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Fusion Protein:CDKL1-DNM2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CDKL1-DNM2
	FusionPDB ID: 15363
	FusionGDB2.0 ID: 15363
		Hgene	Tgene
	Gene symbol	CDKL1	DNM2
	Gene ID	8814	1785
	Gene name	cyclin dependent kinase like 1	dynamin 2
	Synonyms	KKIALRE\|P42	CMT2M\|CMTDI1\|CMTDIB\|DI-CMTB\|DYN2\|DYNII\|LCCS5
	Cytomap	14q21.3	19p13.2
	Type of gene	protein-coding	protein-coding
	Description	cyclin-dependent kinase-like 1cyclin-dependent kinase-like 1 (CDC2-related kinase)protein kinase p42 KKIALREserine/threonine protein kinase KKIALRE	dynamin-2dynamin II
	Modification date	20200313	20200329
	UniProtAcc	Q00532 Main function of 5'-partner protein:	P50570 Main function of 5'-partner protein: FUNCTION: Microtubule-associated force-producing protein involved in producing microtubule bundles and able to bind and hydrolyze GTP. Plays a role in the regulation of neuron morphology, axon growth and formation of neuronal growth cones (By similarity). Plays an important role in vesicular trafficking processes, in particular endocytosis. Involved in cytokinesis (PubMed:12498685). Regulates maturation of apoptotic cell corpse-containing phagosomes by recruiting PIK3C3 to the phagosome membrane (By similarity). {ECO:0000250\|UniProtKB:P39052, ECO:0000250\|UniProtKB:P39054, ECO:0000269\|PubMed:12498685}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000216378, ENST00000395834, ENST00000356146,	ENST00000591819, ENST00000314646, ENST00000355667, ENST00000359692, ENST00000389253, ENST00000408974, ENST00000585892,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 8 X 4=256	19 X 24 X 14=6384
	# samples	8	34
	** MAII score	log2(8/256*10)=-1.67807190511264 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(34/6384*10)=-4.23085400008464 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: CDKL1 [Title/Abstract] AND DNM2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CDKL1 [Title/Abstract] AND DNM2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CDKL1(50862418)-DNM2(10939711), # samples:1
Anticipated loss of major functional domain due to fusion event.	CDKL1-DNM2 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. CDKL1-DNM2 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. CDKL1-DNM2 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. CDKL1-DNM2 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	DNM2	GO:1903526	negative regulation of membrane tubulation	18388313

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr14:50862418/chr19:10939711)
- 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 CDKL1 (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 DNM2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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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)
ENST00000395834	CDKL1	chr14	50862418	-	ENST00000585892	DNM2	chr19	10939711	+	751	199	28	750	241
ENST00000395834	CDKL1	chr14	50862418	-	ENST00000314646	DNM2	chr19	10939711	+	1610	199	28	753	241
ENST00000395834	CDKL1	chr14	50862418	-	ENST00000359692	DNM2	chr19	10939711	+	1591	199	28	753	241
ENST00000395834	CDKL1	chr14	50862418	-	ENST00000389253	DNM2	chr19	10939711	+	1610	199	28	753	241
ENST00000395834	CDKL1	chr14	50862418	-	ENST00000355667	DNM2	chr19	10939711	+	1602	199	28	753	241
ENST00000395834	CDKL1	chr14	50862418	-	ENST00000408974	DNM2	chr19	10939711	+	1131	199	28	753	241
ENST00000216378	CDKL1	chr14	50862418	-	ENST00000585892	DNM2	chr19	10939711	+	1368	816	540	1367	275
ENST00000216378	CDKL1	chr14	50862418	-	ENST00000314646	DNM2	chr19	10939711	+	2227	816	540	1370	276
ENST00000216378	CDKL1	chr14	50862418	-	ENST00000359692	DNM2	chr19	10939711	+	2208	816	540	1370	276
ENST00000216378	CDKL1	chr14	50862418	-	ENST00000389253	DNM2	chr19	10939711	+	2227	816	540	1370	276
ENST00000216378	CDKL1	chr14	50862418	-	ENST00000355667	DNM2	chr19	10939711	+	2219	816	540	1370	276
ENST00000216378	CDKL1	chr14	50862418	-	ENST00000408974	DNM2	chr19	10939711	+	1748	816	540	1370	276

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
ENST00000395834	ENST00000585892	CDKL1	chr14	50862418	-	DNM2	chr19	10939711	+	0.01785874	0.98214126
ENST00000395834	ENST00000314646	CDKL1	chr14	50862418	-	DNM2	chr19	10939711	+	0.037047874	0.9629521
ENST00000395834	ENST00000359692	CDKL1	chr14	50862418	-	DNM2	chr19	10939711	+	0.035395052	0.964605
ENST00000395834	ENST00000389253	CDKL1	chr14	50862418	-	DNM2	chr19	10939711	+	0.037047874	0.9629521
ENST00000395834	ENST00000355667	CDKL1	chr14	50862418	-	DNM2	chr19	10939711	+	0.036727134	0.96327287
ENST00000395834	ENST00000408974	CDKL1	chr14	50862418	-	DNM2	chr19	10939711	+	0.034777347	0.96522266
ENST00000216378	ENST00000585892	CDKL1	chr14	50862418	-	DNM2	chr19	10939711	+	0.033893395	0.9661066
ENST00000216378	ENST00000314646	CDKL1	chr14	50862418	-	DNM2	chr19	10939711	+	0.049475588	0.9505244
ENST00000216378	ENST00000359692	CDKL1	chr14	50862418	-	DNM2	chr19	10939711	+	0.048545774	0.95145416
ENST00000216378	ENST00000389253	CDKL1	chr14	50862418	-	DNM2	chr19	10939711	+	0.049475588	0.9505244
ENST00000216378	ENST00000355667	CDKL1	chr14	50862418	-	DNM2	chr19	10939711	+	0.049352195	0.9506478
ENST00000216378	ENST00000408974	CDKL1	chr14	50862418	-	DNM2	chr19	10939711	+	0.05052462	0.94947535

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 CDKL1-DNM2

+/-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
CDKL1	chr14	50862418	DNM2	chr19	10939711	199	57	IKKIALREIRMLKTKAFIHHELLAYL

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Potential FusionNeoAntigen Information of CDKL1-DNM2 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.

CDKL1-DNM2_50862418_10939711.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)
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B08:01	MLKTKAFI	0.9997	0.8556	10	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B27:04	IRMLKTKAF	0.9997	0.7169	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B27:05	IRMLKTKAF	0.9996	0.8565	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-A30:08	KTKAFIHHE	0.9821	0.72	12	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B08:09	EIRMLKTKA	0.9568	0.7825	7	16
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B14:02	IRMLKTKAF	0.8731	0.6324	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B14:01	IRMLKTKAF	0.8731	0.6324	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B08:01	IRMLKTKAF	0.7736	0.683	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B15:03	IRMLKTKAF	0.4621	0.5018	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B13:02	RMLKTKAFI	0.0512	0.5013	9	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-A30:08	KTKAFIHHEL	0.9958	0.8045	12	22
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B45:01	REIRMLKTKA	0.9255	0.8614	6	16
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B41:01	REIRMLKTKA	0.6795	0.9447	6	16
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B50:01	REIRMLKTKA	0.2522	0.6699	6	16
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B27:04	REIRMLKTKAF	0.9989	0.7475	6	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:05	IRMLKTKAF	0.9943	0.9486	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:95	IRMLKTKAF	0.9927	0.5994	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B27:03	IRMLKTKAF	0.9915	0.8753	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:27	IRMLKTKAF	0.9877	0.8918	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:29	IRMLKTKAF	0.9682	0.9034	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:13	IRMLKTKAF	0.9403	0.812	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:46	IRMLKTKAF	0.8315	0.714	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:19	IRMLKTKAF	0.8249	0.5851	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:67	IRMLKTKAF	0.819	0.8294	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:80	IRMLKTKAF	0.819	0.8294	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:10	IRMLKTKAF	0.8062	0.8754	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B39:12	IRMLKTKAF	0.6789	0.925	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B14:03	IRMLKTKAF	0.2822	0.7753	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C12:16	IRMLKTKAF	0.0774	0.9455	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B40:06	REIRMLKTKA	0.9854	0.6178	6	16
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B08:18	MLKTKAFI	0.9997	0.8556	10	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B27:10	IRMLKTKAF	0.9997	0.8671	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B27:08	IRMLKTKAF	0.9996	0.7176	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B27:06	IRMLKTKAF	0.9993	0.7124	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B27:09	IRMLKTKAF	0.9972	0.7916	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:01	IRMLKTKAF	0.9947	0.5574	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-A30:01	KTKAFIHHE	0.9827	0.837	12	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-A32:01	RMLKTKAFI	0.979	0.9644	9	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:17	IRMLKTKAF	0.8951	0.9308	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C06:08	IRMLKTKAF	0.8822	0.986	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:02	IRMLKTKAF	0.819	0.8294	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:22	IRMLKTKAF	0.7796	0.6997	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B08:18	IRMLKTKAF	0.7736	0.683	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C07:04	IRMLKTKAF	0.7043	0.928	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C06:06	IRMLKTKAF	0.1904	0.9825	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B15:54	IRMLKTKAF	0.1602	0.608	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C03:67	IRMLKTKAF	0.146	0.9522	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C06:17	IRMLKTKAF	0.1291	0.9911	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-C06:02	IRMLKTKAF	0.1291	0.9911	8	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-A30:01	KTKAFIHHEL	0.9958	0.9002	12	22
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B50:04	REIRMLKTKA	0.2522	0.6699	6	16
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	HLA-B50:05	REIRMLKTKA	0.2522	0.6699	6	16

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Potential FusionNeoAntigen Information of CDKL1-DNM2 in HLA II

CDKL1-DNM2_50862418_10939711.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)
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1201	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1201	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1201	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1201	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1201	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1203	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1203	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1203	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1203	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1203	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1204	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1204	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1204	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1204	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1205	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1205	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1205	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1205	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1205	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1206	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1206	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1206	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1206	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1206	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1207	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1207	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1207	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1207	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1207	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1208	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1208	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1208	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1208	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1208	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1209	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1209	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1209	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1209	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1210	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1210	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1210	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1210	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1210	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1211	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1211	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1211	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1211	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1211	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1212	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1212	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1212	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1212	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1212	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1213	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1213	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1213	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1213	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1213	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1214	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1214	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1214	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1214	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1214	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1215	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1215	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1215	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1215	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1215	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1216	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1216	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1216	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1216	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1217	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1217	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1217	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1217	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1217	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1218	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1218	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1218	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1218	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1218	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1219	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1219	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1219	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1219	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1219	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1220	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1220	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1220	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1220	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1221	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1221	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1221	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1221	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1221	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1222	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1222	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1222	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1222	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1223	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1223	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1223	REIRMLKTKAFIHHE	6	21
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1223	IALREIRMLKTKAFI	3	18
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1223	KIALREIRMLKTKAF	2	17
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1377	LREIRMLKTKAFIHH	5	20
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1377	ALREIRMLKTKAFIH	4	19
CDKL1-DNM2	chr14	50862418	chr19	10939711	199	DRB1-1452	LREIRMLKTKAFIHH	5	20

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Fusion breakpoint peptide structures of CDKL1-DNM2

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
7782	REIRMLKTKAFIHH	CDKL1	DNM2	chr14	50862418	chr19	10939711	199

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CDKL1-DNM2

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	7782	REIRMLKTKAFIHH	-7.9962	-8.1096
HLA-B14:02	3BVN	7782	REIRMLKTKAFIHH	-5.70842	-6.74372
HLA-B52:01	3W39	7782	REIRMLKTKAFIHH	-6.83737	-6.95077
HLA-B52:01	3W39	7782	REIRMLKTKAFIHH	-4.4836	-5.5189
HLA-A11:01	4UQ2	7782	REIRMLKTKAFIHH	-10.0067	-10.1201
HLA-A11:01	4UQ2	7782	REIRMLKTKAFIHH	-9.03915	-10.0745
HLA-A24:02	5HGA	7782	REIRMLKTKAFIHH	-6.56204	-6.67544
HLA-A24:02	5HGA	7782	REIRMLKTKAFIHH	-5.42271	-6.45801
HLA-B44:05	3DX8	7782	REIRMLKTKAFIHH	-7.85648	-8.89178
HLA-B44:05	3DX8	7782	REIRMLKTKAFIHH	-5.3978	-5.5112
HLA-A02:01	6TDR	7782	REIRMLKTKAFIHH	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of CDKL1-DNM2

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
CDKL1-DNM2	chr14	50862418	chr19	10939711	10	18	MLKTKAFI	ATGCTCAAGACGAAGGCCTTCATC
CDKL1-DNM2	chr14	50862418	chr19	10939711	12	21	KTKAFIHHE	AAGACGAAGGCCTTCATCCACCACGAG
CDKL1-DNM2	chr14	50862418	chr19	10939711	12	22	KTKAFIHHEL	AAGACGAAGGCCTTCATCCACCACGAGCTG
CDKL1-DNM2	chr14	50862418	chr19	10939711	6	16	REIRMLKTKA	CGGGAAATCCGAATGCTCAAGACGAAGGCC
CDKL1-DNM2	chr14	50862418	chr19	10939711	6	17	REIRMLKTKAF	CGGGAAATCCGAATGCTCAAGACGAAGGCCTTC
CDKL1-DNM2	chr14	50862418	chr19	10939711	7	16	EIRMLKTKA	GAAATCCGAATGCTCAAGACGAAGGCC
CDKL1-DNM2	chr14	50862418	chr19	10939711	8	17	IRMLKTKAF	ATCCGAATGCTCAAGACGAAGGCCTTC
CDKL1-DNM2	chr14	50862418	chr19	10939711	9	18	RMLKTKAFI	CGAATGCTCAAGACGAAGGCCTTCATC

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
CDKL1-DNM2	chr14	50862418	chr19	10939711	2	17	KIALREIRMLKTKAF	AAAATTGCCCTTCGGGAAATCCGAATGCTCAAGACGAAGGCCTTC
CDKL1-DNM2	chr14	50862418	chr19	10939711	3	18	IALREIRMLKTKAFI	ATTGCCCTTCGGGAAATCCGAATGCTCAAGACGAAGGCCTTCATC
CDKL1-DNM2	chr14	50862418	chr19	10939711	4	19	ALREIRMLKTKAFIH	GCCCTTCGGGAAATCCGAATGCTCAAGACGAAGGCCTTCATCCAC
CDKL1-DNM2	chr14	50862418	chr19	10939711	5	20	LREIRMLKTKAFIHH	CTTCGGGAAATCCGAATGCTCAAGACGAAGGCCTTCATCCACCAC
CDKL1-DNM2	chr14	50862418	chr19	10939711	6	21	REIRMLKTKAFIHHE	CGGGAAATCCGAATGCTCAAGACGAAGGCCTTCATCCACCACGAG

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Information of the samples that have these potential fusion neoantigens of CDKL1-DNM2

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
ESCA	CDKL1-DNM2	chr14	50862418	ENST00000395834	chr19	10939711	ENST00000314646	TCGA-V5-AASX

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Potential target of CAR-T therapy development for CDKL1-DNM2

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

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Related Drugs to CDKL1-DNM2

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

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to CDKL1-DNM2

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

	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)