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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:10030)

Fusion Gene Summary for BNC2-ATP7A

check button Fusion gene summary
Fusion gene informationFusion gene name: BNC2-ATP7A
Fusion gene ID: 10030
HgeneTgene
Gene symbol

BNC2

ATP7A

Gene ID

54796

538

Gene namebasonuclin 2ATPase copper transporting alpha
SynonymsBSN2|LUTODSMAX|MK|MNK|SMAX3
Cytomap

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.

Q04656

Ensembl transtripts involved in fusion geneENST00000380672, ENST00000380667, 
ENST00000545497, ENST00000380666, 
ENST00000471301, 		ENST00000350425, 
ENST00000343533, ENST00000341514, 
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 buttonFusion gene breakpoints across BNC2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across ATP7A (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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-3CDSENST00000380672ENST00000350425BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380672ENST00000343533BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380672ENST00000341514BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380667ENST00000350425BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380667ENST00000343533BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380667ENST00000341514BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000545497ENST00000350425BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000545497ENST00000343533BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000545497ENST00000341514BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380666ENST00000350425BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380666ENST00000343533BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000380666ENST00000341514BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000471301ENST00000350425BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000471301ENST00000343533BNC2chr9

16634399

+ATP7AchrX

77166199

+
intron-3CDSENST00000471301ENST00000341514BNC2chr9

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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for BNC2-ATP7A


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.ATP7A

Q04656

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: ATP-driven copper (Cu(+)) ion pump that plays an important role in intracellular copper ion homeostasis (PubMed:10419525, PubMed:11092760, PubMed:28389643). Within a catalytic cycle, acquires Cu(+) ion from donor protein on the cytoplasmic side of the membrane and delivers it to acceptor protein on the lumenal side. The transfer of Cu(+) ion across the membrane is coupled to ATP hydrolysis and is associated with a transient phosphorylation that shifts the pump conformation from inward-facing to outward-facing state (PubMed:10419525, PubMed:19453293, PubMed:19917612, PubMed:31283225, PubMed:28389643). Under physiological conditions, at low cytosolic copper concentration, it is localized at the trans-Golgi network (TGN) where it transfers Cu(+) ions to cuproenzymes of the secretory pathway (PubMed:28389643, PubMed:11092760). Upon elevated cytosolic copper concentrations, it relocalizes to the plasma membrane where it is responsible for the export of excess Cu(+) ions (PubMed:10419525, PubMed:28389643). May play a dual role in neuron function and survival by regulating cooper efflux and neuronal transmission at the synapse as well as by supplying Cu(+) ions to enzymes such as PAM, TYR and SOD3 (PubMed:28389643) (By similarity). In the melanosomes of pigmented cells, provides copper cofactor to TYR to form an active TYR holoenzyme for melanin biosynthesis (By similarity). {ECO:0000250|UniProtKB:Q64430, ECO:0000269|PubMed:10419525, ECO:0000269|PubMed:11092760, ECO:0000269|PubMed:19453293, ECO:0000269|PubMed:19917612, ECO:0000269|PubMed:28389643, ECO:0000269|PubMed:31283225}.

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
TgeneATP7AC0022716Menkes Kinky Hair Syndrome46CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneATP7AC0268353Cutis laxa, x-linked7CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneATP7AC1845359Spinal Muscular Atrophy, Distal, X-Linked 33CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneATP7AC0003496Aortic Rupture2CTD_human
TgeneATP7AC0027854Neurologic Manifestations2CTD_human
TgeneATP7AC0235031Neurologic Symptoms2CTD_human
TgeneATP7AC0422837Neurological observations2CTD_human
TgeneATP7AC0521654Neurologic Deficits2CTD_human
TgeneATP7AC0741160Aortic Aneurysm, Ruptured2CTD_human
TgeneATP7AC0746857Focal Neurologic Deficits2CTD_human
TgeneATP7AC0751377Neurologic Dysfunction2CTD_human
TgeneATP7AC0751378Neurologic Signs2CTD_human
TgeneATP7AC0002871Anemia1CTD_human
TgeneATP7AC0004134Ataxia1CTD_human
TgeneATP7AC0007102Malignant tumor of colon1CTD_human
TgeneATP7AC0009375Colonic Neoplasms1CTD_human
TgeneATP7AC0010495Cutis Laxa1GENOMICS_ENGLAND
TgeneATP7AC0018273Growth Disorders1CTD_human
TgeneATP7AC0019054Hemolysis (disorder)1CTD_human
TgeneATP7AC0019189Hepatitis, Chronic1CTD_human
TgeneATP7AC0019207Hepatoma, Morris1CTD_human
TgeneATP7AC0019208Hepatoma, Novikoff1CTD_human
TgeneATP7AC0020542Pulmonary Hypertension1CTD_human
TgeneATP7AC0022333Jacksonian Seizure1CTD_human
TgeneATP7AC0023904Liver Neoplasms, Experimental1CTD_human
TgeneATP7AC0036572Seizures1CTD_human
TgeneATP7AC0040822Tremor1CTD_human
TgeneATP7AC0040827Saturnine Tremor1CTD_human
TgeneATP7AC0086404Experimental Hepatoma1CTD_human
TgeneATP7AC0149519Chronic Persistent Hepatitis1CTD_human
TgeneATP7AC0149840Senile Tremor1CTD_human
TgeneATP7AC0149958Complex partial seizures1CTD_human
TgeneATP7AC0234370Persistent Tremor1CTD_human
TgeneATP7AC0234371Continuous Tremor1CTD_human
TgeneATP7AC0234372Intermittent Tremor1CTD_human
TgeneATP7AC0234373Fine Tremor1CTD_human
TgeneATP7AC0234374Coarse Tremor1CTD_human
TgeneATP7AC0234375Massive Tremor1CTD_human
TgeneATP7AC0234376Action Tremor1CTD_human
TgeneATP7AC0234377Passive Tremor1CTD_human
TgeneATP7AC0234378Static Tremor1CTD_human
TgeneATP7AC0234379Resting Tremor1CTD_human
TgeneATP7AC0234381Darkness Tremor1CTD_human
TgeneATP7AC0234533Generalized seizures1CTD_human
TgeneATP7AC0234535Clonic Seizures1CTD_human
TgeneATP7AC0234544Todd Paralysis1CTD_human
TgeneATP7AC0235078Tremor, Perioral1CTD_human
TgeneATP7AC0235081Tremor, Limb1CTD_human
TgeneATP7AC0235082Tremor, Muscle1CTD_human
TgeneATP7AC0235083Nerve Tremors1CTD_human
TgeneATP7AC0235574Intravascular hemolysis1CTD_human
TgeneATP7AC0235843Tremor, Neonatal1CTD_human
TgeneATP7AC0240991Ataxia, Sensory1CTD_human
TgeneATP7AC0270824Visual seizure1CTD_human
TgeneATP7AC0270844Tonic Seizures1CTD_human
TgeneATP7AC0270846Epileptic drop attack1CTD_human
TgeneATP7AC0278161Ataxia, Motor1CTD_human
TgeneATP7AC0312854Extravascular Hemolysis1CTD_human
TgeneATP7AC0422850Seizures, Somatosensory1CTD_human
TgeneATP7AC0422852Seizures, Auditory1CTD_human
TgeneATP7AC0422853Olfactory seizure1CTD_human
TgeneATP7AC0422854Gustatory seizure1CTD_human
TgeneATP7AC0422855Vertiginous seizure1CTD_human
TgeneATP7AC0427190Ataxia, Truncal1CTD_human
TgeneATP7AC0494475Tonic - clonic seizures1CTD_human
TgeneATP7AC0520463Chronic active hepatitis1CTD_human
TgeneATP7AC0520966Abnormal coordination1CTD_human
TgeneATP7AC0522224Paralysed1CTD_human
TgeneATP7AC0524611Cryptogenic Chronic Hepatitis1CTD_human
TgeneATP7AC0598589Inherited neuropathies1GENOMICS_ENGLAND
TgeneATP7AC0750937Ataxia, Appendicular1CTD_human
TgeneATP7AC0750940Tremor, Rubral1CTD_human
TgeneATP7AC0751056Non-epileptic convulsion1CTD_human
TgeneATP7AC0751110Single Seizure1CTD_human
TgeneATP7AC0751123Atonic Absence Seizures1CTD_human
TgeneATP7AC0751494Convulsive Seizures1CTD_human
TgeneATP7AC0751495Seizures, Focal1CTD_human
TgeneATP7AC0751496Seizures, Sensory1CTD_human
TgeneATP7AC0751564Pill Rolling Tremor1CTD_human
TgeneATP7AC0751565Tremor, Semirhythmic1CTD_human
TgeneATP7AC1527384Involuntary Quiver1CTD_human
TgeneATP7AC2936380Neointima1CTD_human
TgeneATP7AC2936381Neointima Formation1CTD_human
TgeneATP7AC3495874Nonepileptic Seizures1CTD_human
TgeneATP7AC4048158Convulsions1CTD_human
TgeneATP7AC4316903Absence Seizures1CTD_human
TgeneATP7AC4317109Epileptic Seizures1CTD_human
TgeneATP7AC4317123Myoclonic Seizures1CTD_human
TgeneATP7AC4505436Generalized Absence Seizures1CTD_human