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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:BNIP3L-PMP22 (FusionGDB2 ID:HG665TG5376)

Fusion Gene Summary for BNIP3L-PMP22

check button Fusion gene summary
Fusion gene informationFusion gene name: BNIP3L-PMP22
Fusion gene ID: hg665tg5376
HgeneTgene
Gene symbol

BNIP3L

PMP22

Gene ID

665

5376

Gene nameBCL2 interacting protein 3 likeperipheral myelin protein 22
SynonymsBNIP3a|NIXCIDP|CMT1A|CMT1E|DSS|GAS-3|GAS3|HMSNIA|HNPP|Sp110
Cytomap('BNIP3L')('PMP22')

8p21.2

17p12

Type of geneprotein-codingprotein-coding
DescriptionBCL2/adenovirus E1B 19 kDa protein-interacting protein 3-likeBCL2/adenovirus E1B 19 kDa protein-interacting protein 3ABCL2/adenovirus E1B 19-kd protein-interacting protein 3aBCL2/adenovirus E1B 19kDa interacting protein 3 likeNIP-3-like protein XNIP3peripheral myelin protein 22Charcot-Marie-Tooth neuropathy 1A (greatly reduced nerve conduction velocity, hereditary motor sensory neuropathy Ia)growth arrest-specific protein 3peripheral myelin protein 22 kDa
Modification date2020031320200328
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000380629, ENST00000518611, 
ENST00000520409, ENST00000521254, 
ENST00000523515, 
Fusion gene scores* DoF score7 X 7 X 2=986 X 6 X 2=72
# samples 97
** MAII scorelog2(9/98*10)=-0.122856747785533
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/72*10)=-0.0406419844973459
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BNIP3L [Title/Abstract] AND PMP22 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBNIP3L(26268430)-PMP22(15134169), # 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
HgeneBNIP3L

GO:0043065

positive regulation of apoptotic process

9973195

HgeneBNIP3L

GO:0043066

negative regulation of apoptotic process

10381623

HgeneBNIP3L

GO:0051607

defense response to virus

9973195

TgenePMP22

GO:0008219

cell death

12107182

TgenePMP22

GO:0032060

bleb assembly

12107182



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


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Fusion Gene ORF analysis for BNIP3L-PMP22

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

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 BNIP3L-PMP22


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 BNIP3L-PMP22


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/:26268430/:15134169)
- 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
..
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: 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 BNIP3L-PMP22


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 BNIP3L-PMP22


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 BNIP3L-PMP22


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 BNIP3L-PMP22


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0011195Dejerine-Sottas Disease (disorder)18CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0270911Charcot-Marie-Tooth Disease, Type Ia (disorder)17CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0205713Roussy-Levy Syndrome (disorder)5CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC3495591Charcot-Marie-Tooth Disease, Demyelinating, Type 1e4CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0007959Charcot-Marie-Tooth Disease3CTD_human
TgeneC0270912Charcot-Marie-Tooth Disease, Type Ib3CTD_human
TgeneC0270914Hereditary Motor and Sensory-Neuropathy Type II3CTD_human
TgeneC0393814Hereditary liability to pressure palsies3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0751036Hereditary Motor and Sensory Neuropathy Type I3CTD_human
TgeneC4721453Peripheral Nervous System Diseases2CTD_human
TgeneC0008073Developmental Disabilities1CTD_human
TgeneC0011303Demyelinating Diseases1CTD_human
TgeneC0011304Demyelination1CTD_human
TgeneC0014550Myoclonic Epilepsy1CTD_human
TgeneC0016579Formication1CTD_human
TgeneC0019816Hereditary, Type VII, Motor and Sensory Neuropathy1CTD_human
TgeneC0023944Locked-In Syndrome1CTD_human
TgeneC0027888Hereditary Motor and Sensory Neuropathies1CTD_human
TgeneC0030554Paresthesia1CTD_human
TgeneC0034372Quadriplegia1CTD_human
TgeneC0034933Reflex, Abnormal1CTD_human
TgeneC0085996Child Development Deviations1CTD_human
TgeneC0085997Child Development Disorders, Specific1CTD_human
TgeneC0151572Reflex, Corneal, Decreased1CTD_human
TgeneC0151786Muscle Weakness1CTD_human
TgeneC0151888Hyporeflexia1CTD_human
TgeneC0151889Hyperreflexia1CTD_human
TgeneC0234146Absent reflex1CTD_human
TgeneC0234784Reflex, Gag, Absent1CTD_human
TgeneC0235044Paresthesia, Distal1CTD_human
TgeneC0241772Reflex, Deep Tendon, Absent1CTD_human
TgeneC0270790Quadriparesis1CTD_human
TgeneC0277839Hoffman's Reflex1CTD_human
TgeneC0277850Reflex, Pendular1CTD_human
TgeneC0278211Reflex, Corneal, Absent1CTD_human
TgeneC0338478Idiopathic Myoclonic Epilepsy1CTD_human
TgeneC0338479Symptomatic Myoclonic Epilepsy1CTD_human
TgeneC0392699Dysesthesia1CTD_human
TgeneC0393695Early Childhood Epilepsy, Myoclonic1CTD_human
TgeneC0393702Myoclonic Astatic Epilepsy1CTD_human
TgeneC0393703Myoclonic Absence Epilepsy1CTD_human
TgeneC0426970Spastic Quadriplegia1CTD_human
TgeneC0438414Myoclonic Encephalopathy1CTD_human
TgeneC0522345Reflex, Acoustic, Abnormal1CTD_human
TgeneC0558845Reflex, Ankle, Absent1CTD_human
TgeneC0558846Reflex, Triceps, Absent1CTD_human
TgeneC0558847Reflex, Biceps, Absent1CTD_human
TgeneC0576612Reflex, Anal, Absent1CTD_human
TgeneC0743002Abnormal Deep Tendon Reflex1CTD_human
TgeneC0751120Benign Infantile Myoclonic Epilepsy1CTD_human
TgeneC0751122Infantile Severe Myoclonic Epilepsy1CTD_human
TgeneC0751412Painful Paresthesias1CTD_human
TgeneC0751460Flaccid Quadriplegia1CTD_human
TgeneC0751461Paralysis, Spinal, Quadriplegic1CTD_human
TgeneC0751468Bulbocavernosus Reflex, Decreased1CTD_human
TgeneC0751469Bulbocavernousus Reflex Absent1CTD_human
TgeneC0751470Palmo-Mental Reflex1CTD_human
TgeneC0751471Reflex, Anal, Decreased1CTD_human
TgeneC0751472Reflex, Ankle, Abnormal1CTD_human
TgeneC0751473Reflex, Ankle, Decreased1CTD_human
TgeneC0751474Reflex, Biceps, Abnormal1CTD_human
TgeneC0751475Reflex, Biceps, Decreased1CTD_human
TgeneC0751476Reflex, Gag, Decreased1CTD_human
TgeneC0751477Reflex, Knee, Abnormal1CTD_human
TgeneC0751478Reflex, Knee, Decreased1CTD_human
TgeneC0751479Reflex, Moro, Asymmetric1CTD_human
TgeneC0751480Reflex, Triceps, Abnormal1CTD_human
TgeneC0751481Reflex, Triceps, Decreased1CTD_human
TgeneC0917800Epilepsy, Myoclonic, Infantile1CTD_human
TgeneC2350037Clinically Isolated Syndrome, CNS Demyelinating1CTD_human
TgeneC4551910Acute Inflammatory Demyelinating Polyneuropathy1CTD_human;ORPHANET