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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:BNC2-ATP7A (FusionGDB2 ID:HG54796TG538)

Fusion Gene Summary for BNC2-ATP7A

check button Fusion gene summary
Fusion gene informationFusion gene name: BNC2-ATP7A
Fusion gene ID: hg54796tg538
HgeneTgene
Gene symbol

BNC2

ATP7A

Gene ID

54796

538

Gene namebasonuclin 2ATPase copper transporting alpha
SynonymsBSN2|LUTODSMAX|MK|MNK|SMAX3
Cytomap('BNC2')('ATP7A')

9p22.3-p22.2

Xq21.1

Type of geneprotein-codingprotein-coding
Descriptionzinc finger protein basonuclin-2copper-transporting ATPase 1ATPase, Cu++ transporting, alpha polypeptideCu++-transporting P-type ATPaseMenkes disease-associated proteincopper pump 1
Modification date2020031320200313
UniProtAcc

Q6ZN30

.
Ensembl transtripts involved in fusion geneENST00000380666, ENST00000380667, 
ENST00000380672, ENST00000471301, 
ENST00000545497, 
Fusion gene scores* DoF score12 X 16 X 6=11524 X 7 X 3=84
# samples 167
** MAII scorelog2(16/1152*10)=-2.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/84*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BNC2 [Title/Abstract] AND ATP7A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBNC2(16634399)-ATP7A(77166199), # 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
TgeneATP7A

GO:0051353

positive regulation of oxidoreductase activity

11092760



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/AX69208BNC2chr9

16634399

+ATP7AchrX

77166199

+


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Fusion Gene ORF analysis for BNC2-ATP7A

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-3CDSENST00000380666ENST00000341514BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380666ENST00000343533BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380666ENST00000350425BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380667ENST00000341514BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380667ENST00000343533BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380667ENST00000350425BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380672ENST00000341514BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380672ENST00000343533BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380672ENST00000350425BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000471301ENST00000341514BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000471301ENST00000343533BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000471301ENST00000350425BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000545497ENST00000341514BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000545497ENST00000343533BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000545497ENST00000350425BNC2chr9

16634399

+ATP7AchrX

77166199

+

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 BNC2-ATP7A


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 BNC2-ATP7A


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/:16634399/:77166199)
- 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
BNC2

Q6ZN30

.
FUNCTION: Probable transcription factor specific for skin keratinocytes. May play a role in the differentiation of spermatozoa and oocytes (PubMed:14988505). May also play an important role in early urinary-tract development (PubMed:31051115). {ECO:0000269|PubMed:14988505, ECO:0000269|PubMed:31051115}.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 BNC2-ATP7A


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 BNC2-ATP7A


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 BNC2-ATP7A


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 BNC2-ATP7A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBNC2C0008925Cleft Palate1CTD_human
HgeneBNC2C0238506Congenital posterior urethral valves1GENOMICS_ENGLAND;ORPHANET
HgeneBNC2C0376634Craniofacial Abnormalities1CTD_human
HgeneBNC2C0919267ovarian neoplasm1CTD_human
HgeneBNC2C1140680Malignant neoplasm of ovary1CTD_human
HgeneBNC2C1837218Cleft palate, isolated1CTD_human
TgeneC0022716Menkes Kinky Hair Syndrome46CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0268353Cutis laxa, x-linked7CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC1845359Spinal Muscular Atrophy, Distal, X-Linked 33CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0003496Aortic Rupture2CTD_human
TgeneC0027854Neurologic Manifestations2CTD_human
TgeneC0235031Neurologic Symptoms2CTD_human
TgeneC0422837Neurological observations2CTD_human
TgeneC0521654Neurologic Deficits2CTD_human
TgeneC0741160Aortic Aneurysm, Ruptured2CTD_human
TgeneC0746857Focal Neurologic Deficits2CTD_human
TgeneC0751377Neurologic Dysfunction2CTD_human
TgeneC0751378Neurologic Signs2CTD_human
TgeneC0002871Anemia1CTD_human
TgeneC0004134Ataxia1CTD_human
TgeneC0007102Malignant tumor of colon1CTD_human
TgeneC0009375Colonic Neoplasms1CTD_human
TgeneC0010495Cutis Laxa1GENOMICS_ENGLAND
TgeneC0018273Growth Disorders1CTD_human
TgeneC0019054Hemolysis (disorder)1CTD_human
TgeneC0019189Hepatitis, Chronic1CTD_human
TgeneC0019207Hepatoma, Morris1CTD_human
TgeneC0019208Hepatoma, Novikoff1CTD_human
TgeneC0020542Pulmonary Hypertension1CTD_human
TgeneC0022333Jacksonian Seizure1CTD_human
TgeneC0023904Liver Neoplasms, Experimental1CTD_human
TgeneC0036572Seizures1CTD_human
TgeneC0040822Tremor1CTD_human
TgeneC0040827Saturnine Tremor1CTD_human
TgeneC0086404Experimental Hepatoma1CTD_human
TgeneC0149519Chronic Persistent Hepatitis1CTD_human
TgeneC0149840Senile Tremor1CTD_human
TgeneC0149958Complex partial seizures1CTD_human
TgeneC0234370Persistent Tremor1CTD_human
TgeneC0234371Continuous Tremor1CTD_human
TgeneC0234372Intermittent Tremor1CTD_human
TgeneC0234373Fine Tremor1CTD_human
TgeneC0234374Coarse Tremor1CTD_human
TgeneC0234375Massive Tremor1CTD_human
TgeneC0234376Action Tremor1CTD_human
TgeneC0234377Passive Tremor1CTD_human
TgeneC0234378Static Tremor1CTD_human
TgeneC0234379Resting Tremor1CTD_human
TgeneC0234381Darkness Tremor1CTD_human
TgeneC0234533Generalized seizures1CTD_human
TgeneC0234535Clonic Seizures1CTD_human
TgeneC0234544Todd Paralysis1CTD_human
TgeneC0235078Tremor, Perioral1CTD_human
TgeneC0235081Tremor, Limb1CTD_human
TgeneC0235082Tremor, Muscle1CTD_human
TgeneC0235083Nerve Tremors1CTD_human
TgeneC0235574Intravascular hemolysis1CTD_human
TgeneC0235843Tremor, Neonatal1CTD_human
TgeneC0240991Ataxia, Sensory1CTD_human
TgeneC0270824Visual seizure1CTD_human
TgeneC0270844Tonic Seizures1CTD_human
TgeneC0270846Epileptic drop attack1CTD_human
TgeneC0278161Ataxia, Motor1CTD_human
TgeneC0312854Extravascular Hemolysis1CTD_human
TgeneC0422850Seizures, Somatosensory1CTD_human
TgeneC0422852Seizures, Auditory1CTD_human
TgeneC0422853Olfactory seizure1CTD_human
TgeneC0422854Gustatory seizure1CTD_human
TgeneC0422855Vertiginous seizure1CTD_human
TgeneC0427190Ataxia, Truncal1CTD_human
TgeneC0494475Tonic - clonic seizures1CTD_human
TgeneC0520463Chronic active hepatitis1CTD_human
TgeneC0520966Abnormal coordination1CTD_human
TgeneC0522224Paralysed1CTD_human
TgeneC0524611Cryptogenic Chronic Hepatitis1CTD_human
TgeneC0598589Inherited neuropathies1GENOMICS_ENGLAND
TgeneC0750937Ataxia, Appendicular1CTD_human
TgeneC0750940Tremor, Rubral1CTD_human
TgeneC0751056Non-epileptic convulsion1CTD_human
TgeneC0751110Single Seizure1CTD_human
TgeneC0751123Atonic Absence Seizures1CTD_human
TgeneC0751494Convulsive Seizures1CTD_human
TgeneC0751495Seizures, Focal1CTD_human
TgeneC0751496Seizures, Sensory1CTD_human
TgeneC0751564Pill Rolling Tremor1CTD_human
TgeneC0751565Tremor, Semirhythmic1CTD_human
TgeneC1527384Involuntary Quiver1CTD_human
TgeneC2936380Neointima1CTD_human
TgeneC2936381Neointima Formation1CTD_human
TgeneC3495874Nonepileptic Seizures1CTD_human
TgeneC4048158Convulsions1CTD_human
TgeneC4316903Absence Seizures1CTD_human
TgeneC4317109Epileptic Seizures1CTD_human
TgeneC4317123Myoclonic Seizures1CTD_human
TgeneC4505436Generalized Absence Seizures1CTD_human