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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:NT5C2-LRIT1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: NT5C2-LRIT1
	FusionPDB ID: 60606
	FusionGDB2.0 ID: 60606
		Hgene	Tgene
	Gene symbol	NT5C2	LRIT1
	Gene ID	22978	26103
	Gene name	5'-nucleotidase, cytosolic II	leucine rich repeat, Ig-like and transmembrane domains 1
	Synonyms	GMP\|NT5B\|PNT5\|SPG45\|SPG65\|cN-II	FIGLER9\|LRRC21\|PAL
	Cytomap	10q24.32-q24.33	10q23.1
	Type of gene	protein-coding	protein-coding
	Description	cytosolic purine 5'-nucleotidase5'-nucleotidase (purine), cytosolic type BIMP-specific 5'-NTepididymis secretory sperm binding proteinspastic paraplegia 45 (autosomal recessive)	leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 1fibronectin type III, immunoglobulin and leucine rich repeat domains 9leucine rich repeat containing 21leucine-rich repeat, immunoglobulin-like and transmembra
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000369857, ENST00000343289, ENST00000404739, ENST00000423468, ENST00000470299,	ENST00000372105,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	13 X 8 X 9=936	1 X 1 X 1=1
	# samples	17	1
	** MAII score	log2(17/936*10)=-2.4609737834457 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(1/1*10)=3.32192809488736
Context (manual curation of fusion genes in FusionPDB)	PubMed: NT5C2 [Title/Abstract] AND LRIT1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	NT5C2(104899163)-LRIT1(85994134), # samples:3
Anticipated loss of major functional domain due to fusion event.	NT5C2-LRIT1 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. NT5C2-LRIT1 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. NT5C2-LRIT1 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. NT5C2-LRIT1 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. NT5C2-LRIT1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. NT5C2-LRIT1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. NT5C2-LRIT1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted 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

Fusion gene breakpoints across NT5C2 (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 LRIT1 (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	MESO	TCGA-ZN-A9VQ-01A	NT5C2	chr10	104899163	-	LRIT1	chr10	85994134	-
ChimerDB4	MESO	TCGA-ZN-A9VQ	NT5C2	chr10	104899163	-	LRIT1	chr10	85994134	-

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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)
ENST00000404739	NT5C2	chr10	104899163	-	ENST00000372105	LRIT1	chr10	85994134	-	1816	199	24	1481	485
ENST00000423468	NT5C2	chr10	104899163	-	ENST00000372105	LRIT1	chr10	85994134	-	2028	411	275	1693	472

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
ENST00000404739	ENST00000372105	NT5C2	chr10	104899163	-	LRIT1	chr10	85994134	-	0.007797603	0.9922024
ENST00000423468	ENST00000372105	NT5C2	chr10	104899163	-	LRIT1	chr10	85994134	-	0.004998043	0.995002

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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

>60606_60606_1_NT5C2-LRIT1_NT5C2_chr10_104899163_ENST00000404739_LRIT1_chr10_85994134_ENST00000372105_length(amino acids)=485AA_BP=55
MSTSWSDRLQNAADMPANMDKHALKKYRREAYHRVFVNRSLAMEKIKCFGFDMDYTLAGLQDNPWACDCRLYDLVHLLDGWAPNLAFIET
ELRCASPRSLAGVAFSQLELRKCQGPELHPGVASIRSLLGGTALLRCGATGVPGPEMSWRRANGRPLNGTVHQEVSSDGTSWTLLGLPAV
SHLDSGDYICQAKNFLGASETVISLIVTEPPTSTEHSGSPGALWARTGGGGEAAAYNNKLVARHVPQIPKPAVLATGPSVPSTKEELTLE
HFQMDALGELSDGRAGPSEARMVRSVKVVGDTYHSVSLVWKAPQAKNTTAFSVLYAVFGQHSMRRVIVQPGKTRVTITGLLPKTKYVACV
CVQGLVPRKEQCVIFSTNEVVDAENTQQLINVVVISVAIVIALPLTLLVCCSALQKRCRKCFNKDSTEATVTYVNLERLGYSEDGLEELS

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

>60606_60606_2_NT5C2-LRIT1_NT5C2_chr10_104899163_ENST00000423468_LRIT1_chr10_85994134_ENST00000372105_length(amino acids)=472AA_BP=42
MFVDPVFSSRGSRSLRMSKEGVFVNRSLAMEKIKCFGFDMDYTLAGLQDNPWACDCRLYDLVHLLDGWAPNLAFIETELRCASPRSLAGV
AFSQLELRKCQGPELHPGVASIRSLLGGTALLRCGATGVPGPEMSWRRANGRPLNGTVHQEVSSDGTSWTLLGLPAVSHLDSGDYICQAK
NFLGASETVISLIVTEPPTSTEHSGSPGALWARTGGGGEAAAYNNKLVARHVPQIPKPAVLATGPSVPSTKEELTLEHFQMDALGELSDG
RAGPSEARMVRSVKVVGDTYHSVSLVWKAPQAKNTTAFSVLYAVFGQHSMRRVIVQPGKTRVTITGLLPKTKYVACVCVQGLVPRKEQCV
IFSTNEVVDAENTQQLINVVVISVAIVIALPLTLLVCCSALQKRCRKCFNKDSTEATVTYVNLERLGYSEDGLEELSRHSVSEADRLLSA

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

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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/chr10:104899163/chr10:85994134)
- 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
.	.
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.	FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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

Tgene

LRIT1

chr10:104899163

chr10:85994134

ENST00000372105

201_253

196.33333333333334

624.0

Domain

Note=LRRCT

Tgene

LRIT1

chr10:104899163

chr10:85994134

ENST00000372105

266_335

196.33333333333334

624.0

Domain

Note=Ig-like C2-type

Tgene

LRIT1

chr10:104899163

chr10:85994134

ENST00000372105

430_518

196.33333333333334

624.0

Domain

Fibronectin type-III

Tgene

LRIT1

chr10:104899163

chr10:85994134

ENST00000372105

571_594

196.33333333333334

624.0

Repeat

LRR 6

Tgene

LRIT1

chr10:104899163

chr10:85994134

ENST00000372105

548_623

196.33333333333334

624.0

Topological domain

Cytoplasmic

Tgene

LRIT1

chr10:104899163

chr10:85994134

ENST00000372105

527_547

196.33333333333334

624.0

Transmembrane

Helical

- 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

NT5C2

chr10:104899163

chr10:85994134

ENST00000343289

549_561

58.333333333333336

562.0

Compositional bias

Note=Asp/Glu-rich (acidic)

Hgene

NT5C2

chr10:104899163

chr10:85994134

ENST00000404739

549_561

58.333333333333336

562.0

Compositional bias

Note=Asp/Glu-rich (acidic)

Hgene

NT5C2

chr10:104899163

chr10:85994134

ENST00000343289

202_210

58.333333333333336

562.0

Region

Substrate binding

Hgene

NT5C2

chr10:104899163

chr10:85994134

ENST00000404739

202_210

58.333333333333336

562.0

Region

Substrate binding

Tgene

LRIT1

chr10:104899163

chr10:85994134

ENST00000372105

22_59

196.33333333333334

624.0

Domain

Note=LRRNT

Tgene

LRIT1

chr10:104899163

chr10:85994134

ENST00000372105

108_129

196.33333333333334

624.0

Repeat

Note=LRR 3

Tgene

LRIT1

chr10:104899163

chr10:85994134

ENST00000372105

132_153

196.33333333333334

624.0

Repeat

Note=LRR 4

Tgene

LRIT1

chr10:104899163

chr10:85994134

ENST00000372105

156_177

196.33333333333334

624.0

Repeat

Note=LRR 5

Tgene

LRIT1

chr10:104899163

chr10:85994134

ENST00000372105

60_81

196.33333333333334

624.0

Repeat

Note=LRR 1

Tgene

LRIT1

chr10:104899163

chr10:85994134

ENST00000372105

84_105

196.33333333333334

624.0

Repeat

Note=LRR 2

Tgene

LRIT1

chr10:104899163

chr10:85994134

ENST00000372105

22_526

196.33333333333334

624.0

Topological domain

Lumenal

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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 >>>1019_NT5C2_104899163_LRIT1_85994134_1019_NT5C2_104899163_LRIT1_85994134_ranked_0.pdb	NT5C2	104899163	104899163	ENST00000372105	LRIT1	chr10	85994134	-	MSTSWSDRLQNAADMPANMDKHALKKYRREAYHRVFVNRSLAMEKIKCFGFDMDYTLAGLQDNPWACDCRLYDLVHLLDGWAPNLAFIET ELRCASPRSLAGVAFSQLELRKCQGPELHPGVASIRSLLGGTALLRCGATGVPGPEMSWRRANGRPLNGTVHQEVSSDGTSWTLLGLPAV SHLDSGDYICQAKNFLGASETVISLIVTEPPTSTEHSGSPGALWARTGGGGEAAAYNNKLVARHVPQIPKPAVLATGPSVPSTKEELTLE HFQMDALGELSDGRAGPSEARMVRSVKVVGDTYHSVSLVWKAPQAKNTTAFSVLYAVFGQHSMRRVIVQPGKTRVTITGLLPKTKYVACV CVQGLVPRKEQCVIFSTNEVVDAENTQQLINVVVISVAIVIALPLTLLVCCSALQKRCRKCFNKDSTEATVTYVNLERLGYSEDGLEELS	485

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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.

NT5C2_pLDDT.png

LRIT1_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

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
NT5C2
LRIT1

- 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 NT5C2-LRIT1

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 NT5C2-LRIT1

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