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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:LRRC59-NUP107

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: LRRC59-NUP107
	FusionPDB ID: 49985
	FusionGDB2.0 ID: 49985
		Hgene	Tgene
	Gene symbol	LRRC59	NUP107
	Gene ID	55379	57122
	Gene name	leucine rich repeat containing 59	nucleoporin 107
	Synonyms	PRO1855\|p34	NPHS11\|NUP84\|ODG6\|ODG6; GAMOS7
	Cytomap	17q21.33	12q15
	Type of gene	protein-coding	protein-coding
	Description	leucine-rich repeat-containing protein 59ribosome-binding protein p34	nuclear pore complex protein Nup107nucleoporin 107kDa
	Modification date	20200313	20200313
	UniProtAcc	Q96AG4	P57740
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000225972, ENST00000576448,	ENST00000401003, ENST00000229179, ENST00000378905, ENST00000539906,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	5 X 4 X 2=40	27 X 22 X 9=5346
	# samples	6	37
	** MAII score	log2(6/40*10)=0.584962500721156 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(37/5346*10)=-3.85286266172677 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: LRRC59 [Title/Abstract] AND NUP107 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	LRRC59(48469759)-NUP107(69135593), # samples:3
Anticipated loss of major functional domain due to fusion event.	LRRC59-NUP107 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. LRRC59-NUP107 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	NUP107	GO:0006406	mRNA export from nucleus	11684705

Fusion gene breakpoints across LRRC59 (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 NUP107 (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 Gene Sample Information

Fusion gene information from FusionGDB2.0.

Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	BRCA	TCGA-A8-A0A7-01A	LRRC59	chr17	48469758	-	NUP107	chr12	69135592	+
ChimerDB4	BRCA	TCGA-A8-A0A7-01A	LRRC59	chr17	48469759	-	NUP107	chr12	69135593	+
ChimerDB4	BRCA	TCGA-A8-A0A7	LRRC59	chr17	48469758	-	NUP107	chr12	69135592	+

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Fusion ORF Analysis

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)
ENST00000225972	LRRC59	chr17	48469759	-	ENST00000229179	NUP107	chr12	69135593	+	1484	665	164	940	258
ENST00000225972	LRRC59	chr17	48469759	-	ENST00000378905	NUP107	chr12	69135593	+	1162	665	164	940	258
ENST00000225972	LRRC59	chr17	48469759	-	ENST00000539906	NUP107	chr12	69135593	+	1010	665	164	940	258
ENST00000225972	LRRC59	chr17	48469758	-	ENST00000229179	NUP107	chr12	69135592	+	1484	665	164	940	258
ENST00000225972	LRRC59	chr17	48469758	-	ENST00000378905	NUP107	chr12	69135592	+	1162	665	164	940	258
ENST00000225972	LRRC59	chr17	48469758	-	ENST00000539906	NUP107	chr12	69135592	+	1010	665	164	940	258

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
ENST00000225972	ENST00000229179	LRRC59	chr17	48469759	-	NUP107	chr12	69135593	+	0.001438248	0.9985618
ENST00000225972	ENST00000378905	LRRC59	chr17	48469759	-	NUP107	chr12	69135593	+	0.002263747	0.9977362
ENST00000225972	ENST00000539906	LRRC59	chr17	48469759	-	NUP107	chr12	69135593	+	0.001667115	0.9983329
ENST00000225972	ENST00000229179	LRRC59	chr17	48469758	-	NUP107	chr12	69135592	+	0.001438248	0.9985618
ENST00000225972	ENST00000378905	LRRC59	chr17	48469758	-	NUP107	chr12	69135592	+	0.002263747	0.9977362
ENST00000225972	ENST00000539906	LRRC59	chr17	48469758	-	NUP107	chr12	69135592	+	0.001667115	0.9983329

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>49985_49985_1_LRRC59-NUP107_LRRC59_chr17_48469758_ENST00000225972_NUP107_chr12_69135592_ENST00000229179_length(amino acids)=258AA_BP=167
MTSDISAPFTRRNPGAGARSAGVTMTKAGSKGGNLRDKLDGNELDLSLSDLNEVPVKELAALPKATILDLSCNKLTTLPSDFCGLTHLVK
LDLSKNKLQQLPADFGRLVNLQHLDLLNNKLVTLPVSFAQLKNLKWLDLKDNPLDPVLAKVAGDCLDEKQCKQCANKDAKEDHERTHQMV

--------------------------------------------------------------

>49985_49985_2_LRRC59-NUP107_LRRC59_chr17_48469758_ENST00000225972_NUP107_chr12_69135592_ENST00000378905_length(amino acids)=258AA_BP=167
MTSDISAPFTRRNPGAGARSAGVTMTKAGSKGGNLRDKLDGNELDLSLSDLNEVPVKELAALPKATILDLSCNKLTTLPSDFCGLTHLVK
LDLSKNKLQQLPADFGRLVNLQHLDLLNNKLVTLPVSFAQLKNLKWLDLKDNPLDPVLAKVAGDCLDEKQCKQCANKDAKEDHERTHQMV

--------------------------------------------------------------

>49985_49985_3_LRRC59-NUP107_LRRC59_chr17_48469758_ENST00000225972_NUP107_chr12_69135592_ENST00000539906_length(amino acids)=258AA_BP=167
MTSDISAPFTRRNPGAGARSAGVTMTKAGSKGGNLRDKLDGNELDLSLSDLNEVPVKELAALPKATILDLSCNKLTTLPSDFCGLTHLVK
LDLSKNKLQQLPADFGRLVNLQHLDLLNNKLVTLPVSFAQLKNLKWLDLKDNPLDPVLAKVAGDCLDEKQCKQCANKDAKEDHERTHQMV

--------------------------------------------------------------

>49985_49985_4_LRRC59-NUP107_LRRC59_chr17_48469759_ENST00000225972_NUP107_chr12_69135593_ENST00000229179_length(amino acids)=258AA_BP=167
MTSDISAPFTRRNPGAGARSAGVTMTKAGSKGGNLRDKLDGNELDLSLSDLNEVPVKELAALPKATILDLSCNKLTTLPSDFCGLTHLVK
LDLSKNKLQQLPADFGRLVNLQHLDLLNNKLVTLPVSFAQLKNLKWLDLKDNPLDPVLAKVAGDCLDEKQCKQCANKDAKEDHERTHQMV

--------------------------------------------------------------

>49985_49985_5_LRRC59-NUP107_LRRC59_chr17_48469759_ENST00000225972_NUP107_chr12_69135593_ENST00000378905_length(amino acids)=258AA_BP=167
MTSDISAPFTRRNPGAGARSAGVTMTKAGSKGGNLRDKLDGNELDLSLSDLNEVPVKELAALPKATILDLSCNKLTTLPSDFCGLTHLVK
LDLSKNKLQQLPADFGRLVNLQHLDLLNNKLVTLPVSFAQLKNLKWLDLKDNPLDPVLAKVAGDCLDEKQCKQCANKDAKEDHERTHQMV

--------------------------------------------------------------

>49985_49985_6_LRRC59-NUP107_LRRC59_chr17_48469759_ENST00000225972_NUP107_chr12_69135593_ENST00000539906_length(amino acids)=258AA_BP=167
MTSDISAPFTRRNPGAGARSAGVTMTKAGSKGGNLRDKLDGNELDLSLSDLNEVPVKELAALPKATILDLSCNKLTTLPSDFCGLTHLVK
LDLSKNKLQQLPADFGRLVNLQHLDLLNNKLVTLPVSFAQLKNLKWLDLKDNPLDPVLAKVAGDCLDEKQCKQCANKDAKEDHERTHQMV

--------------------------------------------------------------

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:48469759/chr12:69135593)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
LRRC59 Q96AG4	NUP107 P57740
FUNCTION: Required for nuclear import of FGF1, but not that of FGF2. Might regulate nuclear import of exogenous FGF1 by facilitating interaction with the nuclear import machinery and by transporting cytosolic FGF1 to, and possibly through, the nuclear pores. {ECO:0000269\|PubMed:22321063}.	FUNCTION: Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance (PubMed:12552102, PubMed:15229283, PubMed:30179222). Required for the assembly of peripheral proteins into the NPC (PubMed:15229283, PubMed:12552102). May anchor NUP62 to the NPC (PubMed:15229283). Involved in nephrogenesis (PubMed:30179222). {ECO:0000269\|PubMed:12552102, ECO:0000269\|PubMed:15229283, ECO:0000269\|PubMed:30179222}.

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, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

LRRC59

chr17:48469758

chr12:69135592

ENST00000225972

109_128

143.0

308.0

Repeat

Note=LRR 5

Hgene

LRRC59

chr17:48469758

chr12:69135592

ENST00000225972

10_31

143.0

308.0

Repeat

Note=LRR 1

Hgene

LRRC59

chr17:48469758

chr12:69135592

ENST00000225972

40_62

143.0

308.0

Repeat

Note=LRR 2

Hgene

LRRC59

chr17:48469758

chr12:69135592

ENST00000225972

63_84

143.0

308.0

Repeat

Note=LRR 3

Hgene

LRRC59

chr17:48469758

chr12:69135592

ENST00000225972

86_107

143.0

308.0

Repeat

Note=LRR 4

Hgene

LRRC59

chr17:48469759

chr12:69135593

ENST00000225972

109_128

143.0

308.0

Repeat

Note=LRR 5

Hgene

LRRC59

chr17:48469759

chr12:69135593

ENST00000225972

10_31

143.0

308.0

Repeat

Note=LRR 1

Hgene

LRRC59

chr17:48469759

chr12:69135593

ENST00000225972

40_62

143.0

308.0

Repeat

Note=LRR 2

Hgene

LRRC59

chr17:48469759

chr12:69135593

ENST00000225972

63_84

143.0

308.0

Repeat

Note=LRR 3

Hgene

LRRC59

chr17:48469759

chr12:69135593

ENST00000225972

86_107

143.0

308.0

Repeat

Note=LRR 4

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

LRRC59

chr17:48469758

chr12:69135592

ENST00000225972

148_216

143.0

308.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

LRRC59

chr17:48469759

chr12:69135593

ENST00000225972

148_216

143.0

308.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

LRRC59

chr17:48469758

chr12:69135592

ENST00000225972

248_256

143.0

308.0

Compositional bias

Note=Poly-Leu

Hgene

LRRC59

chr17:48469759

chr12:69135593

ENST00000225972

248_256

143.0

308.0

Compositional bias

Note=Poly-Leu

Hgene

LRRC59

chr17:48469758

chr12:69135592

ENST00000225972

1_244

143.0

308.0

Topological domain

Cytoplasmic

Hgene

LRRC59

chr17:48469758

chr12:69135592

ENST00000225972

266_307

143.0

308.0

Topological domain

Lumenal

Hgene

LRRC59

chr17:48469759

chr12:69135593

ENST00000225972

1_244

143.0

308.0

Topological domain

Cytoplasmic

Hgene

LRRC59

chr17:48469759

chr12:69135593

ENST00000225972

266_307

143.0

308.0

Topological domain

Lumenal

Hgene

LRRC59

chr17:48469758

chr12:69135592

ENST00000225972

245_265

143.0

308.0

Transmembrane

Helical

Hgene

LRRC59

chr17:48469759

chr12:69135593

ENST00000225972

245_265

143.0

308.0

Transmembrane

Helical

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>434_LRRC59_48469758_NUP107_69135592_ranked_0.pdb	LRRC59	48469758	48469758	ENST00000539906	NUP107	chr12	69135592	+	MTSDISAPFTRRNPGAGARSAGVTMTKAGSKGGNLRDKLDGNELDLSLSDLNEVPVKELAALPKATILDLSCNKLTTLPSDFCGLTHLVK LDLSKNKLQQLPADFGRLVNLQHLDLLNNKLVTLPVSFAQLKNLKWLDLKDNPLDPVLAKVAGDCLDEKQCKQCANKDAKEDHERTHQMV	258

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

LRRC59_pLDDT.png

NUP107_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

NUP107

SEH1L, NUP133, NUP85, NUP160, NUP43, NUP37, SEC13, TPR, NUP214, KPNB1, Nup107, Nup98, SIRT7, NUP98, WRNIP1, CUL3, CENPF, NUP153, TP53BP1, PNPT1, EIF4B, CORO1B, MYL1, C1QBP, CPSF6, VCP, PYCARD, CUL7, OBSL1, SUZ12, EED, PNKD, NTRK1, IFI16, SYNE1, APC, PRKDC, RRP1B, NALCN, CD1E, ACTBL2, HSP90AB1, XPO1, SENP1, SENP2, AHCTF1, RANGAP1, H2AFV, NUP50, RANBP2, B9D2, ACLY, RCC1, GLE1, ITPR2, KPNA4, NUP88, RAN, UBE2I, SUMO1, AAAS, RAE1, NUP155, NUP93, NUPL1, WDR1, NXF1, IPO7, NUPL2, NUP205, NUP210, NUP188, NUP62, NXT1, SEC61A1, NUP54, TMEM214, SMPD4, NDC1, KRAS, IP6K3, TMEM209, NUP35, RPUSD3, RGPD8, POM121C, Ranbp2, Ube2i, Rcc1, Kifc1, Nup155, Nup214, FOXA3, FOXI2, FOXK2, FOXL1, FOXP3, FOXQ1, CDC5L, ZNF746, DUSP13, SPAST, UXS1, SIGLECL1, CD70, RAF1, PDHA1, TRIM25, BRCA1, EGLN3, TGFB1, NKX2-1, RNF4, CDC34, BPLF1, EZH2, DCPS, MYC, CDK9, CANX, EZR, LMNA, TOMM20, MGST3, PTRH2, KIAA1429, HIST1H4A, Dppa3, BIRC3, LMBR1L, PLEKHA4, GAPDH, M, nsp16, nsp4, nsp6, ORF6, MAU2, LRRC31, CIT, KIF14, PRC1, TRIM66, FKBP8, PTPN1, RHOT2, SLC25A46, SUMO2, NUPR1, CIC, LGALS9, DYRK1A, BKRF1, DNAJC1, ANAPC2, COX8A, DERL1, EMD, KRT8, LMNB1, LRRC59, RPN1, SEC61B, STIM1, SYNE3, TMPO, NAA40, VPS33A, RGPD1, EFNA4, COMTD1, SLFN11, FBXW7, FBXO32, RCHY1, SIRT6, GLI3,

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
LRRC59
NUP107

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to LRRC59-NUP107

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 LRRC59-NUP107

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	NUP107	C4225228	NEPHROTIC SYNDROME, TYPE 11	2	CTD_human;GENOMICS_ENGLAND;UNIPROT
Tgene	NUP107	C0018051	Gonadal Dysgenesis	1	GENOMICS_ENGLAND
Tgene	NUP107	C0685837	Pure Gonadal Dysgenesis, 46, XX	1	ORPHANET
Tgene	NUP107	C0795949	Galloway Mowat syndrome	1	ORPHANET
Tgene	NUP107	C0949595	Gonadal Dysgenesis, 46,XX	1	ORPHANET
Tgene	NUP107	C1868672	NEPHROTIC SYNDROME, STEROID-RESISTANT, AUTOSOMAL RECESSIVE	1	ORPHANET
Tgene	NUP107	C4748084	OVARIAN DYSGENESIS 6	1	UNIPROT