Home

Download

Statistics

Examples

Help

Contact

Fusion Protein:TNRC18-PRDM16

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: TNRC18-PRDM16
	FusionPDB ID: 92836
	FusionGDB2.0 ID: 92836
		Hgene	Tgene
	Gene symbol	TNRC18	PRDM16
	Gene ID	84629	63976
	Gene name	trinucleotide repeat containing 18	PR/SET domain 16
	Synonyms	CAGL79\|TNRC18A	CMD1LL\|KMT8F\|LVNC8\|MEL1\|PFM13
	Cytomap	7p22.1	1p36.32
	Type of gene	protein-coding	protein-coding
	Description	trinucleotide repeat-containing gene 18 proteinlong CAG trinucleotide repeat-containing gene 79 protein	histone-lysine N-methyltransferase PRDM16MDS1/EVI1-like gene 1PR domain 16PR domain containing 16PR domain zinc finger protein 16transcription factor MEL1
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000399537, ENST00000430969, ENST00000399434,	ENST00000512462, ENST00000270722, ENST00000378391, ENST00000378398, ENST00000441472, ENST00000442529, ENST00000511072, ENST00000514189,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	22 X 26 X 11=6292	9 X 8 X 7=504
	# samples	39	9
	** MAII score	log2(39/6292*10)=-4.01197264166608 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/504*10)=-2.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: TNRC18 [Title/Abstract] AND PRDM16 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: TNRC18 [Title/Abstract] AND PRDM16 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	TNRC18(5460691)-PRDM16(3301716), # samples:1
Anticipated loss of major functional domain due to fusion event.	TNRC18-PRDM16 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. TNRC18-PRDM16 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. TNRC18-PRDM16 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. TNRC18-PRDM16 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	PRDM16	GO:0000122	negative regulation of transcription by RNA polymerase II	19049980
Tgene	PRDM16	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	14656887
Tgene	PRDM16	GO:0045892	negative regulation of transcription, DNA-templated	12816872
Tgene	PRDM16	GO:0045893	positive regulation of transcription, DNA-templated	25578880

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr7:5460691/chr1:3301716)
- 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 TNRC18 (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 PRDM16 (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)
ENST00000399537	TNRC18	chr7	5460691	-	ENST00000511072	PRDM16	chr1	3301716	+	4288	536	551	3634	1027
ENST00000399537	TNRC18	chr7	5460691	-	ENST00000442529	PRDM16	chr1	3301716	+	8677	536	548	3868	1106
ENST00000399537	TNRC18	chr7	5460691	-	ENST00000378398	PRDM16	chr1	3301716	+	8737	536	548	3928	1126
ENST00000399537	TNRC18	chr7	5460691	-	ENST00000441472	PRDM16	chr1	3301716	+	8734	536	548	3925	1125
ENST00000399537	TNRC18	chr7	5460691	-	ENST00000378391	PRDM16	chr1	3301716	+	5482	536	548	3871	1107
ENST00000399537	TNRC18	chr7	5460691	-	ENST00000514189	PRDM16	chr1	3301716	+	4285	536	551	3631	1026
ENST00000399537	TNRC18	chr7	5460691	-	ENST00000270722	PRDM16	chr1	3301716	+	8739	536	548	3928	1126
ENST00000430969	TNRC18	chr7	5460691	-	ENST00000511072	PRDM16	chr1	3301716	+	4288	536	551	3634	1027
ENST00000430969	TNRC18	chr7	5460691	-	ENST00000442529	PRDM16	chr1	3301716	+	8677	536	548	3868	1106
ENST00000430969	TNRC18	chr7	5460691	-	ENST00000378398	PRDM16	chr1	3301716	+	8737	536	548	3928	1126
ENST00000430969	TNRC18	chr7	5460691	-	ENST00000441472	PRDM16	chr1	3301716	+	8734	536	548	3925	1125
ENST00000430969	TNRC18	chr7	5460691	-	ENST00000378391	PRDM16	chr1	3301716	+	5482	536	548	3871	1107
ENST00000430969	TNRC18	chr7	5460691	-	ENST00000514189	PRDM16	chr1	3301716	+	4285	536	551	3631	1026
ENST00000430969	TNRC18	chr7	5460691	-	ENST00000270722	PRDM16	chr1	3301716	+	8739	536	548	3928	1126

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
ENST00000399537	ENST00000511072	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.004897403	0.9951025
ENST00000399537	ENST00000442529	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.001082047	0.99891794
ENST00000399537	ENST00000378398	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.00077486	0.99922514
ENST00000399537	ENST00000441472	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.000779184	0.99922085
ENST00000399537	ENST00000378391	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.001865422	0.9981345
ENST00000399537	ENST00000514189	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.00461019	0.9953898
ENST00000399537	ENST00000270722	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.001370817	0.9986292
ENST00000430969	ENST00000511072	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.004897403	0.9951025
ENST00000430969	ENST00000442529	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.001082047	0.99891794
ENST00000430969	ENST00000378398	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.00077486	0.99922514
ENST00000430969	ENST00000441472	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.000779184	0.99922085
ENST00000430969	ENST00000378391	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.001865422	0.9981345
ENST00000430969	ENST00000514189	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.00461019	0.9953898
ENST00000430969	ENST00000270722	TNRC18	chr7	5460691	-	PRDM16	chr1	3301716	+	0.001370817	0.9986292

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 TNRC18-PRDM16

+/-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

Top

Potential FusionNeoAntigen Information of TNRC18-PRDM16 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.

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)

Top

Potential FusionNeoAntigen Information of TNRC18-PRDM16 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)

Top

Fusion breakpoint peptide structures of TNRC18-PRDM16

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.

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TNRC18-PRDM16

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

Top

Vaccine Design for the FusionNeoAntigens of TNRC18-PRDM16

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

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

Top

Information of the samples that have these potential fusion neoantigens of TNRC18-PRDM16

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

Top

Potential target of CAR-T therapy development for TNRC18-PRDM16

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 TNRC18-PRDM16

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to TNRC18-PRDM16

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)