0033578Prostatic Neoplasms1CTD_human
HgeneB2MC0041755Adverse reaction to drug1CTD_human
HgeneB2MC0079744Diffuse Large B-Cell Lymphoma1CTD_human
HgeneB2MC0079774Peripheral T-Cell Lymphoma1CTD_human
HgeneB2MC0268389Amyloidosis, familial visceral1CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneB2MC0279626Squamous cell carcinoma of esophagus1CTD_human
HgeneB2MC0376358Malignant neoplasm of prostate1CTD_human
HgeneB2MC1858266Bare Lymphocyte Syndrome, Type I1ORPHANET
HgeneB2MC4302669Autosomal dominant beta2-microglobulinic amyloidosis1ORPHANET
TgeneC0472817WHIM syndrome3CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC0027627Neoplasm Metastasis2CTD_human
TgeneC0087031Juvenile-Onset Still Disease2CTD_human
TgeneC0340970Congenital neutropenia2GENOMICS_ENGLAND
TgeneC3495559Juvenile arthritis2CTD_human
TgeneC3714758Juvenile psoriatic arthritis2CTD_human
TgeneC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative2CTD_human
TgeneC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive2CTD_human
TgeneC0003873Rheumatoid Arthritis1CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0007621Neoplastic Cell Transformation1CTD_human
TgeneC0027626Neoplasm Invasiveness1CTD_human
TgeneC0027719Nephrosclerosis1CTD_human
TgeneC0027796Neuralgia1CTD_human
TgeneC0038870Neuralgia, Supraorbital1CTD_human
TgeneC0042656Neuralgia, Vidian1CTD_human
TgeneC0234247Neuralgia, Atypical1CTD_human
TgeneC0234249Neuralgia, Stump1CTD_human
TgeneC0423711Neuralgia, Perineal1CTD_human
TgeneC0423712Neuralgia, Iliohypogastric Nerve1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC0751371Neuralgia, Ilioinguinal1CTD_human
TgeneC0751372Nerve Pain1CTD_human
TgeneC0751373Paroxysmal Nerve Pain1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC1834176MYELOKATHEXIS, ISOLATED1GENOMICS_ENGLAND
TgeneC4704874Mammary Carcinoma, Human1CTD_human