Home

Download

Statistics

Examples

Help

Contact

Fusion Protein:RNF20-LPPR1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RNF20-LPPR1
	FusionPDB ID: 74954
	FusionGDB2.0 ID: 74955
		Hgene	Tgene
	Gene symbol	RNF20	LPPR1
	Gene ID	56254	54886
	Gene name	ring finger protein 20	phospholipid phosphatase related 1
	Synonyms	BRE1\|BRE1A\|hBRE1	LPPR1\|PRG-3
	Cytomap	9q31.1	9q31.1
	Type of gene	protein-coding	protein-coding
	Description	E3 ubiquitin-protein ligase BRE1ABRE1 E3 ubiquitin ligase homologRING-type E3 ubiquitin transferase BRE1Ahomolog of S. cerevisiae BRE1	phospholipid phosphatase-related protein type 1lipid phosphate phosphatase-related protein type 1plasticity related gene 3plasticity-related gene 3 protein
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000481046, ENST00000389120,	ENST00000374874, ENST00000395056, ENST00000494890,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	2 X 2 X 2=8	2 X 4 X 2=16
	# samples	3	4
	** MAII score	log2(3/8*10)=1.90689059560852	log2(4/16*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: RNF20 [Title/Abstract] AND LPPR1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: RNF20 [Title/Abstract] AND LPPR1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	RNF20(104297834)-LPPR1(104032161), # samples:1 RNF20(104297834)-LPPR1(104032162), # samples:1
Anticipated loss of major functional domain due to fusion event.	RNF20-LPPR1 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. RNF20-LPPR1 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
Hgene	RNF20	GO:0000209	protein polyubiquitination	19037095
Hgene	RNF20	GO:0010390	histone monoubiquitination	16307923\|16337599
Hgene	RNF20	GO:0030336	negative regulation of cell migration	18832071
Hgene	RNF20	GO:0033523	histone H2B ubiquitination	16307923\|16337599

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr9:104297834/chr9:104032161)
- 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 RNF20 (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 LPPR1 (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)

ENST00000389120

RNF20

chr9

104297834

ENST00000374874

LPPR1

chr9

104032161

2212

219

1133

373

ENST00000389120

RNF20

chr9

104297834

ENST00000395056

LPPR1

chr9

104032161

2208

219

1133

373

ENST00000389120

RNF20

chr9

104297834

ENST00000374874

LPPR1

chr9

104032162

2212

219

1133

373

ENST00000389120

RNF20

chr9

104297834

ENST00000395056

LPPR1

chr9

104032162

2208

219

1133

373

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
ENST00000389120	ENST00000374874	RNF20	chr9	104297834	+	LPPR1	chr9	104032161	+	0.000681406	0.9993186
ENST00000389120	ENST00000395056	RNF20	chr9	104297834	+	LPPR1	chr9	104032161	+	0.000689865	0.99931014
ENST00000389120	ENST00000374874	RNF20	chr9	104297834	+	LPPR1	chr9	104032162	+	0.000681406	0.9993186
ENST00000389120	ENST00000395056	RNF20	chr9	104297834	+	LPPR1	chr9	104032162	+	0.000689865	0.99931014

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 RNF20-LPPR1

+/-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
RNF20	chr9	104297834	LPPR1	chr9	104032161	219	69	TVETIKLGGVSSTLVIMAGTVLLAYY
RNF20	chr9	104297834	LPPR1	chr9	104032162	219	69	TVETIKLGGVSSTLVIMAGTVLLAYY

Top

Potential FusionNeoAntigen Information of RNF20-LPPR1 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.

RNF20-LPPR1_104297834_104032161.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)
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:22	KLGGVSSTL	0.9811	0.8087	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:13	KLGGVSSTL	0.9712	0.9183	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:27	KLGGVSSTL	0.9607	0.8802	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:30	KLGGVSSTL	0.9557	0.84	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:67	KLGGVSSTL	0.9557	0.84	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:24	KLGGVSSTL	0.9557	0.84	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:60	KLGGVSSTL	0.9553	0.8322	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:11	KLGGVSSTL	0.9548	0.8565	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:38	KLGGVSSTL	0.9347	0.884	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:04	KLGGVSSTL	0.93	0.8589	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:16	KLGGVSSTL	0.9291	0.7949	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:17	KLGGVSSTL	0.9193	0.8019	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:19	KLGGVSSTL	0.7944	0.7031	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:29	KLGGVSSTL	0.7857	0.8422	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:20	KLGGVSSTL	0.7793	0.847	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:35	KLGGVSSTL	0.7631	0.8568	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-B13:01	KLGGVSSTL	0.0889	0.9933	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-B13:02	KLGGVSSTL	0.0846	0.8894	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:02	KLGGVSSTL	0.9825	0.6729	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:05	KLGGVSSTL	0.9695	0.7678	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:01	KLGGVSSTL	0.9557	0.84	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A02:03	KLGGVSSTL	0.9804	0.905	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-A32:01	KLGGVSSTL	0.9347	0.9943	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-B15:73	KLGGVSSTL	0.7944	0.9897	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-B15:30	KLGGVSSTL	0.6676	0.9892	5	14
RNF20-LPPR1	chr9	104297834	chr9	104032161	219	HLA-B40:21	KLGGVSSTL	0.0279	0.6448	5	14

Top

Potential FusionNeoAntigen Information of RNF20-LPPR1 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 RNF20-LPPR1

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
4998	LGGVSSTLVIMAGT	RNF20	LPPR1	chr9	104297834	chr9	104032161	219

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RNF20-LPPR1

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	4998	LGGVSSTLVIMAGT	-8.85616	-8.96956
HLA-B14:02	3BVN	4998	LGGVSSTLVIMAGT	-5.66423	-6.69953
HLA-B52:01	3W39	4998	LGGVSSTLVIMAGT	-6.49489	-6.60829
HLA-B52:01	3W39	4998	LGGVSSTLVIMAGT	-3.99785	-5.03315
HLA-A11:01	4UQ2	4998	LGGVSSTLVIMAGT	-4.90759	-5.94289
HLA-A24:02	5HGA	4998	LGGVSSTLVIMAGT	-7.27887	-7.39227
HLA-A24:02	5HGA	4998	LGGVSSTLVIMAGT	-7.11524	-8.15054
HLA-B27:05	6PYJ	4998	LGGVSSTLVIMAGT	-6.11615	-6.22955
HLA-B27:05	6PYJ	4998	LGGVSSTLVIMAGT	-4.78818	-5.82348
HLA-B44:05	3DX8	4998	LGGVSSTLVIMAGT	-7.22602	-7.33942
HLA-B44:05	3DX8	4998	LGGVSSTLVIMAGT	-4.86671	-5.90201

Top

Vaccine Design for the FusionNeoAntigens of RNF20-LPPR1

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
RNF20-LPPR1	chr9	104297834	chr9	104032161	5	14	KLGGVSSTL	AAGCTAGGAGGTGTCTCTTCAACGCTT

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 RNF20-LPPR1

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
STAD	RNF20-LPPR1	chr9	104297834	ENST00000389120	chr9	104032161	ENST00000374874	TCGA-CD-A487

Top

Potential target of CAR-T therapy development for RNF20-LPPR1

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

LPPR1

chr9:104297834

chr9:104032161

ENST00000374874

127_147

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032161

ENST00000374874

201_218

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032161

ENST00000374874

230_247

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032161

ENST00000374874

257_277

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032161

ENST00000374874

67_87

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032161

ENST00000395056

127_147

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032161

ENST00000395056

201_218

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032161

ENST00000395056

230_247

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032161

ENST00000395056

257_277

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032161

ENST00000395056

67_87

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032162

ENST00000374874

127_147

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032162

ENST00000374874

201_218

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032162

ENST00000374874

230_247

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032162

ENST00000374874

257_277

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032162

ENST00000374874

67_87

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032162

ENST00000395056

127_147

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032162

ENST00000395056

201_218

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032162

ENST00000395056

230_247

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032162

ENST00000395056

257_277

326.0

Transmembrane

Helical

Tgene

LPPR1

chr9:104297834

chr9:104032162

ENST00000395056

67_87

326.0

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

Top

Related Drugs to RNF20-LPPR1

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to RNF20-LPPR1

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)