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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:FRMD3-NTRK2 (FusionGDB2 ID:31213)

Fusion Gene Summary for FRMD3-NTRK2

check button Fusion gene summary
Fusion gene informationFusion gene name: FRMD3-NTRK2
Fusion gene ID: 31213
HgeneTgene
Gene symbol

FRMD3

NTRK2

Gene ID

257019

4915

Gene nameFERM domain containing 3neurotrophic receptor tyrosine kinase 2
Synonyms4.1O|EPB41L4O|EPB41LO|P410EIEE58|GP145-TrkB|OBHD|TRKB|trk-B
Cytomap

9q21.32

9q21.33

Type of geneprotein-codingprotein-coding
DescriptionFERM domain-containing protein 3band 4.1-like protein 4band 4.1-like protein 4Oovary type protein 4.1protein 4.1OBDNF/NT-3 growth factors receptorBDNF-tropomyosine receptor kinase Bneurotrophic tyrosine kinase receptor type 2tropomyosin-related kinase Btyrosine kinase receptor B
Modification date2020031320200313
UniProtAcc

A2A2Y4

Q16620

Ensembl transtripts involved in fusion geneENST00000376438, ENST00000304195, 
ENST00000328788, ENST00000376434, 
ENST00000465485, 		ENST00000376214, 
ENST00000376213, ENST00000395882, 
ENST00000304053, ENST00000376208, 
ENST00000277120, ENST00000323115, 
ENST00000359847, ENST00000395866, 
Fusion gene scores* DoF score5 X 5 X 5=12510 X 9 X 7=630
# samples 510
** MAII scorelog2(5/125*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/630*10)=-2.65535182861255
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FRMD3 [Title/Abstract] AND NTRK2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFRMD3(86152999)-NTRK2(87482157), # samples:1
Anticipated loss of major functional domain due to fusion event.FRMD3-NTRK2 seems lost the major protein functional domain in Tgene partner, which is a kinase due to the frame-shifted ORF.
FRMD3-NTRK2 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 FRMD3 (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 NTRK2 (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
ChimerDB4THCATCGA-ET-A39TFRMD3chr9

86152999

-NTRK2chr9

87482157

+


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Fusion Gene ORF analysis for FRMD3-NTRK2

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
Frame-shiftENST00000376438ENST00000376214FRMD3chr9

86152999

-NTRK2chr9

87482157

+
Frame-shiftENST00000376438ENST00000376213FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000376438ENST00000395882FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000376438ENST00000304053FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000376438ENST00000376208FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000376438ENST00000277120FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000376438ENST00000323115FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000376438ENST00000359847FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000376438ENST00000395866FRMD3chr9

86152999

-NTRK2chr9

87482157

+
Frame-shiftENST00000304195ENST00000376214FRMD3chr9

86152999

-NTRK2chr9

87482157

+
Frame-shiftENST00000304195ENST00000376213FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000304195ENST00000395882FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000304195ENST00000304053FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000304195ENST00000376208FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000304195ENST00000277120FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000304195ENST00000323115FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000304195ENST00000359847FRMD3chr9

86152999

-NTRK2chr9

87482157

+
5CDS-intronENST00000304195ENST00000395866FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-3CDSENST00000328788ENST00000376214FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-3CDSENST00000328788ENST00000376213FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000328788ENST00000395882FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000328788ENST00000304053FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000328788ENST00000376208FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000328788ENST00000277120FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000328788ENST00000323115FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000328788ENST00000359847FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000328788ENST00000395866FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-3CDSENST00000376434ENST00000376214FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-3CDSENST00000376434ENST00000376213FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000376434ENST00000395882FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000376434ENST00000304053FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000376434ENST00000376208FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000376434ENST00000277120FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000376434ENST00000323115FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000376434ENST00000359847FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000376434ENST00000395866FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-3CDSENST00000465485ENST00000376214FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-3CDSENST00000465485ENST00000376213FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000465485ENST00000395882FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000465485ENST00000304053FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000465485ENST00000376208FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000465485ENST00000277120FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000465485ENST00000323115FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000465485ENST00000359847FRMD3chr9

86152999

-NTRK2chr9

87482157

+
intron-intronENST00000465485ENST00000395866FRMD3chr9

86152999

-NTRK2chr9

87482157

+

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 FRMD3-NTRK2


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)
FRMD3chr986152999-NTRK2chr987482157+2.52E-060.9999975
FRMD3chr986152999-NTRK2chr987482157+2.52E-060.9999975

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 FRMD3-NTRK2


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
FRMD3

A2A2Y4

NTRK2

Q16620

FUNCTION: Putative tumor suppressor gene that may be implicated in the origin and progression of lung cancer. {ECO:0000269|PubMed:17260017}.FUNCTION: Receptor tyrosine kinase involved in the development and the maturation of the central and the peripheral nervous systems through regulation of neuron survival, proliferation, migration, differentiation, and synapse formation and plasticity (By similarity). Receptor for BDNF/brain-derived neurotrophic factor and NTF4/neurotrophin-4. Alternatively can also bind NTF3/neurotrophin-3 which is less efficient in activating the receptor but regulates neuron survival through NTRK2 (PubMed:7574684, PubMed:15494731). Upon ligand-binding, undergoes homodimerization, autophosphorylation and activation (PubMed:15494731). Recruits, phosphorylates and/or activates several downstream effectors including SHC1, FRS2, SH2B1, SH2B2 and PLCG1 that regulate distinct overlapping signaling cascades. Through SHC1, FRS2, SH2B1, SH2B2 activates the GRB2-Ras-MAPK cascade that regulates for instance neuronal differentiation including neurite outgrowth. Through the same effectors controls the Ras-PI3 kinase-AKT1 signaling cascade that mainly regulates growth and survival. Through PLCG1 and the downstream protein kinase C-regulated pathways controls synaptic plasticity. Thereby, plays a role in learning and memory by regulating both short term synaptic function and long-term potentiation. PLCG1 also leads to NF-Kappa-B activation and the transcription of genes involved in cell survival. Hence, it is able to suppress anoikis, the apoptosis resulting from loss of cell-matrix interactions. May also play a role in neutrophin-dependent calcium signaling in glial cells and mediate communication between neurons and glia. {ECO:0000250|UniProtKB:P15209, ECO:0000269|PubMed:15494731, ECO:0000269|PubMed:7574684}.

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 FRMD3-NTRK2


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 FRMD3-NTRK2


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 FRMD3-NTRK2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneNTRK2Q16620DB00321AmitriptylineAgonistSmall moleculeApproved
TgeneNTRK2Q16620DB00321AmitriptylineAgonistSmall moleculeApproved
TgeneNTRK2Q16620DB11823EsketamineSmall moleculeApproved|Investigational
TgeneNTRK2Q16620DB11823EsketamineSmall moleculeApproved|Investigational
TgeneNTRK2Q16620DB11986EntrectinibInhibitorSmall moleculeApproved|Investigational
TgeneNTRK2Q16620DB11986EntrectinibInhibitorSmall moleculeApproved|Investigational
TgeneNTRK2Q16620DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgeneNTRK2Q16620DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgeneNTRK2Q16620DB14723LarotrectinibInhibitorSmall moleculeApproved|Investigational
TgeneNTRK2Q16620DB14723LarotrectinibInhibitorSmall moleculeApproved|Investigational

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Related Diseases for FRMD3-NTRK2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneFRMD3C0263454Chloracne1CTD_human
TgeneNTRK2C0011570Mental Depression5PSYGENET
TgeneNTRK2C0011581Depressive disorder5PSYGENET
TgeneNTRK2C0041696Unipolar Depression5PSYGENET
TgeneNTRK2C0525045Mood Disorders5PSYGENET
TgeneNTRK2C1269683Major Depressive Disorder5PSYGENET
TgeneNTRK2C3151303Obesity, Hyperphagia, and Developmental Delay4CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneNTRK2C0005586Bipolar Disorder3CTD_human;PSYGENET
TgeneNTRK2C4693367EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 583GENOMICS_ENGLAND;UNIPROT
TgeneNTRK2C0009171Cocaine Abuse2CTD_human
TgeneNTRK2C0036341Schizophrenia2PSYGENET
TgeneNTRK2C0038220Status Epilepticus2CTD_human
TgeneNTRK2C0236736Cocaine-Related Disorders2CTD_human
TgeneNTRK2C0270823Petit mal status2CTD_human
TgeneNTRK2C0311335Grand Mal Status Epilepticus2CTD_human
TgeneNTRK2C0393734Complex Partial Status Epilepticus2CTD_human
TgeneNTRK2C0600427Cocaine Dependence2CTD_human
TgeneNTRK2C0751217Hyperkinesia, Generalized2CTD_human
TgeneNTRK2C0751522Status Epilepticus, Subclinical2CTD_human
TgeneNTRK2C0751523Non-Convulsive Status Epilepticus2CTD_human
TgeneNTRK2C0751524Simple Partial Status Epilepticus2CTD_human
TgeneNTRK2C3887506Hyperkinesia2CTD_human
TgeneNTRK2C0001973Alcoholic Intoxication, Chronic1PSYGENET
TgeneNTRK2C0004114Astrocytoma1CTD_human
TgeneNTRK2C0004352Autistic Disorder1CTD_human
TgeneNTRK2C0005587Depression, Bipolar1CTD_human
TgeneNTRK2C0008073Developmental Disabilities1CTD_human
TgeneNTRK2C0013415Dysthymic Disorder1PSYGENET
TgeneNTRK2C0017638Glioma1CTD_human
TgeneNTRK2C0020505Hyperphagia1CTD_human
TgeneNTRK2C0024713Manic Disorder1CTD_human
TgeneNTRK2C0027819Neuroblastoma1CTD_human
TgeneNTRK2C0028754Obesity1CTD_human
TgeneNTRK2C0036349Paranoid Schizophrenia1PSYGENET
TgeneNTRK2C0037769West Syndrome1ORPHANET
TgeneNTRK2C0085996Child Development Deviations1CTD_human
TgeneNTRK2C0085997Child Development Disorders, Specific1CTD_human
TgeneNTRK2C0205768Subependymal Giant Cell Astrocytoma1CTD_human
TgeneNTRK2C0259783mixed gliomas1CTD_human
TgeneNTRK2C0280783Juvenile Pilocytic Astrocytoma1CTD_human
TgeneNTRK2C0280785Diffuse Astrocytoma1CTD_human
TgeneNTRK2C0334579Anaplastic astrocytoma1CTD_human
TgeneNTRK2C0334580Protoplasmic astrocytoma1CTD_human
TgeneNTRK2C0334581Gemistocytic astrocytoma1CTD_human
TgeneNTRK2C0334582Fibrillary Astrocytoma1CTD_human
TgeneNTRK2C0334583Pilocytic Astrocytoma1CTD_human
TgeneNTRK2C0338070Childhood Cerebral Astrocytoma1CTD_human
TgeneNTRK2C0338831Manic1CTD_human
TgeneNTRK2C0547065Mixed oligoastrocytoma1CTD_human
TgeneNTRK2C0555198Malignant Glioma1CTD_human
TgeneNTRK2C0678807prenatal alcohol exposure1PSYGENET
TgeneNTRK2C0750935Cerebral Astrocytoma1CTD_human
TgeneNTRK2C0750936Intracranial Astrocytoma1CTD_human
TgeneNTRK2C0752347Lewy Body Disease1CTD_human
TgeneNTRK2C1519086Pilomyxoid astrocytoma1ORPHANET
TgeneNTRK2C1704230Grade I Astrocytoma1CTD_human
TgeneNTRK2C3146244Alcohol Related Birth Defect1PSYGENET