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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:NMNAT3-RBP1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NMNAT3-RBP1
FusionPDB ID: 59447
FusionGDB2.0 ID: 59447
HgeneTgene
Gene symbol

NMNAT3

RBP1

Gene ID

349565

5947

Gene namenicotinamide nucleotide adenylyltransferase 3retinol binding protein 1
SynonymsFKSG76|PNAT-3|PNAT3CRABP-I|CRBP|CRBP1|CRBPI|RBPC
Cytomap

3q23

3q23

Type of geneprotein-codingprotein-coding
Descriptionnicotinamide/nicotinic acid mononucleotide adenylyltransferase 3NMN adenylyltransferase 3NMN/NaMN adenylyltransferase 3NaMN adenylyltransferase 3nicotinamide mononucleotide adenylyltransferase 3nicotinate-nucleotide adenylyltransferase 3pyridine nucretinol-binding protein 1CRBP-Icellular retinol binding protein 1cellular retinol-binding protein Iretinol-binding protein 1, cellular
Modification date2020031320200313
UniProtAcc

Q96T66

.
Ensembl transtripts involved in fusion geneENST idsENST00000296202, ENST00000413939, 
ENST00000512391, ENST00000514703, 
ENST00000406164, ENST00000406824, 
ENST00000339837, ENST00000507242, 
ENST00000511444, 		ENST00000483943, 
ENST00000492918, ENST00000232219, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 3 X 3=364 X 3 X 3=36
# samples 56
** MAII scorelog2(5/36*10)=0.473931188332412
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(6/36*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: NMNAT3 [Title/Abstract] AND RBP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NMNAT3(139346457)-RBP1(139237364), # samples:1
NMNAT3(139346458)-RBP1(139237364), # samples:1
RBP1(139237263)-NMNAT3(139297897), # samples:2
Anticipated loss of major functional domain due to fusion event.NMNAT3-RBP1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
NMNAT3-RBP1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
NMNAT3-RBP1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
NMNAT3-RBP1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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 NMNAT3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across RBP1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4OVTCGA-24-2261-01ANMNAT3chr3

139346458

-RBP1chr3

139237364

-
ChimerDB4OVTCGA-24-2261NMNAT3chr3

139346457

-RBP1chr3

139237364

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000413939NMNAT3chr3139346457-ENST00000232219RBP1chr3139237364-85951076949790
ENST00000296202NMNAT3chr3139346457-ENST00000232219RBP1chr3139237364-84049175047890
ENST00000512391NMNAT3chr3139346457-ENST00000232219RBP1chr3139237364-89955080953790
ENST00000514703NMNAT3chr3139346457-ENST00000232219RBP1chr3139237364-61226352225090
ENST00000413939NMNAT3chr3139346458-ENST00000232219RBP1chr3139237364-85951076949790
ENST00000296202NMNAT3chr3139346458-ENST00000232219RBP1chr3139237364-84049175047890
ENST00000512391NMNAT3chr3139346458-ENST00000232219RBP1chr3139237364-89955080953790
ENST00000514703NMNAT3chr3139346458-ENST00000232219RBP1chr3139237364-61226352225090

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
ENST00000413939ENST00000232219NMNAT3chr3139346457-RBP1chr3139237364-0.627431150.37256888
ENST00000296202ENST00000232219NMNAT3chr3139346457-RBP1chr3139237364-0.693627660.30637234
ENST00000512391ENST00000232219NMNAT3chr3139346457-RBP1chr3139237364-0.51647110.4835289
ENST00000514703ENST00000232219NMNAT3chr3139346457-RBP1chr3139237364-0.52085660.47914344
ENST00000413939ENST00000232219NMNAT3chr3139346458-RBP1chr3139237364-0.627431150.37256888
ENST00000296202ENST00000232219NMNAT3chr3139346458-RBP1chr3139237364-0.693627660.30637234
ENST00000512391ENST00000232219NMNAT3chr3139346458-RBP1chr3139237364-0.51647110.4835289
ENST00000514703ENST00000232219NMNAT3chr3139346458-RBP1chr3139237364-0.52085660.47914344

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>59447_59447_1_NMNAT3-RBP1_NMNAT3_chr3_139346457_ENST00000296202_RBP1_chr3_139237364_ENST00000232219_length(amino acids)=90AA_BP=0
MPGGGWTFLPHAVQRGGSWPTHPADSLGQGCLPGPHCTFLNTCLQTTPSTLISRCSSSPSIHWVQPRPSFSPFCTHWSLSPSQLTVVCLV

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

>59447_59447_2_NMNAT3-RBP1_NMNAT3_chr3_139346457_ENST00000413939_RBP1_chr3_139237364_ENST00000232219_length(amino acids)=90AA_BP=0
MPGGGWTFLPHAVQRGGSWPTHPADSLGQGCLPGPHCTFLNTCLQTTPSTLISRCSSSPSIHWVQPRPSFSPFCTHWSLSPSQLTVVCLV

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

>59447_59447_3_NMNAT3-RBP1_NMNAT3_chr3_139346457_ENST00000512391_RBP1_chr3_139237364_ENST00000232219_length(amino acids)=90AA_BP=0
MPGGGWTFLPHAVQRGGSWPTHPADSLGQGCLPGPHCTFLNTCLQTTPSTLISRCSSSPSIHWVQPRPSFSPFCTHWSLSPSQLTVVCLV

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

>59447_59447_4_NMNAT3-RBP1_NMNAT3_chr3_139346457_ENST00000514703_RBP1_chr3_139237364_ENST00000232219_length(amino acids)=90AA_BP=0
MPGGGWTFLPHAVQRGGSWPTHPADSLGQGCLPGPHCTFLNTCLQTTPSTLISRCSSSPSIHWVQPRPSFSPFCTHWSLSPSQLTVVCLV

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

>59447_59447_5_NMNAT3-RBP1_NMNAT3_chr3_139346458_ENST00000296202_RBP1_chr3_139237364_ENST00000232219_length(amino acids)=90AA_BP=0
MPGGGWTFLPHAVQRGGSWPTHPADSLGQGCLPGPHCTFLNTCLQTTPSTLISRCSSSPSIHWVQPRPSFSPFCTHWSLSPSQLTVVCLV

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

>59447_59447_6_NMNAT3-RBP1_NMNAT3_chr3_139346458_ENST00000413939_RBP1_chr3_139237364_ENST00000232219_length(amino acids)=90AA_BP=0
MPGGGWTFLPHAVQRGGSWPTHPADSLGQGCLPGPHCTFLNTCLQTTPSTLISRCSSSPSIHWVQPRPSFSPFCTHWSLSPSQLTVVCLV

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

>59447_59447_7_NMNAT3-RBP1_NMNAT3_chr3_139346458_ENST00000512391_RBP1_chr3_139237364_ENST00000232219_length(amino acids)=90AA_BP=0
MPGGGWTFLPHAVQRGGSWPTHPADSLGQGCLPGPHCTFLNTCLQTTPSTLISRCSSSPSIHWVQPRPSFSPFCTHWSLSPSQLTVVCLV

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

>59447_59447_8_NMNAT3-RBP1_NMNAT3_chr3_139346458_ENST00000514703_RBP1_chr3_139237364_ENST00000232219_length(amino acids)=90AA_BP=0
MPGGGWTFLPHAVQRGGSWPTHPADSLGQGCLPGPHCTFLNTCLQTTPSTLISRCSSSPSIHWVQPRPSFSPFCTHWSLSPSQLTVVCLV

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

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Fusion Protein Functional Features


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/chr3:139346457/chr3:139237364)
- 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
NMNAT3

Q96T66

.
FUNCTION: Catalyzes the formation of NAD(+) from nicotinamide mononucleotide (NMN) and ATP. Can also use the deamidated form; nicotinic acid mononucleotide (NaMN) as substrate with the same efficiency. Can use triazofurin monophosphate (TrMP) as substrate. Can also use GTP and ITP as nucleotide donors. Also catalyzes the reverse reaction, i.e. the pyrophosphorolytic cleavage of NAD(+). For the pyrophosphorolytic activity, can use NAD(+), NADH, NaAD, nicotinic acid adenine dinucleotide phosphate (NHD), nicotinamide guanine dinucleotide (NGD) as substrates. Fails to cleave phosphorylated dinucleotides NADP(+), NADPH and NaADP(+). Protects against axonal degeneration following injury. {ECO:0000269|PubMed:16118205, ECO:0000269|PubMed:17402747}.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.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000296202-3613_1536.333333333333336253.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000413939-3413_1536.333333333333336164.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000296202-3613_1536.333333333333336253.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000413939-3413_1536.333333333333336164.0Nucleotide bindingATP

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000296202-36135_13736.333333333333336253.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000296202-36203_20636.333333333333336253.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000339837-15135_1370216.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000339837-1513_150216.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000339837-15203_2060216.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000406164-36135_1370216.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000406164-3613_150216.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000406164-36203_2060216.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000413939-34135_13736.333333333333336164.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000413939-34203_20636.333333333333336164.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000296202-36135_13736.333333333333336253.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000296202-36203_20636.333333333333336253.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000339837-15135_1370216.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000339837-1513_150216.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000339837-15203_2060216.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000406164-36135_1370216.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000406164-3613_150216.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000406164-36203_2060216.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000413939-34135_13736.333333333333336164.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000413939-34203_20636.333333333333336164.0Nucleotide bindingATP
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000296202-36147_14836.333333333333336253.0RegionSubstrate binding
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000296202-3653_5536.333333333333336253.0RegionSubstrate binding
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000296202-3690_9336.333333333333336253.0RegionSubstrate binding
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000339837-15147_1480216.0RegionSubstrate binding
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000339837-1553_550216.0RegionSubstrate binding
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000339837-1590_930216.0RegionSubstrate binding
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000406164-36147_1480216.0RegionSubstrate binding
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000406164-3653_550216.0RegionSubstrate binding
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000406164-3690_930216.0RegionSubstrate binding
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000413939-34147_14836.333333333333336164.0RegionSubstrate binding
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000413939-3453_5536.333333333333336164.0RegionSubstrate binding
HgeneNMNAT3chr3:139346457chr3:139237364ENST00000413939-3490_9336.333333333333336164.0RegionSubstrate binding
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000296202-36147_14836.333333333333336253.0RegionSubstrate binding
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000296202-3653_5536.333333333333336253.0RegionSubstrate binding
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000296202-3690_9336.333333333333336253.0RegionSubstrate binding
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000339837-15147_1480216.0RegionSubstrate binding
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000339837-1553_550216.0RegionSubstrate binding
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000339837-1590_930216.0RegionSubstrate binding
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000406164-36147_1480216.0RegionSubstrate binding
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000406164-3653_550216.0RegionSubstrate binding
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000406164-3690_930216.0RegionSubstrate binding
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000413939-34147_14836.333333333333336164.0RegionSubstrate binding
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000413939-3453_5536.333333333333336164.0RegionSubstrate binding
HgeneNMNAT3chr3:139346458chr3:139237364ENST00000413939-3490_9336.333333333333336164.0RegionSubstrate binding


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
NMNAT3
RBP1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to NMNAT3-RBP1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to NMNAT3-RBP1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource