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Fusion Protein:PRDM6-NIPAL4

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PRDM6-NIPAL4
	FusionPDB ID: 68453
	FusionGDB2.0 ID: 68453
		Hgene	Tgene
	Gene symbol	PRDM6	NIPAL4
	Gene ID	93166	348938
	Gene name	PR/SET domain 6	NIPA like domain containing 4
	Synonyms	KMT8C\|PDA3\|PRISM	ARCI6\|ICHTHYIN\|ICHYN
	Cytomap	5q23.2	5q33.3
	Type of gene	protein-coding	protein-coding
	Description	putative histone-lysine N-methyltransferase PRDM6PR domain 6PR domain containing 6PR domain-containing protein 6PR-domain zinc finger protein 6	magnesium transporter NIPA4NIPA-like protein 4non-imprinted in Prader-Willi/Angelman syndrome region protein 4
	Modification date	20200313	20200327
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000407847, ENST00000464424,	ENST00000521390, ENST00000311946, ENST00000435489,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	1 X 1 X 1=1	2 X 1 X 1=2
	# samples	1	1
	** MAII score	log2(1/1*10)=3.32192809488736	log2(1/2*10)=2.32192809488736
Fusion gene context	PubMed: PRDM6 [Title/Abstract] AND NIPAL4 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PRDM6 [Title/Abstract] AND NIPAL4 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PRDM6(122495332)-NIPAL4(156890102), # samples:3
Anticipated loss of major functional domain due to fusion event.	PRDM6-NIPAL4 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. PRDM6-NIPAL4 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. PRDM6-NIPAL4 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. PRDM6-NIPAL4 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:122495332/chr5:156890102)
- 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 PRDM6 (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 NIPAL4 (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)

ENST00000407847

PRDM6

chr5

122495332

ENST00000435489

NIPAL4

chr5

156890102

2828

1567

246

2687

813

ENST00000407847

PRDM6

chr5

122495332

ENST00000311946

NIPAL4

chr5

156890102

4502

1567

246

2744

832

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
ENST00000407847	ENST00000435489	PRDM6	chr5	122495332	+	NIPAL4	chr5	156890102	+	0.013964874	0.9860351
ENST00000407847	ENST00000311946	PRDM6	chr5	122495332	+	NIPAL4	chr5	156890102	+	0.009352864	0.99064714

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 PRDM6-NIPAL4

+/-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
PRDM6	chr5	122495332	NIPAL4	chr5	156890102	1567	441	GIPLQCIAQDENCSLLHLYCSSQEVL

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Potential FusionNeoAntigen Information of PRDM6-NIPAL4 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.

PRDM6-NIPAL4_122495332_156890102.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)
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B39:13	AQDENCSL	0.8342	0.9064	7	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B35:03	IAQDENCSL	0.86	0.7843	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-A02:21	AQDENCSLL	0.6991	0.535	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B39:13	AQDENCSLL	0.6501	0.9288	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B35:04	IAQDENCSL	0.6327	0.8264	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B35:02	IAQDENCSL	0.6327	0.8264	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B38:01	AQDENCSLL	0.6047	0.925	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B38:02	AQDENCSLL	0.5802	0.9364	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B13:01	AQDENCSLL	0.3717	0.8555	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B47:01	AQDENCSLL	0.2476	0.5376	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B44:03	DENCSLLHLY	0.9967	0.8471	9	19
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B13:01	AQDENCSLLHL	0.9868	0.7532	7	18
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C05:09	AQDENCSL	1	0.9346	7	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:15	AQDENCSL	0.9999	0.9474	7	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B39:08	AQDENCSL	0.9435	0.8009	7	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C05:09	AQDENCSLL	0.9997	0.9261	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C04:10	AQDENCSLL	0.9995	0.7339	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C04:07	AQDENCSLL	0.9995	0.7524	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:15	AQDENCSLL	0.9993	0.9437	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C03:19	IAQDENCSL	0.9992	0.9798	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C03:07	IAQDENCSL	0.9987	0.9458	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C03:08	IAQDENCSL	0.9985	0.84	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:15	IAQDENCSL	0.9955	0.9733	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C04:06	IAQDENCSL	0.9885	0.829	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:04	IAQDENCSL	0.9735	0.9628	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:13	IAQDENCSL	0.9735	0.9628	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C04:06	AQDENCSLL	0.9583	0.7738	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C04:14	AQDENCSLL	0.9008	0.7847	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:03	AQDENCSLL	0.8449	0.969	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:04	AQDENCSLL	0.84	0.9372	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:13	AQDENCSLL	0.84	0.9372	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:03	IAQDENCSL	0.7674	0.9818	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B39:09	AQDENCSLL	0.7379	0.594	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B35:12	IAQDENCSL	0.6327	0.8264	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B39:08	AQDENCSLL	0.6156	0.7923	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B39:05	AQDENCSLL	0.5885	0.8821	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C05:09	IAQDENCSLL	0.9996	0.9427	6	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:15	IAQDENCSLL	0.9987	0.9694	6	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:03	IAQDENCSLL	0.7745	0.9849	6	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B39:08	AQDENCSLLHL	0.9802	0.7801	7	18
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C05:01	AQDENCSL	1	0.9346	7	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:02	AQDENCSL	0.9999	0.9474	7	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B39:02	AQDENCSL	0.9489	0.9025	7	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B39:11	AQDENCSL	0.909	0.7328	7	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C05:01	AQDENCSLL	0.9997	0.9261	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C04:03	AQDENCSLL	0.9996	0.8061	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C04:01	AQDENCSLL	0.9995	0.7524	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:02	AQDENCSLL	0.9993	0.9437	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C03:03	IAQDENCSL	0.9992	0.9797	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C03:04	IAQDENCSL	0.9992	0.9797	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C01:03	AQDENCSLL	0.9992	0.9212	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C18:01	AQDENCSLL	0.9992	0.771	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C03:05	IAQDENCSL	0.9982	0.9079	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C03:17	IAQDENCSL	0.9982	0.9516	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C04:03	IAQDENCSL	0.998	0.8521	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:02	IAQDENCSL	0.9955	0.9733	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C03:06	IAQDENCSL	0.9874	0.9802	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B35:13	IAQDENCSL	0.8493	0.7923	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:01	AQDENCSLL	0.8449	0.969	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C16:01	IAQDENCSL	0.8425	0.965	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:01	IAQDENCSL	0.7674	0.9818	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B39:02	AQDENCSLL	0.7644	0.9254	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B07:13	IAQDENCSL	0.7029	0.74	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-A02:06	AQDENCSLL	0.6991	0.535	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B35:09	IAQDENCSL	0.6327	0.8264	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B18:04	ENCSLLHLY	0.6217	0.5667	10	19
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B38:05	AQDENCSLL	0.6047	0.925	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B39:11	AQDENCSLL	0.5841	0.7285	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C07:04	AQDENCSLL	0.5384	0.9214	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B18:11	DENCSLLHL	0.5204	0.5161	9	18
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B15:73	AQDENCSLL	0.4009	0.9031	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C17:01	IAQDENCSL	0.3456	0.8656	6	15
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B15:30	AQDENCSLL	0.3394	0.8331	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B15:09	AQDENCSLL	0.1813	0.6766	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B07:13	AQDENCSLL	0.0288	0.7753	7	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C04:03	IAQDENCSLL	0.9996	0.8511	6	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C05:01	IAQDENCSLL	0.9996	0.9427	6	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:02	IAQDENCSLL	0.9987	0.9694	6	16
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B44:26	DENCSLLHLY	0.9967	0.8471	9	19
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B44:13	DENCSLLHLY	0.9967	0.8471	9	19
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-B44:07	DENCSLLHLY	0.9967	0.8471	9	19
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	1567	HLA-C08:01	IAQDENCSLL	0.7745	0.9849	6	16

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Potential FusionNeoAntigen Information of PRDM6-NIPAL4 in HLA II

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)

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Fusion breakpoint peptide structures of PRDM6-NIPAL4

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
3597	IAQDENCSLLHLYC	PRDM6	NIPAL4	chr5	122495332	chr5	156890102	1567

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PRDM6-NIPAL4

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	3597	IAQDENCSLLHLYC	-6.18902	-6.30242
HLA-B14:02	3BVN	3597	IAQDENCSLLHLYC	-5.51674	-6.55204
HLA-B52:01	3W39	3597	IAQDENCSLLHLYC	-6.26372	-6.37712
HLA-B52:01	3W39	3597	IAQDENCSLLHLYC	-2.88933	-3.92463
HLA-A11:01	4UQ2	3597	IAQDENCSLLHLYC	-8.95966	-9.99496
HLA-A24:02	5HGA	3597	IAQDENCSLLHLYC	-7.97421	-8.08761
HLA-A24:02	5HGA	3597	IAQDENCSLLHLYC	-4.46014	-5.49544
HLA-B44:05	3DX8	3597	IAQDENCSLLHLYC	-4.21738	-4.33078
HLA-B44:05	3DX8	3597	IAQDENCSLLHLYC	-3.79801	-4.83331
HLA-A02:01	6TDR	3597	IAQDENCSLLHLYC	-6.07498	-7.11028

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Vaccine Design for the FusionNeoAntigens of PRDM6-NIPAL4

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
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	10	19	ENCSLLHLY	ATGAAAACTGTTCCCTGCTCCACCTCT
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	6	15	IAQDENCSL	GCATTGCCCAGGATGAAAACTGTTCCC
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	6	16	IAQDENCSLL	GCATTGCCCAGGATGAAAACTGTTCCCTGC
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	7	15	AQDENCSL	TTGCCCAGGATGAAAACTGTTCCC
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	7	16	AQDENCSLL	TTGCCCAGGATGAAAACTGTTCCCTGC
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	7	18	AQDENCSLLHL	TTGCCCAGGATGAAAACTGTTCCCTGCTCCACC
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	9	18	DENCSLLHL	AGGATGAAAACTGTTCCCTGCTCCACC
PRDM6-NIPAL4	chr5	122495332	chr5	156890102	9	19	DENCSLLHLY	AGGATGAAAACTGTTCCCTGCTCCACCTCT

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

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Information of the samples that have these potential fusion neoantigens of PRDM6-NIPAL4

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
KIRC	PRDM6-NIPAL4	chr5	122495332	ENST00000407847	chr5	156890102	ENST00000311946	TCGA-BP-4986-01A

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Potential target of CAR-T therapy development for PRDM6-NIPAL4

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

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000311946

118_138

467.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000311946

165_185

467.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000311946

187_207

467.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000311946

216_236

467.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000311946

258_278

467.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000311946

286_306

467.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000311946

324_344

467.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000311946

356_376

467.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000311946

387_407

467.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000435489

118_138

448.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000435489

165_185

448.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000435489

187_207

448.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000435489

216_236

448.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000435489

258_278

448.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000435489

286_306

448.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000435489

324_344

448.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000435489

356_376

448.0

Transmembrane

Helical

Tgene

NIPAL4

chr5:122495332

chr5:156890102

ENST00000435489

387_407

448.0

Transmembrane

Helical

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 PRDM6-NIPAL4

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 PRDM6-NIPAL4

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)