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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:FCHSD2-NBPF4 (FusionGDB2 ID:29923)

Fusion Gene Summary for FCHSD2-NBPF4

check button Fusion gene summary
Fusion gene informationFusion gene name: FCHSD2-NBPF4
Fusion gene ID: 29923
HgeneTgene
Gene symbol

FCHSD2

NBPF4

Gene ID

9873

148545

Gene nameFCH and double SH3 domains 2NBPF member 4
SynonymsNWK|NWK1|SH3MD3-
Cytomap

11q13.4

1p13.3

Type of geneprotein-codingprotein-coding
DescriptionF-BAR and double SH3 domains protein 2FCH and double SH3 domains protein 2SH3 multiple domains 3SH3 multiple domains protein 3caromnervous wreck homologprotein nervous wreck 1neuroblastoma breakpoint family member 4
Modification date2020031320200313
UniProtAcc

O94868

Q96M43

Ensembl transtripts involved in fusion geneENST00000311172, ENST00000409314, 
ENST00000409418, ENST00000458644, 
ENST00000409853, ENST00000409263, 
ENST00000415641, 
Fusion gene scores* DoF score43 X 26 X 16=178881 X 1 X 1=1
# samples 591
** MAII scorelog2(59/17888*10)=-4.92213332859399
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: FCHSD2 [Title/Abstract] AND NBPF4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFCHSD2(72851076)-NBPF4(108777033), # samples:2
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

check buttonFusion gene breakpoints across FCHSD2 (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 NBPF4 (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
ChimerDB4BRCATCGA-B6-A0I9-01AFCHSD2chr11

72851076

-NBPF4chr1

108777033

-
ChimerDB4BRCATCGA-B6-A0I9-01AFCHSD2chr11

72851076

-NBPF4chr1

108777033

-


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Fusion Gene ORF analysis for FCHSD2-NBPF4

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-3CDSENST00000311172ENST00000415641FCHSD2chr11

72851076

-NBPF4chr1

108777033

-
In-frameENST00000409314ENST00000415641FCHSD2chr11

72851076

-NBPF4chr1

108777033

-
In-frameENST00000409418ENST00000415641FCHSD2chr11

72851076

-NBPF4chr1

108777033

-
5UTR-3CDSENST00000458644ENST00000415641FCHSD2chr11

72851076

-NBPF4chr1

108777033

-
5UTR-3CDSENST00000409853ENST00000415641FCHSD2chr11

72851076

-NBPF4chr1

108777033

-
intron-3CDSENST00000409263ENST00000415641FCHSD2chr11

72851076

-NBPF4chr1

108777033

-

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)
ENST00000409314FCHSD2chr1172851076-ENST00000415641NBPF4chr1108777033-15412881691176335
ENST00000409418FCHSD2chr1172851076-ENST00000415641NBPF4chr1108777033-17565033841391335

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
ENST00000409314ENST00000415641FCHSD2chr1172851076-NBPF4chr1108777033-0.0101538730.9898461
ENST00000409418ENST00000415641FCHSD2chr1172851076-NBPF4chr1108777033-0.0117226930.98827726

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Fusion Genomic Features for FCHSD2-NBPF4


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 FCHSD2-NBPF4


check button Go to

FGviewer for the breakpoints of chr11:72851076-chr1:108777033

.
- 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
FCHSD2

O94868

NBPF4

Q96M43

FUNCTION: Adapter protein that plays a role in endocytosis via clathrin-coated pits. Contributes to the internalization of cell surface receptors, such as integrin ITGB1 and transferrin receptor (PubMed:29887380). Promotes endocytosis of EGFR in cancer cells, and thereby contributes to the down-regulation of EGFR signaling (PubMed:30249660). Recruited to clathrin-coated pits during a mid-to-late stage of assembly, where it is required for normal progress from U-shaped intermediate stage pits to terminal, omega-shaped pits (PubMed:29887380). Binds to membranes enriched in phosphatidylinositol 3,4-bisphosphate or phosphatidylinositol 3,4,5-trisphosphate (PubMed:29887380). When bound to membranes, promotes actin polymerization via its interaction with WAS and/or WASL which leads to the activation of the Arp2/3 complex. Does not promote actin polymerisation in the absence of membranes (PubMed:29887380). {ECO:0000269|PubMed:29887380, ECO:0000269|PubMed:30249660}.

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
TgeneNBPF4chr11:72851076chr1:108777033ENST00000415641815400_503342.6666666666667639.0DomainOlduvai 3

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000311172-119356_3970685.0Coiled coilOntology_term=ECO:0000255
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000409418-220356_39739.666666666666664741.0Coiled coilOntology_term=ECO:0000255
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000409853-116356_3970516.0Coiled coilOntology_term=ECO:0000255
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000311172-119718_7210685.0Compositional biasNote=Poly-Pro
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000409418-220718_72139.666666666666664741.0Compositional biasNote=Poly-Pro
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000409853-116718_7210516.0Compositional biasNote=Poly-Pro
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000311172-119469_5300685.0DomainSH3 1
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000311172-1198_2820685.0DomainF-BAR
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000409418-220469_53039.666666666666664741.0DomainSH3 1
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000409418-2208_28239.666666666666664741.0DomainF-BAR
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000409853-116469_5300516.0DomainSH3 1
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000409853-1168_2820516.0DomainF-BAR
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000311172-119567_6290685.0RegionRequired and sufficient for location at clathrin-coated pits
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000409418-220567_62939.666666666666664741.0RegionRequired and sufficient for location at clathrin-coated pits
HgeneFCHSD2chr11:72851076chr1:108777033ENST00000409853-116567_6290516.0RegionRequired and sufficient for location at clathrin-coated pits
TgeneNBPF4chr11:72851076chr1:108777033ENST0000041564181510_43342.6666666666667639.0Coiled coilOntology_term=ECO:0000255
TgeneNBPF4chr11:72851076chr1:108777033ENST0000041564181569_115342.6666666666667639.0Coiled coilOntology_term=ECO:0000255
TgeneNBPF4chr11:72851076chr1:108777033ENST00000415641815174_261342.6666666666667639.0DomainOlduvai 1
TgeneNBPF4chr11:72851076chr1:108777033ENST00000415641815326_399342.6666666666667639.0DomainOlduvai 2


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Fusion Gene Sequence for FCHSD2-NBPF4


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.
>In-frame_ENST00000409314_ENST00000415641_TCGA-B6-A0I9-01A_FCHSD2_chr11_72851076_-_NBPF4_chr1_108777033_length(transcript)=1541nt_BP=288nt
GTCCGCCTGCCGCCCGCTGGCCTGCTCCCTCCGGGGCAAGTCTTGCTTCTTAAGCGCTCCTTTCACACACGCGCGCGCTCGCTGGGCCGT
CCCCTCCTCTCCGGCCCTCCTCCTCCTCCTGGTCCTTGCTAACGCTGCCGTCGGGGAGGATTGATGTCCCTTCAGCATCATGCAGCCGCC
GCCGAGGAAGGTGAAAGTTACACAAGAACTGAAAAACATTCAAGTTGAGCAGATGACAAAACTTCAAGCCAAACATCAAGCAGAATGTGA
TTTGCTTGAAGATATGAGGCTCAGCAGGGGACCGCTGAGAGTGGACAAGCATGAAATCCCCCAGGAGTCACTGGATGGATGTTGCTTGAC
TCCTTCCATCCTTCCTGACCTGACTCCCTCCTACCACCCTTATTGGAGCACTTTGTACTCTTTTGAAGACAAGCAAGTCAGCTTGGCTCT
TGTAGACAAAATTAAAAAGGATCAAGAGGAGATAGAAGACCAAAGCCCACCATGCCCCAGGCTCAGCCAGGAGCTGCCAGAGGTGAAGGA
GCAGGAAGTCCCAGAGGACTCTGTGAATGAAGTTTACTTGACTCCCTCAGTTCACCATGACGTGTCTGACTGCCACCAGCCTTATAGCAG
CACCTTGTCCTCATTGGAGGATCAGCTTGCCTGCTCTGCTCTGGATGTAGCCTCCCCCACCGAGGCGGCCTGTCCCCAAGGGACTTGGAG
TGGAGACTTGAGCCACCACCAGTCAGAGGTGCAAGTTTCACAGGCACAGCTGGAACCAAGCACCCTGGTGCCCAGTTGTCTGCGACTACA
GCTGGATCAAGGGTTCCACTGTGGGAACGGCTTGGCCCAGCGGGGCCTTTCCTCCACCACCTGCAGCTTCTCAGCCAATGCTGATTCTGG
GAACCAATGGCCCTTCCAAGAGCTGGTTTTAGAGCCCTCTCTGGGGATGAAGAACCCTCCCCAGCTGGAAGATGATGCACTTGAAGGCTC
AGCAAGCAACACACAAGGGCGTCAAGTCACTGGCCGGATTCGTGCCTCCCTTGTCCTGATACTGAAGACCATCAGAAGAAGACTCCCGTT
CAGCAAGTGGAGACTGGCATTCAGATTCGCTGGCCCGCATGCTGAGAGCGCAGAGATACCAAATACTGCTGGAAGGACGCAAAGGATGGC
AGGATGAAAGAATGTCACAAAAAGCAGCTTTTCCACTTGATAAAAACAACTAAAACAGCAAAGCAAGTTTAAGTCCAAACACAATACTGC
AGGGGTCCTTCACTGAGGATTGAATTTCAGACACAGAATACTCTTGATGACTTCAAGCCACTATGCTCCTTTGATTTGAGAAGCCACATT
CCATCCCCCTCCAATTGTGATCAATACCTAGGGAGACCAATGCCCAGATGGACAAATAGCATTGACCGGCGTTAGCCCTGTTTCTCAATT
CCCATCGTGTAGAGAACAGGAGTCCGCAGCTGCTGGCAGGAGACAGCATGTCAGCCGGGACTCTGCCAGGGCAGAGTATGAGCAATGCCA

>In-frame_ENST00000409314_ENST00000415641_TCGA-B6-A0I9-01A_FCHSD2_chr11_72851076_-_NBPF4_chr1_108777033_length(amino acids)=335AA_start in transcript=169_stop in transcript=1176
MQPPPRKVKVTQELKNIQVEQMTKLQAKHQAECDLLEDMRLSRGPLRVDKHEIPQESLDGCCLTPSILPDLTPSYHPYWSTLYSFEDKQV
SLALVDKIKKDQEEIEDQSPPCPRLSQELPEVKEQEVPEDSVNEVYLTPSVHHDVSDCHQPYSSTLSSLEDQLACSALDVASPTEAACPQ
GTWSGDLSHHQSEVQVSQAQLEPSTLVPSCLRLQLDQGFHCGNGLAQRGLSSTTCSFSANADSGNQWPFQELVLEPSLGMKNPPQLEDDA

--------------------------------------------------------------
>In-frame_ENST00000409418_ENST00000415641_TCGA-B6-A0I9-01A_FCHSD2_chr11_72851076_-_NBPF4_chr1_108777033_length(transcript)=1756nt_BP=503nt
GGCGGCGCAGGCGGCCGACCGGGAGCGCGGACAACGCGGCTGCGGCTAACCCGCCGCCCGGCCGGCTGAGACCCTCGCGCCCCTGCTCCT
GGGGCCCCCGCCCCCTCGCCGTCTCCGCCTCCTTCCTCACACACCCCCGGGCCGCCCGGGCCGCCCGGGCCCCAAGCCTTCCCGGTGCTC
CTCCCTCGTCTCCTCACACTCGCTCTCTGGCTGGGGTCCGCCTGCCGCCCGCTGGCCTGCTCCCTCCGGGGCAAGTCTTGCTTCTTAAGC
GCTCCTTTCACACACGCGCGCGCTCGCTGGGCCGTCCCCTCCTCTCCGGCCCTCCTCCTCCTCCTGGTCCTTGCTAACGCTGCCGTCGGG
GAGGATTGATGTCCCTTCAGCATCATGCAGCCGCCGCCGAGGAAGGTGAAAGTTACACAAGAACTGAAAAACATTCAAGTTGAGCAGATG
ACAAAACTTCAAGCCAAACATCAAGCAGAATGTGATTTGCTTGAAGATATGAGGCTCAGCAGGGGACCGCTGAGAGTGGACAAGCATGAA
ATCCCCCAGGAGTCACTGGATGGATGTTGCTTGACTCCTTCCATCCTTCCTGACCTGACTCCCTCCTACCACCCTTATTGGAGCACTTTG
TACTCTTTTGAAGACAAGCAAGTCAGCTTGGCTCTTGTAGACAAAATTAAAAAGGATCAAGAGGAGATAGAAGACCAAAGCCCACCATGC
CCCAGGCTCAGCCAGGAGCTGCCAGAGGTGAAGGAGCAGGAAGTCCCAGAGGACTCTGTGAATGAAGTTTACTTGACTCCCTCAGTTCAC
CATGACGTGTCTGACTGCCACCAGCCTTATAGCAGCACCTTGTCCTCATTGGAGGATCAGCTTGCCTGCTCTGCTCTGGATGTAGCCTCC
CCCACCGAGGCGGCCTGTCCCCAAGGGACTTGGAGTGGAGACTTGAGCCACCACCAGTCAGAGGTGCAAGTTTCACAGGCACAGCTGGAA
CCAAGCACCCTGGTGCCCAGTTGTCTGCGACTACAGCTGGATCAAGGGTTCCACTGTGGGAACGGCTTGGCCCAGCGGGGCCTTTCCTCC
ACCACCTGCAGCTTCTCAGCCAATGCTGATTCTGGGAACCAATGGCCCTTCCAAGAGCTGGTTTTAGAGCCCTCTCTGGGGATGAAGAAC
CCTCCCCAGCTGGAAGATGATGCACTTGAAGGCTCAGCAAGCAACACACAAGGGCGTCAAGTCACTGGCCGGATTCGTGCCTCCCTTGTC
CTGATACTGAAGACCATCAGAAGAAGACTCCCGTTCAGCAAGTGGAGACTGGCATTCAGATTCGCTGGCCCGCATGCTGAGAGCGCAGAG
ATACCAAATACTGCTGGAAGGACGCAAAGGATGGCAGGATGAAAGAATGTCACAAAAAGCAGCTTTTCCACTTGATAAAAACAACTAAAA
CAGCAAAGCAAGTTTAAGTCCAAACACAATACTGCAGGGGTCCTTCACTGAGGATTGAATTTCAGACACAGAATACTCTTGATGACTTCA
AGCCACTATGCTCCTTTGATTTGAGAAGCCACATTCCATCCCCCTCCAATTGTGATCAATACCTAGGGAGACCAATGCCCAGATGGACAA
ATAGCATTGACCGGCGTTAGCCCTGTTTCTCAATTCCCATCGTGTAGAGAACAGGAGTCCGCAGCTGCTGGCAGGAGACAGCATGTCAGC

>In-frame_ENST00000409418_ENST00000415641_TCGA-B6-A0I9-01A_FCHSD2_chr11_72851076_-_NBPF4_chr1_108777033_length(amino acids)=335AA_start in transcript=384_stop in transcript=1391
MQPPPRKVKVTQELKNIQVEQMTKLQAKHQAECDLLEDMRLSRGPLRVDKHEIPQESLDGCCLTPSILPDLTPSYHPYWSTLYSFEDKQV
SLALVDKIKKDQEEIEDQSPPCPRLSQELPEVKEQEVPEDSVNEVYLTPSVHHDVSDCHQPYSSTLSSLEDQLACSALDVASPTEAACPQ
GTWSGDLSHHQSEVQVSQAQLEPSTLVPSCLRLQLDQGFHCGNGLAQRGLSSTTCSFSANADSGNQWPFQELVLEPSLGMKNPPQLEDDA

--------------------------------------------------------------

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Fusion Gene PPI Analysis for FCHSD2-NBPF4


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 FCHSD2-NBPF4


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 FCHSD2-NBPF4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneFCHSD2C0087031Juvenile-Onset Still Disease1CTD_human
HgeneFCHSD2C3495559Juvenile arthritis1CTD_human
HgeneFCHSD2C3714758Juvenile psoriatic arthritis1CTD_human
HgeneFCHSD2C4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
HgeneFCHSD2C4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human