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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:SNX29-CLEC16A

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SNX29-CLEC16A
FusionPDB ID: 84947
FusionGDB2.0 ID: 84947
HgeneTgene
Gene symbol

SNX29

CLEC16A

Gene ID

92017

23274

Gene namesorting nexin 29C-type lectin domain containing 16A
SynonymsA-388D4.1|RUNDC2AGop-1|KIAA0350
Cytomap

16p13.13-p13.12

16p13.13

Type of geneprotein-codingprotein-coding
Descriptionsorting nexin-29RUN domain containing 2ARUN domain-containing protein 2Aprotein CLEC16AC-type lectin domain family 16 member A
Modification date2020031320200313
UniProtAcc.

Q2KHT3

Main function of 5'-partner protein: FUNCTION: Regulator of mitophagy through the upstream regulation of the RNF41/NRDP1-PRKN pathway. Mitophagy is a selective form of autophagy necessary for mitochondrial quality control. The RNF41/NRDP1-PRKN pathway regulates autophagosome-lysosome fusion during late mitophagy. May protect RNF41/NRDP1 from proteosomal degradation, RNF41/NRDP1 which regulates proteosomal degradation of PRKN. Plays a key role in beta cells functions by regulating mitophagy/autophagy and mitochondrial health. {ECO:0000269|PubMed:24949970}.
Ensembl transtripts involved in fusion geneENST idsENST00000306030, ENST00000323433, 
ENST00000566228, ENST00000568359, 
ENST00000381822, ENST00000409552, 
ENST00000465491, ENST00000409790, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score21 X 18 X 11=415814 X 13 X 10=1820
# samples 2517
** MAII scorelog2(25/4158*10)=-4.05588975819628
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/1820*10)=-3.42033179894836
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: SNX29 [Title/Abstract] AND CLEC16A [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SNX29 [Title/Abstract] AND CLEC16A [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SNX29(12571716)-CLEC16A(11272192), # samples:1
SNX29(12172772)-CLEC16A(11114050), # samples:1
Anticipated loss of major functional domain due to fusion event.SNX29-CLEC16A 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.
SNX29-CLEC16A 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.
SNX29-CLEC16A 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.
SNX29-CLEC16A 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.
SNX29-CLEC16A seems lost the major protein functional domain in Hgene partner, which is a CGC 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 button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr16:12571716/chr16:11272192)
- 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 buttonRetention analysis results 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, are available here.

check buttonFusion gene breakpoints across SNX29 (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 CLEC16A (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 Amino Acid Sequences


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)
ENST00000566228SNX29chr1612172772-ENST00000409790CLEC16Achr1611114050+682914716933291086
ENST00000566228SNX29chr1612172772-ENST00000409552CLEC16Achr1611114050+30071471692942957
ENST00000323433SNX29chr1612172772-ENST00000409790CLEC16Achr1611114050+5661303292161710
ENST00000323433SNX29chr1612172772-ENST00000409552CLEC16Achr1611114050+1839303291774581
ENST00000306030SNX29chr1612172772-ENST00000409790CLEC16Achr1611114050+5661303292161710
ENST00000306030SNX29chr1612172772-ENST00000409552CLEC16Achr1611114050+1839303291774581

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
ENST00000566228ENST00000409790SNX29chr1612172772-CLEC16Achr1611114050+0.0017550860.9982449
ENST00000566228ENST00000409552SNX29chr1612172772-CLEC16Achr1611114050+0.0089254740.9910745
ENST00000323433ENST00000409790SNX29chr1612172772-CLEC16Achr1611114050+0.0063774880.9936225
ENST00000323433ENST00000409552SNX29chr1612172772-CLEC16Achr1611114050+0.0165214350.98347855
ENST00000306030ENST00000409790SNX29chr1612172772-CLEC16Achr1611114050+0.0063774880.9936225
ENST00000306030ENST00000409552SNX29chr1612172772-CLEC16Achr1611114050+0.0165214350.98347855

check button Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for SNX29-CLEC16A

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
SNX29chr1612172772CLEC16Achr16111140501471468LPSASVPESMTIKIEMVIMERSKLSE
SNX29chr1612172772CLEC16Achr161111405030392LPSASVPESMTIKIEMVIMERSKLSE

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Potential FusionNeoAntigen Information of SNX29-CLEC16A in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
SNX29-CLEC16A_12172772_11114050.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B57:03MTIKIEMVI0.99620.9193918
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B15:16MTIKIEMVI0.99590.6493918
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B15:17MTIKIEMVI0.99550.8477918
SNX29-CLEC16Achr1612172772chr1611114050303HLA-A02:13SMTIKIEMV0.9870.5034817
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B35:03ESMTIKIEM0.98160.7658716
SNX29-CLEC16Achr1612172772chr1611114050303HLA-A74:09KIEMVIMER0.96250.64241221
SNX29-CLEC16Achr1612172772chr1611114050303HLA-A74:03KIEMVIMER0.96250.64241221
SNX29-CLEC16Achr1612172772chr1611114050303HLA-A74:11KIEMVIMER0.96250.64241221
SNX29-CLEC16Achr1612172772chr1611114050303HLA-A31:02KIEMVIMER0.89610.62661221
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B35:03VPESMTIKI0.8930.8523514
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B35:04VPESMTIKI0.87440.8991514
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B35:02VPESMTIKI0.87440.8991514
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B35:02ESMTIKIEM0.87410.8044716
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B35:04ESMTIKIEM0.87410.8044716
SNX29-CLEC16Achr1612172772chr1611114050303HLA-A31:01KIEMVIMER0.9670.5911221
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B51:07VPESMTIKI0.95390.6747514
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B35:12VPESMTIKI0.87440.8991514
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B35:12ESMTIKIEM0.87410.8044716
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B39:10VPESMTIKI0.1310.8228514
SNX29-CLEC16Achr1612172772chr1611114050303HLA-C01:17SVPESMTIKI0.72910.8861414
SNX29-CLEC16Achr1612172772chr1611114050303HLA-C15:02MTIKIEMVI0.99960.9161918
SNX29-CLEC16Achr1612172772chr1611114050303HLA-A25:01ESMTIKIEM0.99830.7871716
SNX29-CLEC16Achr1612172772chr1611114050303HLA-A68:02MTIKIEMVI0.99660.6236918
SNX29-CLEC16Achr1612172772chr1611114050303HLA-A69:01MTIKIEMVI0.99350.6653918
SNX29-CLEC16Achr1612172772chr1611114050303HLA-A74:01KIEMVIMER0.96250.64241221
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B35:13VPESMTIKI0.90430.8556514
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B35:09VPESMTIKI0.87440.8991514
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B35:09ESMTIKIEM0.87410.8044716
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B67:01VPESMTIKI0.22450.5796514
SNX29-CLEC16Achr1612172772chr1611114050303HLA-A68:02ESMTIKIEMV0.99920.5207717
SNX29-CLEC16Achr1612172772chr1611114050303HLA-A69:01ESMTIKIEMV0.99820.5265717
SNX29-CLEC16Achr1612172772chr1611114050303HLA-B67:01VPESMTIKIEM0.9620.6338516

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Potential FusionNeoAntigen Information of SNX29-CLEC16A in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
SNX29-CLEC16A_12172772_11114050.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1113IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1113TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1117IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1117TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1118IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1134IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1152IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1152TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1157IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1172IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1184IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1189IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1192IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1192TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1204IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1209IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1306IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1344IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1354IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1377IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1401IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1401TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1404IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1404TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1405IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1405TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1406IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1408IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1408TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1411IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1411TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1412IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1417IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1418IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1418TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1420IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1421IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1423IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1423TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1426IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1426TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1428IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1429IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1431IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1431TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1432IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1432TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1433IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1434IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1434TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1435IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1435TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1438IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1439IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1443IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1443TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1445IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1445TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1449IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1450IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1452IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1454IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1454TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1455IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1456IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1456TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1458IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1458TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1459IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1459TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1460IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1460TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1461IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1461TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1462IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1462TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1464IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1464TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1465IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1465TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1470IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1471IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1471TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1472IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1472TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1473IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1474IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1475IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1475TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1480IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1481IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1481TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1482IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1483IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1486IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1486TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1487IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1487TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1488IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1488TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1490IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1490TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1491IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1491TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1495IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1496IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1496TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1497IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1497TIKIEMVIMERSKLS1025
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1499IKIEMVIMERSKLSE1126
SNX29-CLEC16Achr1612172772chr1611114050303DRB1-1499TIKIEMVIMERSKLS1025

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Fusion breakpoint peptide structures of SNX29-CLEC16A

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
6596PESMTIKIEMVIMESNX29CLEC16Achr1612172772chr1611114050303

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SNX29-CLEC16A

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score
HLA-B14:023BVN6596PESMTIKIEMVIME-7.9962-8.1096
HLA-B14:023BVN6596PESMTIKIEMVIME-5.70842-6.74372
HLA-B52:013W396596PESMTIKIEMVIME-6.83737-6.95077
HLA-B52:013W396596PESMTIKIEMVIME-4.4836-5.5189
HLA-A11:014UQ26596PESMTIKIEMVIME-10.0067-10.1201
HLA-A11:014UQ26596PESMTIKIEMVIME-9.03915-10.0745
HLA-A24:025HGA6596PESMTIKIEMVIME-6.56204-6.67544
HLA-A24:025HGA6596PESMTIKIEMVIME-5.42271-6.45801
HLA-B44:053DX86596PESMTIKIEMVIME-7.85648-8.89178
HLA-B44:053DX86596PESMTIKIEMVIME-5.3978-5.5112
HLA-A02:016TDR6596PESMTIKIEMVIME-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of SNX29-CLEC16A

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence
SNX29-CLEC16Achr1612172772chr16111140501221KIEMVIMERTTAAGATCGAGATGGTGATCATGGAGC
SNX29-CLEC16Achr1612172772chr1611114050414SVPESMTIKICCTCAGTGCCAGAGTCCATGACAATTAAGA
SNX29-CLEC16Achr1612172772chr1611114050514VPESMTIKICAGTGCCAGAGTCCATGACAATTAAGA
SNX29-CLEC16Achr1612172772chr1611114050516VPESMTIKIEMCAGTGCCAGAGTCCATGACAATTAAGATCGAGA
SNX29-CLEC16Achr1612172772chr1611114050716ESMTIKIEMCAGAGTCCATGACAATTAAGATCGAGA
SNX29-CLEC16Achr1612172772chr1611114050717ESMTIKIEMVCAGAGTCCATGACAATTAAGATCGAGATGG
SNX29-CLEC16Achr1612172772chr1611114050817SMTIKIEMVAGTCCATGACAATTAAGATCGAGATGG
SNX29-CLEC16Achr1612172772chr1611114050918MTIKIEMVICCATGACAATTAAGATCGAGATGGTGA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
SNX29-CLEC16Achr1612172772chr16111140501025TIKIEMVIMERSKLSTGACAATTAAGATCGAGATGGTGATCATGGAGCGTAGCAAGCTCT
SNX29-CLEC16Achr1612172772chr16111140501126IKIEMVIMERSKLSECAATTAAGATCGAGATGGTGATCATGGAGCGTAGCAAGCTCTCAG

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Information of the samples that have these potential fusion neoantigens of SNX29-CLEC16A

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample
UCECSNX29-CLEC16Achr1612172772ENST00000306030chr1611114050ENST00000409552TCGA-A5-A7WJ-01A

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Potential target of CAR-T therapy development for SNX29-CLEC16A

check button Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to SNX29-CLEC16A

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 SNX29-CLEC16A

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