Home

Download

Statistics

Examples

Help

Contact

Fusion Protein:AFAP1-RET

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: AFAP1-RET
	FusionPDB ID: 2631
	FusionGDB2.0 ID: 2631
		Hgene	Tgene
	Gene symbol	AFAP1	RET
	Gene ID	60312	5979
	Gene name	actin filament associated protein 1	ret proto-oncogene
	Synonyms	AFAP\|AFAP-110\|AFAP110	CDHF12\|CDHR16\|HSCR1\|MEN2A\|MEN2B\|MTC1\|PTC\|RET-ELE1
	Cytomap	4p16.1	10q11.21
	Type of gene	protein-coding	protein-coding
	Description	actin filament-associated protein 1110 kDa actin filament-associated proteinactin filament-associated protein, 110 kDa	proto-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 medullary
	Modification date	20200313	20200322
	UniProtAcc	Q8N4X5 Main function of 5'-partner protein: FUNCTION: May play a role in a signaling cascade by enhancing the kinase activity of SRC. Contributes to SRC-regulated transcription activation. {ECO:0000269\|PubMed:17412687}.	RTL1 Main function of 5'-partner protein: 1358
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000358461, ENST00000360265, ENST00000382543, ENST00000420658, ENST00000513842,	ENST00000340058, ENST00000355710,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	11 X 17 X 7=1309	32 X 31 X 11=10912
	# samples	19	48
	** MAII score	log2(19/1309*10)=-2.78439377361429 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(48/10912*10)=-4.50673733341565 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: AFAP1 [Title/Abstract] AND RET [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: AFAP1 [Title/Abstract] AND RET [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	AFAP1(7870348)-RET(43612031), # samples:1
Anticipated loss of major functional domain due to fusion event.	AFAP1-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. AFAP1-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. AFAP1-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. AFAP1-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.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	RET	GO:0030155	regulation of cell adhesion	21357690
Tgene	RET	GO:0030335	positive regulation of cell migration	20702524
Tgene	RET	GO:0033619	membrane protein proteolysis	21357690
Tgene	RET	GO:0033630	positive regulation of cell adhesion mediated by integrin	20702524
Tgene	RET	GO:0035860	glial cell-derived neurotrophic factor receptor signaling pathway	28953886
Tgene	RET	GO:0043410	positive regulation of MAPK cascade	28846099

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr4:7870348/chr10:43612031)
- 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.

Retention 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.

Fusion gene breakpoints across AFAP1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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

Top

Fusion Amino Acid Sequences

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000360265	AFAP1	chr4	7870348	-	ENST00000355710	RET	chr10	43612031	+	3751	460	187	1668	493
ENST00000360265	AFAP1	chr4	7870348	-	ENST00000340058	RET	chr10	43612031	+	2293	460	187	1542	451
ENST00000358461	AFAP1	chr4	7870348	-	ENST00000355710	RET	chr10	43612031	+	3789	498	273	1706	477
ENST00000358461	AFAP1	chr4	7870348	-	ENST00000340058	RET	chr10	43612031	+	2331	498	273	1580	435
ENST00000420658	AFAP1	chr4	7870348	-	ENST00000355710	RET	chr10	43612031	+	3789	498	273	1706	477
ENST00000420658	AFAP1	chr4	7870348	-	ENST00000340058	RET	chr10	43612031	+	2331	498	273	1580	435
ENST00000382543	AFAP1	chr4	7870348	-	ENST00000355710	RET	chr10	43612031	+	3520	229	4	1437	477
ENST00000382543	AFAP1	chr4	7870348	-	ENST00000340058	RET	chr10	43612031	+	2062	229	4	1311	435

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000360265	ENST00000355710	AFAP1	chr4	7870348	-	RET	chr10	43612031	+	0.000547004	0.999453
ENST00000360265	ENST00000340058	AFAP1	chr4	7870348	-	RET	chr10	43612031	+	0.00149675	0.9985033
ENST00000358461	ENST00000355710	AFAP1	chr4	7870348	-	RET	chr10	43612031	+	0.000687138	0.9993129
ENST00000358461	ENST00000340058	AFAP1	chr4	7870348	-	RET	chr10	43612031	+	0.001822425	0.9981775
ENST00000420658	ENST00000355710	AFAP1	chr4	7870348	-	RET	chr10	43612031	+	0.000687138	0.9993129
ENST00000420658	ENST00000340058	AFAP1	chr4	7870348	-	RET	chr10	43612031	+	0.001822425	0.9981775
ENST00000382543	ENST00000355710	AFAP1	chr4	7870348	-	RET	chr10	43612031	+	0.000530692	0.99946934
ENST00000382543	ENST00000340058	AFAP1	chr4	7870348	-	RET	chr10	43612031	+	0.001650721	0.9983493

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

Top

Fusion Protein Breakpoint Sequences for AFAP1-RET

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
AFAP1	chr4	7870348	RET	chr10	43612031	229	75	PQMPLPEIPQPWLEDPKWEFPRKNLV
AFAP1	chr4	7870348	RET	chr10	43612031	460	91	PQMPLPEIPQPWLEDPKWEFPRKNLV
AFAP1	chr4	7870348	RET	chr10	43612031	498	75	PQMPLPEIPQPWLEDPKWEFPRKNLV

Top

Potential FusionNeoAntigen Information of AFAP1-RET in HLA I

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.

AFAP1-RET_7870348_43612031.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B18:01	LEDPKWEF	0.9978	0.9723	12	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B53:01	PWLEDPKW	0.959	0.5778	10	18
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B53:01	QPWLEDPKW	0.9775	0.736	9	18
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B15:02	WLEDPKWEF	0.8914	0.9543	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B45:01	LEDPKWEFP	0.8761	0.9561	12	21
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B35:08	QPWLEDPKW	0.7967	0.9345	9	18
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B13:01	WLEDPKWEF	0.3391	0.9181	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B41:01	LEDPKWEFP	0.2376	0.9347	12	21
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B35:05	QPWLEDPKWEF	0.9981	0.7291	9	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B35:08	QPWLEDPKWEF	0.9973	0.9202	9	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B53:01	IPQPWLEDPKW	0.9968	0.5572	7	18
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B35:01	QPWLEDPKWEF	0.9964	0.8957	9	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B53:01	QPWLEDPKWEF	0.9913	0.7223	9	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B82:01	QPWLEDPKWEF	0.9774	0.7638	9	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B39:08	LEDPKWEF	0.983	0.8617	12	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-C04:07	WLEDPKWEF	0.9989	0.846	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-C04:10	WLEDPKWEF	0.9989	0.818	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-C05:09	WLEDPKWEF	0.9989	0.9689	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-C08:15	WLEDPKWEF	0.9979	0.9714	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B15:31	WLEDPKWEF	0.8957	0.9209	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B15:21	WLEDPKWEF	0.8942	0.9407	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B15:05	WLEDPKWEF	0.8705	0.9141	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-C04:14	WLEDPKWEF	0.7117	0.8247	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B18:04	LEDPKWEF	0.9983	0.9742	12	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B18:06	LEDPKWEF	0.9979	0.9785	12	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B18:05	LEDPKWEF	0.9978	0.9723	12	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B18:08	LEDPKWEF	0.9977	0.9708	12	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B18:03	LEDPKWEF	0.9971	0.9698	12	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B18:11	LEDPKWEF	0.9954	0.9528	12	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B41:03	LEDPKWEF	0.9388	0.6451	12	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-C04:03	WLEDPKWEF	0.999	0.8875	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-C04:01	WLEDPKWEF	0.9989	0.846	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-C05:01	WLEDPKWEF	0.9989	0.9689	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-C18:01	WLEDPKWEF	0.9982	0.8608	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-C08:02	WLEDPKWEF	0.9979	0.9714	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B53:02	QPWLEDPKW	0.9779	0.7279	9	18
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B35:20	WLEDPKWEF	0.8663	0.9622	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B15:13	QPWLEDPKW	0.8662	0.9672	9	18
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B15:13	WLEDPKWEF	0.7596	0.7525	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-C04:04	WLEDPKWEF	0.5966	0.9088	11	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B51:06	QPWLEDPKW	0.3282	0.722	9	18
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B35:17	QPWLEDPKWEF	0.9986	0.8326	9	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B35:30	QPWLEDPKWEF	0.9986	0.8326	9	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B53:02	IPQPWLEDPKW	0.9979	0.6492	7	18
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B35:24	QPWLEDPKWEF	0.9972	0.8623	9	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B35:77	QPWLEDPKWEF	0.9964	0.8957	9	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B35:23	QPWLEDPKWEF	0.9963	0.9158	9	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B53:02	QPWLEDPKWEF	0.9934	0.7199	9	20
AFAP1-RET	chr4	7870348	chr10	43612031	498	HLA-B82:02	QPWLEDPKWEF	0.9774	0.7638	9	20

Top

Potential FusionNeoAntigen Information of AFAP1-RET in HLA II

AFAP1-RET_7870348_43612031.msa

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA II	FusionNeoAntigen peptide	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-0305	PQPWLEDPKWEFPRK	8	23
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-0305	IPQPWLEDPKWEFPR	7	22
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-0305	QPWLEDPKWEFPRKN	9	24
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-0305	EIPQPWLEDPKWEFP	6	21
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-0310	PQPWLEDPKWEFPRK	8	23
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-0338	PQPWLEDPKWEFPRK	8	23
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-0338	IPQPWLEDPKWEFPR	7	22
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-0340	PQPWLEDPKWEFPRK	8	23
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-0340	IPQPWLEDPKWEFPR	7	22
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-0340	QPWLEDPKWEFPRKN	9	24
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-0340	EIPQPWLEDPKWEFP	6	21
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-1179	PQPWLEDPKWEFPRK	8	23
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-1333	PQPWLEDPKWEFPRK	8	23
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB1-1493	PQPWLEDPKWEFPRK	8	23
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB3-0114	PQPWLEDPKWEFPRK	8	23
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB3-0114	IPQPWLEDPKWEFPR	7	22
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB3-0114	EIPQPWLEDPKWEFP	6	21
AFAP1-RET	chr4	7870348	chr10	43612031	498	DRB3-0114	QPWLEDPKWEFPRKN	9	24

Top

Fusion breakpoint peptide structures of AFAP1-RET

3D 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 name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
1802	EIPQPWLEDPKWEF	AFAP1	RET	chr4	7870348	chr10	43612031	498

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of AFAP1-RET

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	1802	EIPQPWLEDPKWEF	-7.9962	-8.1096
HLA-B14:02	3BVN	1802	EIPQPWLEDPKWEF	-5.70842	-6.74372
HLA-B52:01	3W39	1802	EIPQPWLEDPKWEF	-6.83737	-6.95077
HLA-B52:01	3W39	1802	EIPQPWLEDPKWEF	-4.4836	-5.5189
HLA-A11:01	4UQ2	1802	EIPQPWLEDPKWEF	-10.0067	-10.1201
HLA-A11:01	4UQ2	1802	EIPQPWLEDPKWEF	-9.03915	-10.0745
HLA-A24:02	5HGA	1802	EIPQPWLEDPKWEF	-6.56204	-6.67544
HLA-A24:02	5HGA	1802	EIPQPWLEDPKWEF	-5.42271	-6.45801
HLA-B44:05	3DX8	1802	EIPQPWLEDPKWEF	-7.85648	-8.89178
HLA-B44:05	3DX8	1802	EIPQPWLEDPKWEF	-5.3978	-5.5112
HLA-A02:01	6TDR	1802	EIPQPWLEDPKWEF	-3.37154	-4.40684

Top

Vaccine Design for the FusionNeoAntigens of AFAP1-RET

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
AFAP1-RET	chr4	7870348	chr10	43612031	10	18	PWLEDPKW	CCCTGGCTGGAGGATCCAAAGTGG
AFAP1-RET	chr4	7870348	chr10	43612031	11	20	WLEDPKWEF	TGGCTGGAGGATCCAAAGTGGGAATTC
AFAP1-RET	chr4	7870348	chr10	43612031	12	20	LEDPKWEF	CTGGAGGATCCAAAGTGGGAATTC
AFAP1-RET	chr4	7870348	chr10	43612031	12	21	LEDPKWEFP	CTGGAGGATCCAAAGTGGGAATTCCCT
AFAP1-RET	chr4	7870348	chr10	43612031	7	18	IPQPWLEDPKW	ATCCCTCAGCCCTGGCTGGAGGATCCAAAGTGG
AFAP1-RET	chr4	7870348	chr10	43612031	9	18	QPWLEDPKW	CAGCCCTGGCTGGAGGATCCAAAGTGG
AFAP1-RET	chr4	7870348	chr10	43612031	9	20	QPWLEDPKWEF	CAGCCCTGGCTGGAGGATCCAAAGTGGGAATTC

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide	FusionNEoAntigen RNA sequence
AFAP1-RET	chr4	7870348	chr10	43612031	6	21	EIPQPWLEDPKWEFP	GAGATCCCTCAGCCCTGGCTGGAGGATCCAAAGTGGGAATTCCCT
AFAP1-RET	chr4	7870348	chr10	43612031	7	22	IPQPWLEDPKWEFPR	ATCCCTCAGCCCTGGCTGGAGGATCCAAAGTGGGAATTCCCTCGG
AFAP1-RET	chr4	7870348	chr10	43612031	8	23	PQPWLEDPKWEFPRK	CCTCAGCCCTGGCTGGAGGATCCAAAGTGGGAATTCCCTCGGAAG
AFAP1-RET	chr4	7870348	chr10	43612031	9	24	QPWLEDPKWEFPRKN	CAGCCCTGGCTGGAGGATCCAAAGTGGGAATTCCCTCGGAAGAAC

Top

Information of the samples that have these potential fusion neoantigens of AFAP1-RET

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 type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
N/A	AFAP1-RET	chr4	7870348	ENST00000358461	chr10	43612031	ENST00000340058	X56348

Top

Potential target of CAR-T therapy development for AFAP1-RET

Predicted 3D structure. We used RoseTTAFold.

Retention 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'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

Top

Related Drugs to AFAP1-RET

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to AFAP1-RET

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

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Tgene	RET	C1833921	Familial medullary thyroid carcinoma	23	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	RET	C3888239	HIRSCHSPRUNG DISEASE, SUSCEPTIBILITY TO, 1	16	GENOMICS_ENGLAND;UNIPROT
Tgene	RET	C0025268	Multiple Endocrine Neoplasia Type 2a	15	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	RET	C1708353	Hereditary Paraganglioma-Pheochromocytoma Syndrome	12	CLINGEN
Tgene	RET	C0025269	Multiple Endocrine Neoplasia Type 2b	10	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	RET	C0238463	Papillary thyroid carcinoma	3	CTD_human;ORPHANET
Tgene	RET	C1275808	Congenital central hypoventilation	3	CTD_human;GENOMICS_ENGLAND;UNIPROT
Tgene	RET	C1859049	CCHS WITH HIRSCHSPRUNG DISEASE	3	CTD_human;ORPHANET
Tgene	RET	C0009402	Colorectal Carcinoma	2	CTD_human;UNIPROT
Tgene	RET	C0009404	Colorectal Neoplasms	2	CTD_human
Tgene	RET	C0019569	Hirschsprung Disease	2	CTD_human
Tgene	RET	C0027662	Multiple Endocrine Neoplasia	2	CTD_human;GENOMICS_ENGLAND
Tgene	RET	C0085758	Aganglionosis, Colonic	2	CTD_human
Tgene	RET	C0266294	Unilateral agenesis of kidney	2	ORPHANET
Tgene	RET	C1257840	Aganglionosis, Rectosigmoid Colon	2	CTD_human
Tgene	RET	C3661523	Congenital Intestinal Aganglionosis	2	CTD_human
Tgene	RET	C0006413	Burkitt Lymphoma	1	CTD_human
Tgene	RET	C0031511	Pheochromocytoma	1	CGI;CTD_human;GENOMICS_ENGLAND;UNIPROT
Tgene	RET	C0038220	Status Epilepticus	1	CTD_human
Tgene	RET	C0040136	Thyroid Neoplasm	1	CGI;CTD_human
Tgene	RET	C0151468	Thyroid Gland Follicular Adenoma	1	CTD_human
Tgene	RET	C0206693	Medullary carcinoma	1	CTD_human
Tgene	RET	C0238462	Medullary carcinoma of thyroid	1	CGI;CTD_human
Tgene	RET	C0270823	Petit mal status	1	CTD_human
Tgene	RET	C0311335	Grand Mal Status Epilepticus	1	CTD_human
Tgene	RET	C0343640	African Burkitt's lymphoma	1	CTD_human
Tgene	RET	C0393734	Complex Partial Status Epilepticus	1	CTD_human
Tgene	RET	C0549473	Thyroid carcinoma	1	CGI;CTD_human;UNIPROT
Tgene	RET	C0740340	Amyloidosis, Familial	1	CTD_human
Tgene	RET	C0751522	Status Epilepticus, Subclinical	1	CTD_human
Tgene	RET	C0751523	Non-Convulsive Status Epilepticus	1	CTD_human
Tgene	RET	C0751524	Simple Partial Status Epilepticus	1	CTD_human
Tgene	RET	C1257877	Pheochromocytoma, Extra-Adrenal	1	CTD_human
Tgene	RET	C1609433	Congenital absence of kidneys syndrome	1	CTD_human;GENOMICS_ENGLAND;ORPHANET
Tgene	RET	C3501843	Nonmedullary Thyroid Carcinoma	1	CTD_human
Tgene	RET	C3501844	Familial Nonmedullary Thyroid Cancer	1	CTD_human
Tgene	RET	C4721444	Burkitt Leukemia	1	CTD_human

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)