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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:NTRK2-LAP3 (FusionGDB2 ID:60328)

Fusion Gene Summary for NTRK2-LAP3

check button Fusion gene summary
Fusion gene informationFusion gene name: NTRK2-LAP3
Fusion gene ID: 60328
HgeneTgene
Gene symbol

NTRK2

LAP3

Gene ID

4915

51056

Gene nameneurotrophic receptor tyrosine kinase 2leucine aminopeptidase 3
SynonymsEIEE58|GP145-TrkB|OBHD|TRKB|trk-BHEL-S-106|LAP|LAPEP|PEPS
Cytomap

9q21.33

4p15.32

Type of geneprotein-codingprotein-coding
DescriptionBDNF/NT-3 growth factors receptorBDNF-tropomyosine receptor kinase Bneurotrophic tyrosine kinase receptor type 2tropomyosin-related kinase Btyrosine kinase receptor Bcytosol aminopeptidaseLAP-3epididymis secretory protein Li 106leucyl aminopeptidasepeptidase Sproline aminopeptidaseprolyl aminopeptidase
Modification date2020031320200313
UniProtAcc.

P28838

Ensembl transtripts involved in fusion geneENST00000376214, ENST00000376213, 
ENST00000395882, ENST00000304053, 
ENST00000376208, ENST00000277120, 
ENST00000323115, ENST00000359847, 
ENST00000395866, 		ENST00000226299, 
ENST00000606142, ENST00000503467, 
Fusion gene scores* DoF score8 X 8 X 5=3208 X 7 X 7=392
# samples 88
** MAII scorelog2(8/320*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/392*10)=-2.29278174922785
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NTRK2 [Title/Abstract] AND LAP3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNTRK2(87430621)-LAP3(17585225), # samples:1
Anticipated loss of major functional domain due to fusion event.NTRK2-LAP3 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
NTRK2-LAP3 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
NTRK2-LAP3 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
NTRK2-LAP3 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

check buttonFusion gene breakpoints across NTRK2 (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 LAP3 (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
ChimerDB4LGGTCGA-DB-5278-01ANTRK2chr9

87430621

-LAP3chr4

17585225

+


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Fusion Gene ORF analysis for NTRK2-LAP3

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-3CDSENST00000376214ENST00000226299NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-3CDSENST00000376214ENST00000606142NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-intronENST00000376214ENST00000503467NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-3CDSENST00000376213ENST00000226299NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-3CDSENST00000376213ENST00000606142NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-intronENST00000376213ENST00000503467NTRK2chr9

87430621

-LAP3chr4

17585225

+
Frame-shiftENST00000395882ENST00000226299NTRK2chr9

87430621

-LAP3chr4

17585225

+
Frame-shiftENST00000395882ENST00000606142NTRK2chr9

87430621

-LAP3chr4

17585225

+
5CDS-intronENST00000395882ENST00000503467NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-3CDSENST00000304053ENST00000226299NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-3CDSENST00000304053ENST00000606142NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-intronENST00000304053ENST00000503467NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-3CDSENST00000376208ENST00000226299NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-3CDSENST00000376208ENST00000606142NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-intronENST00000376208ENST00000503467NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-3CDSENST00000277120ENST00000226299NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-3CDSENST00000277120ENST00000606142NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-intronENST00000277120ENST00000503467NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-3CDSENST00000323115ENST00000226299NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-3CDSENST00000323115ENST00000606142NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-intronENST00000323115ENST00000503467NTRK2chr9

87430621

-LAP3chr4

17585225

+
Frame-shiftENST00000359847ENST00000226299NTRK2chr9

87430621

-LAP3chr4

17585225

+
Frame-shiftENST00000359847ENST00000606142NTRK2chr9

87430621

-LAP3chr4

17585225

+
5CDS-intronENST00000359847ENST00000503467NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-3CDSENST00000395866ENST00000226299NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-3CDSENST00000395866ENST00000606142NTRK2chr9

87430621

-LAP3chr4

17585225

+
intron-intronENST00000395866ENST00000503467NTRK2chr9

87430621

-LAP3chr4

17585225

+

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 NTRK2-LAP3


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 NTRK2-LAP3


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
.LAP3

P28838

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: Cytolosic metallopeptidase that catalyzes the removal of unsubstituted N-terminal hydrophobic amino acids from various peptides. The presence of Zn(2+) ions is essential for the peptidase activity, and the association with other cofactors can modulate the substrate spectificity of the enzyme. For instance, in the presence of Mn(2+), it displays a specific Cys-Gly hydrolyzing activity of Cys-Gly-S-conjugates. Involved in the metabolism of glutathione and in the degradation of glutathione S-conjugates, which may play a role in the control of the cell redox status. {ECO:0000250|UniProtKB:P00727}.

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 NTRK2-LAP3


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 NTRK2-LAP3


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 NTRK2-LAP3


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 NTRK2-LAP3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneNTRK2C0011570Mental Depression5PSYGENET
HgeneNTRK2C0011581Depressive disorder5PSYGENET
HgeneNTRK2C0041696Unipolar Depression5PSYGENET
HgeneNTRK2C0525045Mood Disorders5PSYGENET
HgeneNTRK2C1269683Major Depressive Disorder5PSYGENET
HgeneNTRK2C3151303Obesity, Hyperphagia, and Developmental Delay4CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneNTRK2C0005586Bipolar Disorder3CTD_human;PSYGENET
HgeneNTRK2C4693367EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 583GENOMICS_ENGLAND;UNIPROT
HgeneNTRK2C0009171Cocaine Abuse2CTD_human
HgeneNTRK2C0036341Schizophrenia2PSYGENET
HgeneNTRK2C0038220Status Epilepticus2CTD_human
HgeneNTRK2C0236736Cocaine-Related Disorders2CTD_human
HgeneNTRK2C0270823Petit mal status2CTD_human
HgeneNTRK2C0311335Grand Mal Status Epilepticus2CTD_human
HgeneNTRK2C0393734Complex Partial Status Epilepticus2CTD_human
HgeneNTRK2C0600427Cocaine Dependence2CTD_human
HgeneNTRK2C0751217Hyperkinesia, Generalized2CTD_human
HgeneNTRK2C0751522Status Epilepticus, Subclinical2CTD_human
HgeneNTRK2C0751523Non-Convulsive Status Epilepticus2CTD_human
HgeneNTRK2C0751524Simple Partial Status Epilepticus2CTD_human
HgeneNTRK2C3887506Hyperkinesia2CTD_human
HgeneNTRK2C0001973Alcoholic Intoxication, Chronic1PSYGENET
HgeneNTRK2C0004114Astrocytoma1CTD_human
HgeneNTRK2C0004352Autistic Disorder1CTD_human
HgeneNTRK2C0005587Depression, Bipolar1CTD_human
HgeneNTRK2C0008073Developmental Disabilities1CTD_human
HgeneNTRK2C0013415Dysthymic Disorder1PSYGENET
HgeneNTRK2C0017638Glioma1CTD_human
HgeneNTRK2C0020505Hyperphagia1CTD_human
HgeneNTRK2C0024713Manic Disorder1CTD_human
HgeneNTRK2C0027819Neuroblastoma1CTD_human
HgeneNTRK2C0028754Obesity1CTD_human
HgeneNTRK2C0036349Paranoid Schizophrenia1PSYGENET
HgeneNTRK2C0037769West Syndrome1ORPHANET
HgeneNTRK2C0085996Child Development Deviations1CTD_human
HgeneNTRK2C0085997Child Development Disorders, Specific1CTD_human
HgeneNTRK2C0205768Subependymal Giant Cell Astrocytoma1CTD_human
HgeneNTRK2C0259783mixed gliomas1CTD_human
HgeneNTRK2C0280783Juvenile Pilocytic Astrocytoma1CTD_human
HgeneNTRK2C0280785Diffuse Astrocytoma1CTD_human
HgeneNTRK2C0334579Anaplastic astrocytoma1CTD_human
HgeneNTRK2C0334580Protoplasmic astrocytoma1CTD_human
HgeneNTRK2C0334581Gemistocytic astrocytoma1CTD_human
HgeneNTRK2C0334582Fibrillary Astrocytoma1CTD_human
HgeneNTRK2C0334583Pilocytic Astrocytoma1CTD_human
HgeneNTRK2C0338070Childhood Cerebral Astrocytoma1CTD_human
HgeneNTRK2C0338831Manic1CTD_human
HgeneNTRK2C0547065Mixed oligoastrocytoma1CTD_human
HgeneNTRK2C0555198Malignant Glioma1CTD_human
HgeneNTRK2C0678807prenatal alcohol exposure1PSYGENET
HgeneNTRK2C0750935Cerebral Astrocytoma1CTD_human
HgeneNTRK2C0750936Intracranial Astrocytoma1CTD_human
HgeneNTRK2C0752347Lewy Body Disease1CTD_human
HgeneNTRK2C1519086Pilomyxoid astrocytoma1ORPHANET
HgeneNTRK2C1704230Grade I Astrocytoma1CTD_human
HgeneNTRK2C3146244Alcohol Related Birth Defect1PSYGENET
TgeneLAP3C0019193Hepatitis, Toxic1CTD_human
TgeneLAP3C0860207Drug-Induced Liver Disease1CTD_human
TgeneLAP3C1262760Hepatitis, Drug-Induced1CTD_human
TgeneLAP3C3658290Drug-Induced Acute Liver Injury1CTD_human
TgeneLAP3C4277682Chemical and Drug Induced Liver Injury1CTD_human
TgeneLAP3C4279912Chemically-Induced Liver Toxicity1CTD_human