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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:RET-CCDC6

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RET-CCDC6
FusionPDB ID: 73555
FusionGDB2.0 ID: 73555
HgeneTgene
Gene symbol

RET

CCDC6

Gene ID

5979

8030

Gene nameret proto-oncogenecoiled-coil domain containing 6
SynonymsCDHF12|CDHR16|HSCR1|MEN2A|MEN2B|MTC1|PTC|RET-ELE1D10S170|H4|PTC|TPC|TST1
Cytomap

10q11.21

10q21.2

Type of geneprotein-codingprotein-coding
Descriptionproto-oncogene tyrosine-protein kinase receptor RetRET receptor tyrosine kinasecadherin family member 12cadherin-related family member 16proto-oncogene c-Retrearranged during transfectionret proto-oncogene (multiple endocrine neoplasia and medullarycoiled-coil domain-containing protein 6papillary thyroid carcinoma-encoded protein
Modification date2020032220200327
UniProtAcc

RTL1

Main function of 5'-partner protein: 1358

A6NI79

Main function of 5'-partner protein: FUNCTION: May act as a scaffold to regulate the recruitment and assembly of spindle midzone components. Required for the localization of AURKB and PLK1 to the spindle midzone. {ECO:0000305|PubMed:20962590}.
Ensembl transtripts involved in fusion geneENST idsENST00000340058, ENST00000355710, 
ENST00000263102, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score9 X 6 X 4=21612 X 8 X 6=576
# samples 914
** MAII scorelog2(9/216*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/576*10)=-2.04064198449735
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: RET [Title/Abstract] AND CCDC6 [Title/Abstract] AND fusion [Title/Abstract]

RET, ROS1 and ALK fusions in lung cancer (pmid: 22327623)
Fusion neoantigen context

PubMed: RET [Title/Abstract] AND CCDC6 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CCDC6(61665880)-RET(43612032), # samples:54
RET(43610184)-CCDC6(61612460), # samples:2
Anticipated loss of major functional domain due to fusion event.CCDC6-RET 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.
CCDC6-RET 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.
RET-CCDC6 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.
RET-CCDC6 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.
RET-CCDC6 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.
RET-CCDC6 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.
CCDC6-RET seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
CCDC6-RET seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CCDC6-RET seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
CCDC6-RET seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CCDC6-RET seems lost the major protein functional domain in Tgene partner, which is a kinase 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
HgeneRET

GO:0030155

regulation of cell adhesion

21357690

HgeneRET

GO:0030335

positive regulation of cell migration

20702524

HgeneRET

GO:0033619

membrane protein proteolysis

21357690

HgeneRET

GO:0033630

positive regulation of cell adhesion mediated by integrin

20702524

HgeneRET

GO:0035860

glial cell-derived neurotrophic factor receptor signaling pathway

28953886

HgeneRET

GO:0043410

positive regulation of MAPK cascade

28846099



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/chr10:61665880/chr10:43612032)
- 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 RET (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 CCDC6 (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)
ENST00000355710RETchr1043610184+ENST00000263102CCDC6chr1061612460-7644236823234891085
ENST00000340058RETchr1043610184+ENST00000263102CCDC6chr1061612460-7592231618034371085

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
ENST00000355710ENST00000263102RETchr1043610184+CCDC6chr1061612460-0.0007875080.9992125
ENST00000340058ENST00000263102RETchr1043610184+CCDC6chr1061612460-0.0007427130.99925727

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 RET-CCDC6

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
RETchr1043610184CCDC6chr10616124602316712MENQVSVDAFKILQARAEQEEEFISN
RETchr1043610184CCDC6chr10616124602368712MENQVSVDAFKILQARAEQEEEFISN

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Potential FusionNeoAntigen Information of RET-CCDC6 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.
RET-CCDC6_43610184_61612460.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)
RET-CCDC6chr1043610184chr10616124602316HLA-B08:09DAFKILQA0.9950.7711715
RET-CCDC6chr1043610184chr10616124602316HLA-A31:02SVDAFKILQAR0.9720.6387516
RET-CCDC6chr1043610184chr10616124602316HLA-A74:09SVDAFKILQAR0.97020.6786516
RET-CCDC6chr1043610184chr10616124602316HLA-A74:03SVDAFKILQAR0.97020.6786516
RET-CCDC6chr1043610184chr10616124602316HLA-A74:11SVDAFKILQAR0.97020.6786516
RET-CCDC6chr1043610184chr10616124602316HLA-B51:07DAFKILQA0.99970.7653715
RET-CCDC6chr1043610184chr10616124602316HLA-B78:01DAFKILQA0.99950.5297715
RET-CCDC6chr1043610184chr10616124602316HLA-A31:01SVDAFKILQAR0.97780.6009516
RET-CCDC6chr1043610184chr10616124602316HLA-B78:02DAFKILQA0.99970.6686715
RET-CCDC6chr1043610184chr10616124602316HLA-A74:01SVDAFKILQAR0.97020.6786516

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Potential FusionNeoAntigen Information of RET-CCDC6 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.
RET-CCDC6_43610184_61612460.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)
RET-CCDC6chr1043610184chr10616124602316DRB1-0101VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0103VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0103SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0105VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0107VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0109VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0111VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0113VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0115VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0115SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0117VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0119VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0121VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0125VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0127VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0129VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0131VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0405VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0405SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0409VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0417VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0424VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0424SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0429VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0429SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0430VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0430SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0445VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0445SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0447VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0447SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0447DAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB1-0448VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0448SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0454VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0454SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0454DAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB1-0457VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0457SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0477VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0477SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0480VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0480SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0480DAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB1-0482VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0482SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0482DAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB1-0482VSVDAFKILQARAEQ419
RET-CCDC6chr1043610184chr10616124602316DRB1-0483VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0483SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0484VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0484SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0486VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0486SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0486DAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB1-0486VSVDAFKILQARAEQ419
RET-CCDC6chr1043610184chr10616124602316DRB1-0487VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0489VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0489SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0801VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0801SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0803VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0803SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0805VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0805SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0807VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0807SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0808VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0808SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0811VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0811SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0813VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0814VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0814SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0815VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0816VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0816SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0818VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0818SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0819VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0823VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0823SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0824VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0825VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0825SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0826VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0826SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0827VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0827SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0829VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0830VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0832VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0832SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0832DAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB1-0832VSVDAFKILQARAEQ419
RET-CCDC6chr1043610184chr10616124602316DRB1-0833VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0833SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0834VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0834SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0835VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0835SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0836VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0836SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0837VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0837SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0837DAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB1-0838VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0838SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0839VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0839SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-0840VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0903VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0903DAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB1-0908VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-0908DAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB1-1001VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1001SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-1001DAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB1-1003VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1003SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-1003DAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB1-1105VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1130VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1130SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-1172VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1216VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1216SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-1216DAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB1-1216VSVDAFKILQARAEQ419
RET-CCDC6chr1043610184chr10616124602316DRB1-1222VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1222SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-13100VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1313VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1321VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1330VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1346VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1349VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1355VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1413VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1422VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1425VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1446VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1453VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1463VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1463SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-1485VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1485SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-1601VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1602VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1603VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1604VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1604SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-1605VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1607VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1608VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1609VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1609SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-1610VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1610SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB1-1611VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1612VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1614VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB1-1616VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB5-0101VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB5-0102VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB5-0102SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB5-0102DAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB5-0102VSVDAFKILQARAEQ419
RET-CCDC6chr1043610184chr10616124602316DRB5-0103VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB5-0103SVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB5-0104VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB5-0105VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB5-0108NVDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB5-0108NSVDAFKILQARAEQE520
RET-CCDC6chr1043610184chr10616124602316DRB5-0108NDAFKILQARAEQEEE722
RET-CCDC6chr1043610184chr10616124602316DRB5-0108NVSVDAFKILQARAEQ419
RET-CCDC6chr1043610184chr10616124602316DRB5-0113VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB5-0114VDAFKILQARAEQEE621
RET-CCDC6chr1043610184chr10616124602316DRB5-0203VDAFKILQARAEQEE621

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Fusion breakpoint peptide structures of RET-CCDC6

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
9826VDAFKILQARAEQERETCCDC6chr1043610184chr10616124602316

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RET-CCDC6

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-B14:023BVN9826VDAFKILQARAEQE-7.9962-8.1096
HLA-B14:023BVN9826VDAFKILQARAEQE-5.70842-6.74372
HLA-B52:013W399826VDAFKILQARAEQE-6.83737-6.95077
HLA-B52:013W399826VDAFKILQARAEQE-4.4836-5.5189
HLA-A11:014UQ29826VDAFKILQARAEQE-10.0067-10.1201
HLA-A11:014UQ29826VDAFKILQARAEQE-9.03915-10.0745
HLA-A24:025HGA9826VDAFKILQARAEQE-6.56204-6.67544
HLA-A24:025HGA9826VDAFKILQARAEQE-5.42271-6.45801
HLA-B44:053DX89826VDAFKILQARAEQE-7.85648-8.89178
HLA-B44:053DX89826VDAFKILQARAEQE-5.3978-5.5112
HLA-A02:016TDR9826VDAFKILQARAEQE-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of RET-CCDC6

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
RET-CCDC6chr1043610184chr1061612460516SVDAFKILQARTCCGTGGATGCCTTCAAGATCCTGCAAGCCAGG
RET-CCDC6chr1043610184chr1061612460715DAFKILQAGATGCCTTCAAGATCCTGCAAGCC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
RET-CCDC6chr1043610184chr1061612460419VSVDAFKILQARAEQGTCTCCGTGGATGCCTTCAAGATCCTGCAAGCCAGGGCTGAGCAG
RET-CCDC6chr1043610184chr1061612460520SVDAFKILQARAEQETCCGTGGATGCCTTCAAGATCCTGCAAGCCAGGGCTGAGCAGGAA
RET-CCDC6chr1043610184chr1061612460621VDAFKILQARAEQEEGTGGATGCCTTCAAGATCCTGCAAGCCAGGGCTGAGCAGGAAGAA
RET-CCDC6chr1043610184chr1061612460722DAFKILQARAEQEEEGATGCCTTCAAGATCCTGCAAGCCAGGGCTGAGCAGGAAGAAGAA

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Information of the samples that have these potential fusion neoantigens of RET-CCDC6

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
THCARET-CCDC6chr1043610184ENST00000340058chr1061612460ENST00000263102TCGA-DJ-A4V5-01A

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Potential target of CAR-T therapy development for RET-CCDC6

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
HgeneRETchr10:43610184chr10:61612460ENST00000340058+1119636_6577121073.0TransmembraneHelical
HgeneRETchr10:43610184chr10:61612460ENST00000355710+1120636_6577121115.0TransmembraneHelical

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 RET-CCDC6

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 RET-CCDC6

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
HgeneRETC1833921Familial medullary thyroid carcinoma23CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneRETC3888239HIRSCHSPRUNG DISEASE, SUSCEPTIBILITY TO, 116GENOMICS_ENGLAND;UNIPROT
HgeneRETC0025268Multiple Endocrine Neoplasia Type 2a15CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneRETC1708353Hereditary Paraganglioma-Pheochromocytoma Syndrome12CLINGEN
HgeneRETC0025269Multiple Endocrine Neoplasia Type 2b10CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneRETC0238463Papillary thyroid carcinoma3CTD_human;ORPHANET
HgeneRETC1275808Congenital central hypoventilation3CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneRETC1859049CCHS WITH HIRSCHSPRUNG DISEASE3CTD_human;ORPHANET
HgeneRETC0009402Colorectal Carcinoma2CTD_human;UNIPROT
HgeneRETC0009404Colorectal Neoplasms2CTD_human
HgeneRETC0019569Hirschsprung Disease2CTD_human
HgeneRETC0027662Multiple Endocrine Neoplasia2CTD_human;GENOMICS_ENGLAND
HgeneRETC0085758Aganglionosis, Colonic2CTD_human
HgeneRETC0266294Unilateral agenesis of kidney2ORPHANET
HgeneRETC1257840Aganglionosis, Rectosigmoid Colon2CTD_human
HgeneRETC3661523Congenital Intestinal Aganglionosis2CTD_human
HgeneRETC0006413Burkitt Lymphoma1CTD_human
HgeneRETC0031511Pheochromocytoma1CGI;CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneRETC0038220Status Epilepticus1CTD_human
HgeneRETC0040136Thyroid Neoplasm1CGI;CTD_human
HgeneRETC0151468Thyroid Gland Follicular Adenoma1CTD_human
HgeneRETC0206693Medullary carcinoma1CTD_human
HgeneRETC0238462Medullary carcinoma of thyroid1CGI;CTD_human
HgeneRETC0270823Petit mal status1CTD_human
HgeneRETC0311335Grand Mal Status Epilepticus1CTD_human
HgeneRETC0343640African Burkitt's lymphoma1CTD_human
HgeneRETC0393734Complex Partial Status Epilepticus1CTD_human
HgeneRETC0549473Thyroid carcinoma1CGI;CTD_human;UNIPROT
HgeneRETC0740340Amyloidosis, Familial1CTD_human
HgeneRETC0751522Status Epilepticus, Subclinical1CTD_human
HgeneRETC0751523Non-Convulsive Status Epilepticus1CTD_human
HgeneRETC0751524Simple Partial Status Epilepticus1CTD_human
HgeneRETC1257877Pheochromocytoma, Extra-Adrenal1CTD_human
HgeneRETC1609433Congenital absence of kidneys syndrome1CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneRETC3501843Nonmedullary Thyroid Carcinoma1CTD_human
HgeneRETC3501844Familial Nonmedullary Thyroid Cancer1CTD_human
HgeneRETC4721444Burkitt Leukemia1CTD_human
TgeneCCDC6C0238463Papillary thyroid carcinoma2CTD_human;ORPHANET
TgeneCCDC6C3501843Nonmedullary Thyroid Carcinoma1CTD_human
TgeneCCDC6C3501844Familial Nonmedullary Thyroid Cancer1CTD_human