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Center for Computational Systems Medicine level3
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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 Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Potential Active Site Information

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Potentially Interacting Small Molecules through Virtual Screening

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Biochemical Features of Small Molecules with ADME

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Drug Toxicity Information

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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:SND1-BRAF

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SND1-BRAF
FusionPDB ID: 84466
FusionGDB2.0 ID: 84466
HgeneTgene
Gene symbol

SND1

BRAF

Gene ID

27044

673

Gene namestaphylococcal nuclease and tudor domain containing 1B-Raf proto-oncogene, serine/threonine kinase
SynonymsTDRD11|Tudor-SN|p100B-RAF1|B-raf|BRAF1|NS7|RAFB1
Cytomap

7q32.1

7q34

Type of geneprotein-codingprotein-coding
Descriptionstaphylococcal nuclease domain-containing protein 1EBNA2 coactivator p100testis tissue sperm-binding protein Li 82Ptudor domain-containing protein 11serine/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
Modification date2020031320200329
UniProtAcc

Q7KZF4

P15056

Ensembl transtripts involved in fusion geneENST idsENST00000467238, ENST00000354725, 
ENST00000288602, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score17 X 19 X 10=323048 X 58 X 16=44544
# samples 2169
** MAII scorelog2(21/3230*10)=-3.94307293191516
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(69/44544*10)=-6.0124909441832
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: SND1 [Title/Abstract] AND BRAF [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)BRAF(140487348)-SND1(127724776), # samples:3
SND1(127361454)-BRAF(140487384), # samples:5
Anticipated loss of major functional domain due to fusion event.BRAF-SND1 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-SND1 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.
SND1-BRAF 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.
SND1-BRAF 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.
SND1-BRAF 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.
SND1-BRAF 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
HgeneSND1

GO:0010587

miRNA catabolic process

28546213

TgeneBRAF

GO:0000186

activation of MAPKK activity

29433126

TgeneBRAF

GO:0006468

protein phosphorylation

17563371

TgeneBRAF

GO:0010828

positive regulation of glucose transmembrane transport

23010278

TgeneBRAF

GO:0033138

positive regulation of peptidyl-serine phosphorylation

19667065

TgeneBRAF

GO:0043066

negative regulation of apoptotic process

19667065

TgeneBRAF

GO:0070374

positive regulation of ERK1 and ERK2 cascade

22065586

TgeneBRAF

GO:0071277

cellular response to calcium ion

18567582

TgeneBRAF

GO:0090150

establishment of protein localization to membrane

23010278


check buttonFusion gene breakpoints across SND1 (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 BRAF (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
ChimerDB4THCATCGA-DJ-A3UZ-01ASND1chr7

127361454

-BRAFchr7

140487384

-
ChimerDB4THCATCGA-DJ-A3UZ-01ASND1chr7

127361454

+BRAFchr7

140487384

-
ChimerDB4THCATCGA-EL-A3ZK-01ASND1chr7

127721553

-BRAFchr7

140482957

-
ChimerDB4THCATCGA-EL-A3ZK-01ASND1chr7

127721553

+BRAFchr7

140482957

-
ChimerDB4THCATCGA-FY-A40N-01ASND1chr7

127361454

-BRAFchr7

140487384

-
ChimerDB4THCATCGA-FY-A40N-01ASND1chr7

127361454

+BRAFchr7

140487384

-
ChimerKB3..SND1chr7

127361454

+BRAFchr7

140487384

-
ChimerKB3..SND1chr7

127631110

+BRAFchr7

140433809

-
ChimerKB3..SND1chr7

127721553

+BRAFchr7

140482957

-
ChiTaRS5.0N/AJX013981SND1chr7

127631110

+BRAFchr7

140487386

-


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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)
ENST00000354725SND1chr7127361454+ENST00000288602BRAFchr7140487384-262513461402506788
ENST00000354725SND1chr7127721553+ENST00000288602BRAFchr7140482957-3546230414034271095
ENST00000354725SND1chr7127361454+ENST00000288602BRAFchr7140487384-262513461402506788
ENST00000354725SND1chr7127721553+ENST00000288602BRAFchr7140482957-3546230414034271095
ENST00000354725SND1chr7127631110+ENST00000288602BRAFchr7140487386-325219731403133997

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
ENST00000354725ENST00000288602SND1chr7127361454+BRAFchr7140487384-0.0051007860.9948992
ENST00000354725ENST00000288602SND1chr7127721553+BRAFchr7140482957-0.0013746380.9986254
ENST00000354725ENST00000288602SND1chr7127631110+BRAFchr7140487386-0.0016971320.9983028

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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

>84466_84466_1_SND1-BRAF_SND1_chr7_127361454_ENST00000354725_BRAF_chr7_140487384_ENST00000288602_length(amino acids)=788AA_BP=402
MTPPVRPAAPLVAFASPHMASSAQSGGSSGGPAVPTVQRGIIKMVLSGCAIIVRGQPRGGPPPERQINLSNIRAGNLARRAAATQPDAKD
TPDEPWAFPAREFLRKKLIGKEVCFTIENKTPQGREYGMIYLGKDTNGENIAESLVAEGLATRREGMRANNPEQNRLSECEEQAKAAKKG
MWSEGNGSHTIRDLKYTIENPRHFVDSHHQKPVNAIIEHVRDGSVVRALLLPDYYLVTVMLSGIKCPTFRREADGSETPEPFAAEAKFFT
ESRLLQRDVQIILESCHNQNILGTILHPNGNITELLLKEGFARCVDWSIAVYTRGAEKLRAAERFAKERRLRIWRDYVAPTANLDQKDKQ
FVAKVMQVLNADAIVVKLNSGDYKTIHLSSIRPPRLEGENTQDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSPGPQRERKS
SSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMG
YSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSH
QFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLK

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

>84466_84466_2_SND1-BRAF_SND1_chr7_127631110_ENST00000354725_BRAF_chr7_140487386_ENST00000288602_length(amino acids)=997AA_BP=611
MTPPVRPAAPLVAFASPHMASSAQSGGSSGGPAVPTVQRGIIKMVLSGCAIIVRGQPRGGPPPERQINLSNIRAGNLARRAAATQPDAKD
TPDEPWAFPAREFLRKKLIGKEVCFTIENKTPQGREYGMIYLGKDTNGENIAESLVAEGLATRREGMRANNPEQNRLSECEEQAKAAKKG
MWSEGNGSHTIRDLKYTIENPRHFVDSHHQKPVNAIIEHVRDGSVVRALLLPDYYLVTVMLSGIKCPTFRREADGSETPEPFAAEAKFFT
ESRLLQRDVQIILESCHNQNILGTILHPNGNITELLLKEGFARCVDWSIAVYTRGAEKLRAAERFAKERRLRIWRDYVAPTANLDQKDKQ
FVAKVMQVLNADAIVVKLNSGDYKTIHLSSIRPPRLEGENTQDKNKKLRPLYDIPYMFEAREFLRKKLIGKKVNVTVDYIRPASPATETV
PAFSERTCATVTIGGINIAEALVSKGLATVIRYRQDDDQRSSHYDELLAAEARAIKNGKGLHSKKEVPIHRVADISGDTQKAKQFLPFLQ
RAGRSEAVVEYVFSGSRLKLYLPKETCLITFLLAGIECPRGARNLPGLVQEGEPFSEEATLFTKELVLQREDLIRDQGFRGDGGSTTGLS
ATPPASLPGSLTNVKALQKSPGPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTA
PTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKS
NNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMV
GRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGG

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

>84466_84466_3_SND1-BRAF_SND1_chr7_127721553_ENST00000354725_BRAF_chr7_140482957_ENST00000288602_length(amino acids)=1095AA_BP=721
MTPPVRPAAPLVAFASPHMASSAQSGGSSGGPAVPTVQRGIIKMVLSGCAIIVRGQPRGGPPPERQINLSNIRAGNLARRAAATQPDAKD
TPDEPWAFPAREFLRKKLIGKEVCFTIENKTPQGREYGMIYLGKDTNGENIAESLVAEGLATRREGMRANNPEQNRLSECEEQAKAAKKG
MWSEGNGSHTIRDLKYTIENPRHFVDSHHQKPVNAIIEHVRDGSVVRALLLPDYYLVTVMLSGIKCPTFRREADGSETPEPFAAEAKFFT
ESRLLQRDVQIILESCHNQNILGTILHPNGNITELLLKEGFARCVDWSIAVYTRGAEKLRAAERFAKERRLRIWRDYVAPTANLDQKDKQ
FVAKVMQVLNADAIVVKLNSGDYKTIHLSSIRPPRLEGENTQDKNKKLRPLYDIPYMFEAREFLRKKLIGKKVNVTVDYIRPASPATETV
PAFSERTCATVTIGGINIAEALVSKGLATVIRYRQDDDQRSSHYDELLAAEARAIKNGKGLHSKKEVPIHRVADISGDTQKAKQFLPFLQ
RAGRSEAVVEYVFSGSRLKLYLPKETCLITFLLAGIECPRGARNLPGLVQEGEPFSEEATLFTKELVLQREVEVEVESMDKAGNFIGWLH
IDGANLSVLLVEHALSKVHFTAERSSYYKSLLSAEEAAKQKKEKVWAHYEEQPVEEVMPVLEEKERSASYKPVFVTEITDDLHFYVQDVE
TGSTTGLSATPPASLPGSLTNVKALQKSPGPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVA
VKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKS
IIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINN
RDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPKIHRSASEPSLNRAGFQTEDFSLYACASP

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

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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/chr7:140487348/chr7:127724776)
- 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
SND1

Q7KZF4

BRAF

P15056

FUNCTION: Endonuclease that mediates miRNA decay of both protein-free and AGO2-loaded miRNAs (PubMed:28546213, PubMed:18453631). As part of its function in miRNA decay, regulates mRNAs involved in G1-to-S phase transition (PubMed:28546213). Functions as a bridging factor between STAT6 and the basal transcription factor (PubMed:12234934). Plays a role in PIM1 regulation of MYB activity (PubMed:9809063). Functions as a transcriptional coactivator for STAT5 (By similarity). {ECO:0000250|UniProtKB:Q78PY7, ECO:0000269|PubMed:12234934, ECO:0000269|PubMed:18453631, ECO:0000269|PubMed:28546213, ECO:0000269|PubMed:9809063}.; FUNCTION: (Microbial infection) Functions as a transcriptional coactivator for the Epstein-Barr virus nuclear antigen 2 (EBNA2). {ECO:0000269|PubMed:7651391}.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}.

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
HgeneSND1chr7:127361454chr7:140487384ENST00000354725+102418_166384.0911.0DomainTNase-like 1
HgeneSND1chr7:127361454chr7:140487384ENST00000354725+1024193_328384.0911.0DomainTNase-like 2
HgeneSND1chr7:127631110chr7:140487386ENST00000354725+162418_166593.0911.0DomainTNase-like 1
HgeneSND1chr7:127631110chr7:140487386ENST00000354725+1624193_328593.0911.0DomainTNase-like 2
HgeneSND1chr7:127631110chr7:140487386ENST00000354725+1624341_496593.0911.0DomainTNase-like 3
HgeneSND1chr7:127721553chr7:140482957ENST00000354725+182418_166703.3333333333334911.0DomainTNase-like 1
HgeneSND1chr7:127721553chr7:140482957ENST00000354725+1824193_328703.3333333333334911.0DomainTNase-like 2
HgeneSND1chr7:127721553chr7:140482957ENST00000354725+1824341_496703.3333333333334911.0DomainTNase-like 3
HgeneSND1chr7:127721553chr7:140482957ENST00000354725+1824525_660703.3333333333334911.0DomainTNase-like 4
HgeneSND1chr7:127361454chr7:140487384ENST00000354725+1024321_325384.0911.0MotifNuclear localization signal
HgeneSND1chr7:127631110chr7:140487386ENST00000354725+1624321_325593.0911.0MotifNuclear localization signal
HgeneSND1chr7:127631110chr7:140487386ENST00000354725+1624388_392593.0911.0MotifNuclear localization signal
HgeneSND1chr7:127721553chr7:140482957ENST00000354725+1824321_325703.3333333333334911.0MotifNuclear localization signal
HgeneSND1chr7:127721553chr7:140482957ENST00000354725+1824388_392703.3333333333334911.0MotifNuclear localization signal
TgeneBRAFchr7:127361454chr7:140487384ENST00000288602718428_432380.0767.0Compositional biasNote=Poly-Ser
TgeneBRAFchr7:127631110chr7:140487386ENST00000288602718428_432380.0767.0Compositional biasNote=Poly-Ser
TgeneBRAFchr7:127721553chr7:140482957ENST00000288602818428_432392.3333333333333767.0Compositional biasNote=Poly-Ser
TgeneBRAFchr7:127361454chr7:140487384ENST00000288602718457_717380.0767.0DomainProtein kinase
TgeneBRAFchr7:127631110chr7:140487386ENST00000288602718457_717380.0767.0DomainProtein kinase
TgeneBRAFchr7:127721553chr7:140482957ENST00000288602818457_717392.3333333333333767.0DomainProtein kinase
TgeneBRAFchr7:127361454chr7:140487384ENST00000288602718463_471380.0767.0Nucleotide bindingATP
TgeneBRAFchr7:127631110chr7:140487386ENST00000288602718463_471380.0767.0Nucleotide bindingATP
TgeneBRAFchr7:127721553chr7:140482957ENST00000288602818463_471392.3333333333333767.0Nucleotide bindingATP

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSND1chr7:127361454chr7:140487384ENST00000354725+1024341_496384.0911.0DomainTNase-like 3
HgeneSND1chr7:127361454chr7:140487384ENST00000354725+1024525_660384.0911.0DomainTNase-like 4
HgeneSND1chr7:127361454chr7:140487384ENST00000354725+1024729_787384.0911.0DomainTudor
HgeneSND1chr7:127631110chr7:140487386ENST00000354725+1624525_660593.0911.0DomainTNase-like 4
HgeneSND1chr7:127631110chr7:140487386ENST00000354725+1624729_787593.0911.0DomainTudor
HgeneSND1chr7:127721553chr7:140482957ENST00000354725+1824729_787703.3333333333334911.0DomainTudor
HgeneSND1chr7:127361454chr7:140487384ENST00000354725+1024388_392384.0911.0MotifNuclear localization signal
TgeneBRAFchr7:127361454chr7:140487384ENST00000288602718122_129380.0767.0Compositional biasNote=Poly-Ser
TgeneBRAFchr7:127361454chr7:140487384ENST000002886027186_11380.0767.0Compositional biasNote=Poly-Gly
TgeneBRAFchr7:127631110chr7:140487386ENST00000288602718122_129380.0767.0Compositional biasNote=Poly-Ser
TgeneBRAFchr7:127631110chr7:140487386ENST000002886027186_11380.0767.0Compositional biasNote=Poly-Gly
TgeneBRAFchr7:127721553chr7:140482957ENST00000288602818122_129392.3333333333333767.0Compositional biasNote=Poly-Ser
TgeneBRAFchr7:127721553chr7:140482957ENST000002886028186_11392.3333333333333767.0Compositional biasNote=Poly-Gly
TgeneBRAFchr7:127361454chr7:140487384ENST00000288602718155_227380.0767.0DomainRBD
TgeneBRAFchr7:127631110chr7:140487386ENST00000288602718155_227380.0767.0DomainRBD
TgeneBRAFchr7:127721553chr7:140482957ENST00000288602818155_227392.3333333333333767.0DomainRBD
TgeneBRAFchr7:127361454chr7:140487384ENST00000288602718234_280380.0767.0Zinc fingerPhorbol-ester/DAG-type
TgeneBRAFchr7:127631110chr7:140487386ENST00000288602718234_280380.0767.0Zinc fingerPhorbol-ester/DAG-type
TgeneBRAFchr7:127721553chr7:140482957ENST00000288602818234_280392.3333333333333767.0Zinc fingerPhorbol-ester/DAG-type


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file (643) >>>643.pdbFusion protein BP residue: 402
CIF file (643) >>>643.cif		SND1chr7127361454+BRAFchr7140487384-
MTPPVRPAAPLVAFASPHMASSAQSGGSSGGPAVPTVQRGIIKMVLSGCA
IIVRGQPRGGPPPERQINLSNIRAGNLARRAAATQPDAKDTPDEPWAFPA
REFLRKKLIGKEVCFTIENKTPQGREYGMIYLGKDTNGENIAESLVAEGL
ATRREGMRANNPEQNRLSECEEQAKAAKKGMWSEGNGSHTIRDLKYTIEN
PRHFVDSHHQKPVNAIIEHVRDGSVVRALLLPDYYLVTVMLSGIKCPTFR
READGSETPEPFAAEAKFFTESRLLQRDVQIILESCHNQNILGTILHPNG
NITELLLKEGFARCVDWSIAVYTRGAEKLRAAERFAKERRLRIWRDYVAP
TANLDQKDKQFVAKVMQVLNADAIVVKLNSGDYKTIHLSSIRPPRLEGEN
TQDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSPGPQRERKS
SSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHG
DVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIV
TQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLK
SNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQ
DKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDL
SKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPKIHRSA
788
3D view using mol* of 643 (AA BP:402)
PDB file (801) >>>801.pdbFusion protein BP residue: 721
CIF file (801) >>>801.cif		SND1chr7127721553+BRAFchr7140482957-
MTPPVRPAAPLVAFASPHMASSAQSGGSSGGPAVPTVQRGIIKMVLSGCA
IIVRGQPRGGPPPERQINLSNIRAGNLARRAAATQPDAKDTPDEPWAFPA
REFLRKKLIGKEVCFTIENKTPQGREYGMIYLGKDTNGENIAESLVAEGL
ATRREGMRANNPEQNRLSECEEQAKAAKKGMWSEGNGSHTIRDLKYTIEN
PRHFVDSHHQKPVNAIIEHVRDGSVVRALLLPDYYLVTVMLSGIKCPTFR
READGSETPEPFAAEAKFFTESRLLQRDVQIILESCHNQNILGTILHPNG
NITELLLKEGFARCVDWSIAVYTRGAEKLRAAERFAKERRLRIWRDYVAP
TANLDQKDKQFVAKVMQVLNADAIVVKLNSGDYKTIHLSSIRPPRLEGEN
TQDKNKKLRPLYDIPYMFEAREFLRKKLIGKKVNVTVDYIRPASPATETV
PAFSERTCATVTIGGINIAEALVSKGLATVIRYRQDDDQRSSHYDELLAA
EARAIKNGKGLHSKKEVPIHRVADISGDTQKAKQFLPFLQRAGRSEAVVE
YVFSGSRLKLYLPKETCLITFLLAGIECPRGARNLPGLVQEGEPFSEEAT
LFTKELVLQREVEVEVESMDKAGNFIGWLHIDGANLSVLLVEHALSKVHF
TAERSSYYKSLLSAEEAAKQKKEKVWAHYEEQPVEEVMPVLEEKERSASY
KPVFVTEITDDLHFYVQDVETGSTTGLSATPPASLPGSLTNVKALQKSPG
PQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTV
YKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYST
KPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKS
IIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMA
PEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGR
GYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSL
1095
3D view using mol* of 801 (AA BP:721)


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
SND1_pLDDT.png
all structure
all structure
BRAF_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
SND1_BRAF_643_pLDDT.png (AA BP:402)
all structure
SND1_BRAF_643_pLDDT_and_active_sites.png (AA BP:402)
all structure
SND1_BRAF_643_violinplot.png (AA BP:402)
all structure
SND1_BRAF_801_pLDDT.png (AA BP:721)
all structure
SND1_BRAF_801_pLDDT_and_active_sites.png (AA BP:721)
all structure
SND1_BRAF_801_violinplot.png (AA BP:721)
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots
SND1_BRAF_801.png
all structure

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Potential Active Site Information


check button The potential binding sites of these fusion proteins were identified using SiteMap, a module of the Schrodinger suite.
Fusion AA seq ID in FusionPDBSite scoreSizeD scoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues
6431.091161.122236.3270.4960.7921.0640.8080.8980.90.574Chain A: 490,597,598,599,600,620,623,624,627,632,6
33,634,635,636,637,638,639,641,642,643,646,655,659
,660,663,684
8011.02893341.0923906.2060.63380.65290.79330.67090.73440.91350.8544Chain A: 245,246,247,248,260,261,262,312,313,314,3
15,316,317,319,320,326,327,330,333,334,337,338,343
,344,345,346,347,348,349,350,351,352,353,354,359,4
36,437,438,439,440,482,483,484,485,486,487,488,489
,490,491,492,493,494,495,496,498,499

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Potentially Interacting Small Molecules through Virtual Screening


check button The FDA-approved small molecule library molecules were subjected to virtual screening using the Glide.
Fusion AA seq ID in FusionPDBZINC IDDrugBank IDDrug nameDocking scoreGlide gscore

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check button Drug information from DrugBank of the top 20 interacting small molecules.
ZINC IDDrugBank IDDrug nameDrug typeSMILESDrug group

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Biochemical Features of Small Molecules


check button ADME (Absorption, Distribution, Metabolism, and Excretion) of drugs using QikProp(v3.9)
ZINC IDmol_MWdipoleSASAFOSAFISAPISAWPSAvolumedonorHBaccptHBIPHuman Oral AbsorptionPercent Human Oral AbsorptionRule Of FiveRule Of Three


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Drug Toxicity Information


check button Toxicity information of individual drugs using eToxPred
ZINC IDSmileSurface AccessibilityToxicity


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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,
SND1IKBKE, SNW1, RBPJ, GTF2E2, GTF2E1, MYB, PIM1, STAT6, POLR2A, USP22, PDPK1, PRKAA1, UBA5, LZTR1, DHX9, CREBBP, RBM39, SIRT7, HHV8GK18_gp81, CUL3, CDK2, CAND1, APP, RPS3, HNRNPM, TOMM22, RPL19, MYBBP1A, SMNDC1, RPS20, NENF, RPL4, VDAC2, ILF2, SRSF3, HNRNPU, RPN1, HNRNPR, SSR3, FN1, VCAM1, CSNK2A1, ITGA4, G3BP1, PRPF8, RNU1-1, RNU2-1, RNU4-1, RNU6-1, RNU5A-1, MAK, TARDBP, EIF3CL, RPS11, RPS2, RPS6, RPS9, DDX3X, RPL23A, RPL35, RPS16, RPS26, RPS27, RPS3A, SHFM1, LIN28A, HUWE1, RAPGEF2, MDM2, CUL7, OBSL1, CCDC8, UBE2I, ESR1, MMP28, TDRD3, TXNDC5, NTRK1, NPM1, RPL10, CNOT1, Eif3a, Pabpc1, Rpl35, Srp72, Rrbp1, MCM2, U2AF2, CDH1, PTP4A1, MTDH, PA2G4, TRAP1, ANXA5, SNRPB2, EIF5B, GPI, IDH2, PDIA3, UBE2N, MRPL12, CRNN, ZNF207, CPNE3, CS, PYGL, SF3A3, DNAJC8, PLS3, CPSF6, NANS, SF3A1, ECHS1, SRP68, MYL12B, AIMP1, CYLD, DLD, DLST, PDHA1, SOD1, TRIM25, BRCA1, YAP1, EFTUD2, AAR2, PIH1D1, CHD3, ESR2, HEXIM1, AGR2, RECQL4, WWP1, MYC, CANX, GRWD1, KIAA1429, ATG16L1, NR2C2, AGRN, BMH2, BMH1, BRF1, AASS, P4HA1, HSP90AA1, HSP90AB1, LRPPRC, HADHA, ATP5C1, SHMT2, MCFD2, ATP5F1, VCP, CTNNB1, BCAP31, DLAT, EPRS, ILF3, PARP1, SFPQ, ALDH16A1, BCL2L13, CCT7, CORO1C, GFM1, PNPT1, SQSTM1, MAB21L2, SNRNP70, GSK3B, ANO7, BIRC3, STAU1, LMBR1L, NFX1, WWP2, Hsp22, TRIM28, PLEKHA4, PINK1, HCVgp1, ZC3H18, FGFR1, EMC4, HNRNPC, M, nsp4, nsp6, nsp8, ORF7b, CAPRIN1, LARP4B, MEX3B, SYNCRIP, TOP3B, UNK, USP10, SDCCAG3, CIT, ANLN, PTGER4, KIF14, FKBP8, PTPN1, ORF9b, LRRC59, SUMO2, NDN, HULC, NUPR1, BRD4, Apc2, LGALS9, IFI16, BKRF1, ASXL1, DNAJC1, DNAJC25, SEC63, H2AFX, TFDP1, MAX, LINC00624, CD274, ISG15, UFL1, DDRGK1, TP53, CKAP4, ELOVL5, EMD, GORASP1, MAPRE1, METTL7A, RPS24, SEC61B, SEC62, SERBP1, SSR1, STIM1, STX4, TMPO, FZR1, HOXA1, NAA40, BGLT3, PSMC3, ARFGAP1, PRPS2, SPINT2, FAM221B, BDH2, SYT6, EP300, CTIF, RCHY1, CCNF, MAP1LC3B, SLFN11, PDE4B, SIRT6,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
SND1all structure
BRAFall structure


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 SND1-BRAF


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID
SND1BRAFResistance To C-Met Inhibitor Pf-04217903PubMed22745804

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Related Diseases to SND1-BRAF


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID
SND1BRAFGastric CancerPubMed22745804
SND1BRAFPancreatic AdenocarcinomaMyCancerGenome
SND1BRAFThyroid Gland Papillary CarcinomaMyCancerGenome
SND1BRAFProstate AdenocarcinomaMyCancerGenome
SND1BRAFLow-Grade GliomaMyCancerGenome
SND1BRAFNosMyCancerGenome
SND1BRAFPancreatic Acinar Cell CarcinomaMyCancerGenome

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSND1C0004352Autistic Disorder1CTD_human
HgeneSND1C0024121Lung Neoplasms1CTD_human
HgeneSND1C0242379Malignant neoplasm of lung1CTD_human
TgeneBRAFC0025202melanoma24CGI;CTD_human;UNIPROT
TgeneBRAFC1275081Cardio-facio-cutaneous syndrome14CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneBRAFC0009402Colorectal Carcinoma8CTD_human;UNIPROT
TgeneBRAFC0028326Noonan Syndrome8CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneBRAFC0238463Papillary thyroid carcinoma8CTD_human;ORPHANET
TgeneBRAFC0040136Thyroid Neoplasm6CGI;CTD_human
TgeneBRAFC0151468Thyroid Gland Follicular Adenoma6CTD_human
TgeneBRAFC0175704LEOPARD Syndrome6CLINGEN;GENOMICS_ENGLAND
TgeneBRAFC0549473Thyroid carcinoma6CGI;CTD_human
TgeneBRAFC3150970NOONAN SYNDROME 75CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneBRAFC0009404Colorectal Neoplasms4CTD_human
TgeneBRAFC3150971LEOPARD SYNDROME 34CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneBRAFC1519086Pilomyxoid astrocytoma3ORPHANET
TgeneBRAFC0004565Melanoma, B162CTD_human
TgeneBRAFC0009075Melanoma, Cloudman S912CTD_human
TgeneBRAFC0018598Melanoma, Harding-Passey2CTD_human
TgeneBRAFC0023443Hairy Cell Leukemia2CGI;ORPHANET
TgeneBRAFC0025205Melanoma, Experimental2CTD_human
TgeneBRAFC0033578Prostatic Neoplasms2CTD_human
TgeneBRAFC0152013Adenocarcinoma of lung (disorder)2CGI;CTD_human
TgeneBRAFC0376358Malignant neoplasm of prostate2CTD_human
TgeneBRAFC0587248Costello syndrome (disorder)2CLINGEN;CTD_human
TgeneBRAFC3501843Nonmedullary Thyroid Carcinoma2CTD_human
TgeneBRAFC3501844Familial Nonmedullary Thyroid Cancer2CTD_human
TgeneBRAFC0002448Ameloblastoma1CTD_human
TgeneBRAFC0004114Astrocytoma1CTD_human
TgeneBRAFC0010276Craniopharyngioma1CTD_human;ORPHANET
TgeneBRAFC0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
TgeneBRAFC0017638Glioma1CGI;CTD_human
TgeneBRAFC0019621Histiocytosis, Langerhans-Cell1CGI;ORPHANET
TgeneBRAFC0022665Kidney Neoplasm1CTD_human
TgeneBRAFC0023903Liver neoplasms1CTD_human
TgeneBRAFC0024232Lymphatic Metastasis1CTD_human
TgeneBRAFC0024694Mandibular Neoplasms1CTD_human
TgeneBRAFC0027659Neoplasms, Experimental1CTD_human
TgeneBRAFC0027962Melanocytic nevus1GENOMICS_ENGLAND
TgeneBRAFC0036920Sezary Syndrome1CTD_human
TgeneBRAFC0041409Turner Syndrome, Male1CTD_human
TgeneBRAFC0079773Lymphoma, T-Cell, Cutaneous1CTD_human
TgeneBRAFC0205768Subependymal Giant Cell Astrocytoma1CTD_human
TgeneBRAFC0206686Adrenocortical carcinoma1CTD_human
TgeneBRAFC0206754Neuroendocrine Tumors1CTD_human
TgeneBRAFC0259783mixed gliomas1CTD_human
TgeneBRAFC0278875Adult Craniopharyngioma1CTD_human
TgeneBRAFC0280783Juvenile Pilocytic Astrocytoma1CTD_human
TgeneBRAFC0280785Diffuse Astrocytoma1CTD_human
TgeneBRAFC0334579Anaplastic astrocytoma1CGI;CTD_human
TgeneBRAFC0334580Protoplasmic astrocytoma1CTD_human
TgeneBRAFC0334581Gemistocytic astrocytoma1CTD_human
TgeneBRAFC0334582Fibrillary Astrocytoma1CTD_human
TgeneBRAFC0334583Pilocytic Astrocytoma1CGI;CTD_human
TgeneBRAFC0338070Childhood Cerebral Astrocytoma1CTD_human
TgeneBRAFC0345904Malignant neoplasm of liver1CTD_human
TgeneBRAFC0376407Granulomatous Slack Skin1CTD_human
TgeneBRAFC0406803Syringocystadenoma Papilliferum1GENOMICS_ENGLAND
TgeneBRAFC0431128Papillary craniopharyngioma1CTD_human
TgeneBRAFC0431129Adamantinous Craniopharyngioma1CTD_human
TgeneBRAFC0547065Mixed oligoastrocytoma1CTD_human
TgeneBRAFC0555198Malignant Glioma1CTD_human
TgeneBRAFC0596263Carcinogenesis1CTD_human
TgeneBRAFC0684249Carcinoma of lung1CGI;UNIPROT
TgeneBRAFC0740457Malignant neoplasm of kidney1CTD_human
TgeneBRAFC0750935Cerebral Astrocytoma1CTD_human
TgeneBRAFC0750936Intracranial Astrocytoma1CTD_human
TgeneBRAFC0751061Craniopharyngioma, Child1CTD_human
TgeneBRAFC0920269Microsatellite Instability1CTD_human
TgeneBRAFC1527404Female Pseudo-Turner Syndrome1CTD_human
TgeneBRAFC1704230Grade I Astrocytoma1CTD_human
TgeneBRAFC1721098Replication Error Phenotype1CTD_human
TgeneBRAFC2239176Liver carcinoma1CTD_human
TgeneBRAFC4551484Leopard Syndrome 11GENOMICS_ENGLAND
TgeneBRAFC4551602Noonan Syndrome 11CTD_human
TgeneBRAFC4721532Lymphoma, Non-Hodgkin, Familial1UNIPROT
TgeneBRAFC4733333familial non-medullary thyroid cancer1GENOMICS_ENGLAND