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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:BRAF-NUDT9

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: BRAF-NUDT9
FusionPDB ID: 10129
FusionGDB2.0 ID: 10129
HgeneTgene
Gene symbol

BRAF

NUDT9

Gene ID

673

53343

Gene nameB-Raf proto-oncogene, serine/threonine kinasenudix hydrolase 9
SynonymsB-RAF1|B-raf|BRAF1|NS7|RAFB1NUDT10
Cytomap

7q34

4q22.1

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase B-raf94 kDa B-raf proteinB-Raf proto-oncogene serine/threonine-protein kinase (p94)B-Raf serine/threonine-proteinmurine sarcoma viral (v-raf) oncogene homolog B1proto-oncogene B-Rafv-raf murine sarcoma viral oncogene ADP-ribose pyrophosphatase, mitochondrialADP-ribose diphosphataseADP-ribose phosphohydrolaseADP-ribose pyrosphosphatase NUDT9ADPR-PPaseadenosine diphosphoribose pyrophosphatasenucleoside diphosphate linked moiety X-type motif 9nudix (nucleoside dip
Modification date2020032920200313
UniProtAcc

P15056

.
Ensembl transtripts involved in fusion geneENST idsENST00000288602, ENST00000515371, 
ENST00000302174, ENST00000473942, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score28 X 21 X 11=64682 X 3 X 1=6
# samples 323
** MAII scorelog2(32/6468*10)=-4.3371758685863
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/6*10)=2.32192809488736
Context (manual curation of fusion genes in FusionPDB)

PubMed: BRAF [Title/Abstract] AND NUDT9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)BRAF(140624366)-NUDT9(88372741), # samples:1
Anticipated loss of major functional domain due to fusion event.BRAF-NUDT9 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.
BRAF-NUDT9 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.
BRAF-NUDT9 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.
BRAF-NUDT9 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
HgeneBRAF

GO:0000186

activation of MAPKK activity

29433126

HgeneBRAF

GO:0006468

protein phosphorylation

17563371

HgeneBRAF

GO:0010828

positive regulation of glucose transmembrane transport

23010278

HgeneBRAF

GO:0033138

positive regulation of peptidyl-serine phosphorylation

19667065

HgeneBRAF

GO:0043066

negative regulation of apoptotic process

19667065

HgeneBRAF

GO:0070374

positive regulation of ERK1 and ERK2 cascade

22065586

HgeneBRAF

GO:0071277

cellular response to calcium ion

18567582

HgeneBRAF

GO:0090150

establishment of protein localization to membrane

23010278


check buttonFusion gene breakpoints across BRAF (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 NUDT9 (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
ChimerDB4STADTCGA-BR-8366-01ABRAFchr7

140624366

-NUDT9chr4

88372741

+


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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)
ENST00000288602BRAFchr7140624366-ENST00000302174NUDT9chr488372741+93419961609182
ENST00000288602BRAFchr7140624366-ENST00000473942NUDT9chr488372741+204319961609182

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
ENST00000288602ENST00000302174BRAFchr7140624366-NUDT9chr488372741+0.0007581660.9992418
ENST00000288602ENST00000473942BRAFchr7140624366-NUDT9chr488372741+0.000386820.9996132

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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

>10129_10129_1_BRAF-NUDT9_BRAF_chr7_140624366_ENST00000288602_NUDT9_chr4_88372741_ENST00000302174_length(amino acids)=182AA_BP=46
MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEGMVDPGEKISATLKREFGEEALNSLQKTSAEKREIEEKLHKLFS
QDHLVIYKGYVDDPRNTDNAWMETEAVNYHDETGEIMDNLMLEAGDDAGKVKWVDINDKLKLYASHSQFIKLVAEKRDAHWSEDSEADCH

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

>10129_10129_2_BRAF-NUDT9_BRAF_chr7_140624366_ENST00000288602_NUDT9_chr4_88372741_ENST00000473942_length(amino acids)=182AA_BP=46
MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEGMVDPGEKISATLKREFGEEALNSLQKTSAEKREIEEKLHKLFS
QDHLVIYKGYVDDPRNTDNAWMETEAVNYHDETGEIMDNLMLEAGDDAGKVKWVDINDKLKLYASHSQFIKLVAEKRDAHWSEDSEADCH

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

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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/chr7:140624366/chr4:88372741)
- 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
BRAF

P15056

.
FUNCTION: Protein kinase involved in the transduction of mitogenic signals from the cell membrane to the nucleus (Probable). Phosphorylates MAP2K1, and thereby activates the MAP kinase signal transduction pathway (PubMed:21441910, PubMed:29433126). May play a role in the postsynaptic responses of hippocampal neurons (PubMed:1508179). {ECO:0000269|PubMed:1508179, ECO:0000269|PubMed:21441910, ECO:0000269|PubMed:29433126, ECO:0000305}.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
HgeneBRAFchr7:140624366chr4:88372741ENST00000288602-1186_1146.0767.0Compositional biasNote=Poly-Gly
TgeneNUDT9chr7:140624366chr4:88372741ENST0000047394248178_334164.0301.0DomainNudix hydrolase
TgeneNUDT9chr7:140624366chr4:88372741ENST0000030217448215_237214.0351.0MotifNote=Nudix box
TgeneNUDT9chr7:140624366chr4:88372741ENST0000047394248215_237164.0301.0MotifNote=Nudix box

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneBRAFchr7:140624366chr4:88372741ENST00000288602-118122_12946.0767.0Compositional biasNote=Poly-Ser
HgeneBRAFchr7:140624366chr4:88372741ENST00000288602-118428_43246.0767.0Compositional biasNote=Poly-Ser
HgeneBRAFchr7:140624366chr4:88372741ENST00000288602-118155_22746.0767.0DomainRBD
HgeneBRAFchr7:140624366chr4:88372741ENST00000288602-118457_71746.0767.0DomainProtein kinase
HgeneBRAFchr7:140624366chr4:88372741ENST00000288602-118463_47146.0767.0Nucleotide bindingATP
HgeneBRAFchr7:140624366chr4:88372741ENST00000288602-118234_28046.0767.0Zinc fingerPhorbol-ester/DAG-type
TgeneNUDT9chr7:140624366chr4:88372741ENST0000030217448178_334214.0351.0DomainNudix hydrolase


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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
BRAFYWHAB, YWHAG, YWHAQ, YWHAZ, SFN, HRAS, AKT1, MAPK3, RAP1GAP, RAF1, MRAS, RAP1A, PAK2, TERF1, CCDC88A, NEDD4L, Nedd4, MAP2K1, RNF149, KSR1, BRAP, PRKCE, RPS6KB2, HSP90AA1, BRAF, YWHAE, HSPA5, MAP2K2, HSPA1A, HSPA8, YWHAH, HSPA9, ARAF, CDC37, HSP90AB1, PHKB, LIMK1, IQGAP1, MAPK1, BAD, LIPF, MUS81, Vps4b, FBXW7, FGFR2, BRCA2, VHL, FNTA, HDAC2, PIK3CA, EGFR, PTEN, FNIP1, FNIP2, RAB3GAP1, KRAS, KIAA0141, FKBPL, ARMCX3, KCNC4, RPTOR, CYLD, NRAS, HSPA4, DNAJB6, PDCD11, PIP5K1A, DNAJC15, VANGL1, DNAJC11, FKBP5, HSPA4L, HSP90B1, GNAI2, DNAJC13, GNAS, PPP2CB, HSD11B2, DNAJB11, PLD2, RAP1B, WDR6, CPNE3, MYOF, COPA, UBLCP1, PPP1CA, RAD50, PIP4K2C, PHB, VIM, PGAM1, DNAJA1, MAP2K7, SPRY2, ALDOA, AP2B1, ATP5A1, SSB, IGF1R, JUP, PPP6C, PARP1, HSPB1, NME2, PRDX2, CCT7, RAB1A, FARSA, FASN, EPRS, TRAF2, REST, KIAA1429, NANOG, ITCH, SMURF2, WWP1, WWP2, PPP2CA, PPP2R2A, AURKA, LATS2, MAP2K3, MAP2K6, RASSF1, STK11, TERT, PEBP1, CRBN, FAR1, PSMC4, UBA52, UBB, UBC, RPS27A, HSPA6, HSP90AB3P, DSP, ATAD3A, ATAD3B, P4HB, SDF2L1, SLC25A22, SPTBN4, TMEM33, CTSB, NCL, HPX, TXNDC12, SLC25A11, NDUFA4, CTSV, FBP1, HSD17B3, ZNF189, ZNF510, KIF14, SRC, TRAP1, JTB, S100P, USP28,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
BRAFall structure
NUDT9


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 BRAF-NUDT9


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 BRAF-NUDT9


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
HgeneBRAFC0025202melanoma24CGI;CTD_human;UNIPROT
HgeneBRAFC1275081Cardio-facio-cutaneous syndrome14CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneBRAFC0009402Colorectal Carcinoma8CTD_human;UNIPROT
HgeneBRAFC0028326Noonan Syndrome8CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneBRAFC0238463Papillary thyroid carcinoma8CTD_human;ORPHANET
HgeneBRAFC0040136Thyroid Neoplasm6CGI;CTD_human
HgeneBRAFC0151468Thyroid Gland Follicular Adenoma6CTD_human
HgeneBRAFC0175704LEOPARD Syndrome6CLINGEN;GENOMICS_ENGLAND
HgeneBRAFC0549473Thyroid carcinoma6CGI;CTD_human
HgeneBRAFC3150970NOONAN SYNDROME 75CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneBRAFC0009404Colorectal Neoplasms4CTD_human
HgeneBRAFC3150971LEOPARD SYNDROME 34CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneBRAFC1519086Pilomyxoid astrocytoma3ORPHANET
HgeneBRAFC0004565Melanoma, B162CTD_human
HgeneBRAFC0009075Melanoma, Cloudman S912CTD_human
HgeneBRAFC0018598Melanoma, Harding-Passey2CTD_human
HgeneBRAFC0023443Hairy Cell Leukemia2CGI;ORPHANET
HgeneBRAFC0025205Melanoma, Experimental2CTD_human
HgeneBRAFC0033578Prostatic Neoplasms2CTD_human
HgeneBRAFC0152013Adenocarcinoma of lung (disorder)2CGI;CTD_human
HgeneBRAFC0376358Malignant neoplasm of prostate2CTD_human
HgeneBRAFC0587248Costello syndrome (disorder)2CLINGEN;CTD_human
HgeneBRAFC3501843Nonmedullary Thyroid Carcinoma2CTD_human
HgeneBRAFC3501844Familial Nonmedullary Thyroid Cancer2CTD_human
HgeneBRAFC0002448Ameloblastoma1CTD_human
HgeneBRAFC0004114Astrocytoma1CTD_human
HgeneBRAFC0010276Craniopharyngioma1CTD_human;ORPHANET
HgeneBRAFC0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
HgeneBRAFC0017638Glioma1CGI;CTD_human
HgeneBRAFC0019621Histiocytosis, Langerhans-Cell1CGI;ORPHANET
HgeneBRAFC0022665Kidney Neoplasm1CTD_human
HgeneBRAFC0023903Liver neoplasms1CTD_human
HgeneBRAFC0024232Lymphatic Metastasis1CTD_human
HgeneBRAFC0024694Mandibular Neoplasms1CTD_human
HgeneBRAFC0027659Neoplasms, Experimental1CTD_human
HgeneBRAFC0027962Melanocytic nevus1GENOMICS_ENGLAND
HgeneBRAFC0036920Sezary Syndrome1CTD_human
HgeneBRAFC0041409Turner Syndrome, Male1CTD_human
HgeneBRAFC0079773Lymphoma, T-Cell, Cutaneous1CTD_human
HgeneBRAFC0205768Subependymal Giant Cell Astrocytoma1CTD_human
HgeneBRAFC0206686Adrenocortical carcinoma1CTD_human
HgeneBRAFC0206754Neuroendocrine Tumors1CTD_human
HgeneBRAFC0259783mixed gliomas1CTD_human
HgeneBRAFC0278875Adult Craniopharyngioma1CTD_human
HgeneBRAFC0280783Juvenile Pilocytic Astrocytoma1CTD_human
HgeneBRAFC0280785Diffuse Astrocytoma1CTD_human
HgeneBRAFC0334579Anaplastic astrocytoma1CGI;CTD_human
HgeneBRAFC0334580Protoplasmic astrocytoma1CTD_human
HgeneBRAFC0334581Gemistocytic astrocytoma1CTD_human
HgeneBRAFC0334582Fibrillary Astrocytoma1CTD_human
HgeneBRAFC0334583Pilocytic Astrocytoma1CGI;CTD_human
HgeneBRAFC0338070Childhood Cerebral Astrocytoma1CTD_human
HgeneBRAFC0345904Malignant neoplasm of liver1CTD_human
HgeneBRAFC0376407Granulomatous Slack Skin1CTD_human
HgeneBRAFC0406803Syringocystadenoma Papilliferum1GENOMICS_ENGLAND
HgeneBRAFC0431128Papillary craniopharyngioma1CTD_human
HgeneBRAFC0431129Adamantinous Craniopharyngioma1CTD_human
HgeneBRAFC0547065Mixed oligoastrocytoma1CTD_human
HgeneBRAFC0555198Malignant Glioma1CTD_human
HgeneBRAFC0596263Carcinogenesis1CTD_human
HgeneBRAFC0684249Carcinoma of lung1CGI;UNIPROT
HgeneBRAFC0740457Malignant neoplasm of kidney1CTD_human
HgeneBRAFC0750935Cerebral Astrocytoma1CTD_human
HgeneBRAFC0750936Intracranial Astrocytoma1CTD_human
HgeneBRAFC0751061Craniopharyngioma, Child1CTD_human
HgeneBRAFC0920269Microsatellite Instability1CTD_human
HgeneBRAFC1527404Female Pseudo-Turner Syndrome1CTD_human
HgeneBRAFC1704230Grade I Astrocytoma1CTD_human
HgeneBRAFC1721098Replication Error Phenotype1CTD_human
HgeneBRAFC2239176Liver carcinoma1CTD_human
HgeneBRAFC4551484Leopard Syndrome 11GENOMICS_ENGLAND
HgeneBRAFC4551602Noonan Syndrome 11CTD_human
HgeneBRAFC4721532Lymphoma, Non-Hodgkin, Familial1UNIPROT
HgeneBRAFC4733333familial non-medullary thyroid cancer1GENOMICS_ENGLAND