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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:NIPBL-C5orf42

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: NIPBL-C5orf42
	FusionPDB ID: 59192
	FusionGDB2.0 ID: 59192
		Hgene	Tgene
	Gene symbol	NIPBL	C5orf42
	Gene ID	25836	65250
	Gene name	NIPBL cohesin loading factor	ciliogenesis and planar polarity effector 1
	Synonyms	CDLS\|CDLS1\|IDN3\|IDN3-B\|Scc2	C5orf42\|Hug\|JBTS17\|OFD6
	Cytomap	5p13.2	5p13.2
	Type of gene	protein-coding	protein-coding
	Description	nipped-B-like proteinNipped-B homologSCC2 homologdelanginsister chromatid cohesion 2 homolog	ciliogenesis and planar polarity effector 1protein JBTS17transmembrane protein ENSP00000382582
	Modification date	20200313	20200313
	UniProtAcc	Q6KC79	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000504430, ENST00000282516, ENST00000448238,	ENST00000274258, ENST00000425232, ENST00000508244, ENST00000512288,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	26 X 13 X 16=5408	7 X 8 X 5=280
	# samples	43	7
	** MAII score	log2(43/5408*10)=-3.65268658669272 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/280*10)=-2 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: NIPBL [Title/Abstract] AND C5orf42 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	NIPBL(36962376)-C5orf42(37115151), # samples:4 C5orf42(37138821)-NIPBL(36995723), # samples:1
Anticipated loss of major functional domain due to fusion event.	NIPBL-C5orf42 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. NIPBL-C5orf42 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. C5orf42-NIPBL seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF. C5orf42-NIPBL seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
Hgene	NIPBL	GO:0000122	negative regulation of transcription by RNA polymerase II	18854353
Hgene	NIPBL	GO:0031065	positive regulation of histone deacetylation	18854353
Hgene	NIPBL	GO:0045892	negative regulation of transcription, DNA-templated	18854353
Hgene	NIPBL	GO:0071921	cohesin loading	22628566

Fusion gene breakpoints across NIPBL (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 C5orf42 (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	ESCA	TCGA-L5-A8NI-01A	NIPBL	chr5	36962376	-	C5orf42	chr5	37115151	-
ChimerDB4	ESCA	TCGA-L5-A8NI	NIPBL	chr5	36962376	+	C5orf42	chr5	37115151	-

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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)
ENST00000282516	NIPBL	chr5	36962376	+	ENST00000508244	C5orf42	chr5	37115151	-	2929	1109	499	1554	351
ENST00000282516	NIPBL	chr5	36962376	+	ENST00000274258	C5orf42	chr5	37115151	-	2929	1109	499	1554	351
ENST00000282516	NIPBL	chr5	36962376	+	ENST00000425232	C5orf42	chr5	37115151	-	2929	1109	499	1554	351
ENST00000448238	NIPBL	chr5	36962376	+	ENST00000508244	C5orf42	chr5	37115151	-	2898	1078	468	1523	351
ENST00000448238	NIPBL	chr5	36962376	+	ENST00000274258	C5orf42	chr5	37115151	-	2898	1078	468	1523	351
ENST00000448238	NIPBL	chr5	36962376	+	ENST00000425232	C5orf42	chr5	37115151	-	2898	1078	468	1523	351

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
ENST00000282516	ENST00000508244	NIPBL	chr5	36962376	+	C5orf42	chr5	37115151	-	0.000860835	0.9991392
ENST00000282516	ENST00000274258	NIPBL	chr5	36962376	+	C5orf42	chr5	37115151	-	0.000860835	0.9991392
ENST00000282516	ENST00000425232	NIPBL	chr5	36962376	+	C5orf42	chr5	37115151	-	0.000860835	0.9991392
ENST00000448238	ENST00000508244	NIPBL	chr5	36962376	+	C5orf42	chr5	37115151	-	0.000873012	0.999127
ENST00000448238	ENST00000274258	NIPBL	chr5	36962376	+	C5orf42	chr5	37115151	-	0.000873012	0.999127
ENST00000448238	ENST00000425232	NIPBL	chr5	36962376	+	C5orf42	chr5	37115151	-	0.000873012	0.999127

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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

>59192_59192_1_NIPBL-C5orf42_NIPBL_chr5_36962376_ENST00000282516_C5orf42_chr5_37115151_ENST00000274258_length(amino acids)=351AA_BP=203
MNGDMPHVPITTLAGIASLTDLLNQLPLPSPLPATTTKSLLFNARIAEEVNCLLACRDDNLVSQLVHSLNQVSTDHIELKDNLGSDDPEG
DIPVLLQAVLARSPNVFREKSMQNRYVQSGMMMSQYKLSQNSMHSSPASSNYQQTTISHSPSSRFVPPQTSSGNRFMPQQNSPVPSPYAP
QSPAGYMPYSHPSSYTTHPQMQQGTATFTIQKKAGGAKAAVRKATQSPVTFQKGSNAPCHSLQHTKKHGSAGLAPQTKQVCVEYEREETV

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

>59192_59192_2_NIPBL-C5orf42_NIPBL_chr5_36962376_ENST00000282516_C5orf42_chr5_37115151_ENST00000425232_length(amino acids)=351AA_BP=203
MNGDMPHVPITTLAGIASLTDLLNQLPLPSPLPATTTKSLLFNARIAEEVNCLLACRDDNLVSQLVHSLNQVSTDHIELKDNLGSDDPEG
DIPVLLQAVLARSPNVFREKSMQNRYVQSGMMMSQYKLSQNSMHSSPASSNYQQTTISHSPSSRFVPPQTSSGNRFMPQQNSPVPSPYAP
QSPAGYMPYSHPSSYTTHPQMQQGTATFTIQKKAGGAKAAVRKATQSPVTFQKGSNAPCHSLQHTKKHGSAGLAPQTKQVCVEYEREETV

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

>59192_59192_3_NIPBL-C5orf42_NIPBL_chr5_36962376_ENST00000282516_C5orf42_chr5_37115151_ENST00000508244_length(amino acids)=351AA_BP=203
MNGDMPHVPITTLAGIASLTDLLNQLPLPSPLPATTTKSLLFNARIAEEVNCLLACRDDNLVSQLVHSLNQVSTDHIELKDNLGSDDPEG
DIPVLLQAVLARSPNVFREKSMQNRYVQSGMMMSQYKLSQNSMHSSPASSNYQQTTISHSPSSRFVPPQTSSGNRFMPQQNSPVPSPYAP
QSPAGYMPYSHPSSYTTHPQMQQGTATFTIQKKAGGAKAAVRKATQSPVTFQKGSNAPCHSLQHTKKHGSAGLAPQTKQVCVEYEREETV

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

>59192_59192_4_NIPBL-C5orf42_NIPBL_chr5_36962376_ENST00000448238_C5orf42_chr5_37115151_ENST00000274258_length(amino acids)=351AA_BP=203
MNGDMPHVPITTLAGIASLTDLLNQLPLPSPLPATTTKSLLFNARIAEEVNCLLACRDDNLVSQLVHSLNQVSTDHIELKDNLGSDDPEG
DIPVLLQAVLARSPNVFREKSMQNRYVQSGMMMSQYKLSQNSMHSSPASSNYQQTTISHSPSSRFVPPQTSSGNRFMPQQNSPVPSPYAP
QSPAGYMPYSHPSSYTTHPQMQQGTATFTIQKKAGGAKAAVRKATQSPVTFQKGSNAPCHSLQHTKKHGSAGLAPQTKQVCVEYEREETV

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

>59192_59192_5_NIPBL-C5orf42_NIPBL_chr5_36962376_ENST00000448238_C5orf42_chr5_37115151_ENST00000425232_length(amino acids)=351AA_BP=203
MNGDMPHVPITTLAGIASLTDLLNQLPLPSPLPATTTKSLLFNARIAEEVNCLLACRDDNLVSQLVHSLNQVSTDHIELKDNLGSDDPEG
DIPVLLQAVLARSPNVFREKSMQNRYVQSGMMMSQYKLSQNSMHSSPASSNYQQTTISHSPSSRFVPPQTSSGNRFMPQQNSPVPSPYAP
QSPAGYMPYSHPSSYTTHPQMQQGTATFTIQKKAGGAKAAVRKATQSPVTFQKGSNAPCHSLQHTKKHGSAGLAPQTKQVCVEYEREETV

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

>59192_59192_6_NIPBL-C5orf42_NIPBL_chr5_36962376_ENST00000448238_C5orf42_chr5_37115151_ENST00000508244_length(amino acids)=351AA_BP=203
MNGDMPHVPITTLAGIASLTDLLNQLPLPSPLPATTTKSLLFNARIAEEVNCLLACRDDNLVSQLVHSLNQVSTDHIELKDNLGSDDPEG
DIPVLLQAVLARSPNVFREKSMQNRYVQSGMMMSQYKLSQNSMHSSPASSNYQQTTISHSPSSRFVPPQTSSGNRFMPQQNSPVPSPYAP
QSPAGYMPYSHPSSYTTHPQMQQGTATFTIQKKAGGAKAAVRKATQSPVTFQKGSNAPCHSLQHTKKHGSAGLAPQTKQVCVEYEREETV

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

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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/chr5:36962376/chr5:37115151)
- 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
NIPBL Q6KC79	.
FUNCTION: Plays an important role in the loading of the cohesin complex on to DNA. Forms a heterodimeric complex (also known as cohesin loading complex) with MAU2/SCC4 which mediates the loading of the cohesin complex onto chromatin (PubMed:22628566, PubMed:28914604). Plays a role in cohesin loading at sites of DNA damage. Its recruitment to double-strand breaks (DSBs) sites occurs in a CBX3-, RNF8- and RNF168-dependent manner whereas its recruitment to UV irradiation-induced DNA damage sites occurs in a ATM-, ATR-, RNF8- and RNF168-dependent manner (PubMed:28167679). Along with ZNF609, promotes cortical neuron migration during brain development by regulating the transcription of crucial genes in this process. Preferentially binds promoters containing paused RNA polymerase II. Up-regulates the expression of SEMA3A, NRP1, PLXND1 and GABBR2 genes, among others (By similarity). {ECO:0000250\|UniProtKB:Q6KCD5, ECO:0000269\|PubMed:22628566, ECO:0000269\|PubMed:28167679, ECO:0000269\|PubMed:28914604}.	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

- 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

NIPBL

chr5:36962376

chr5:37115151

ENST00000282516

418_462

203.33333333333334

2805.0

Compositional bias

Note=Gln-rich

Hgene

NIPBL

chr5:36962376

chr5:37115151

ENST00000448238

418_462

203.33333333333334

2698.0

Compositional bias

Note=Gln-rich

Hgene

NIPBL

chr5:36962376

chr5:37115151

ENST00000282516

996_1009

203.33333333333334

2805.0

Motif

PxVxL motif

Hgene

NIPBL

chr5:36962376

chr5:37115151

ENST00000448238

996_1009

203.33333333333334

2698.0

Motif

PxVxL motif

Hgene

NIPBL

chr5:36962376

chr5:37115151

ENST00000282516

1767_1805

203.33333333333334

2805.0

Repeat

Note=HEAT 1

Hgene

NIPBL

chr5:36962376

chr5:37115151

ENST00000282516

1843_1881

203.33333333333334

2805.0

Repeat

Note=HEAT 2

Hgene

NIPBL

chr5:36962376

chr5:37115151

ENST00000282516

1945_1984

203.33333333333334

2805.0

Repeat

Note=HEAT 3

Hgene

NIPBL

chr5:36962376

chr5:37115151

ENST00000282516

2227_2267

203.33333333333334

2805.0

Repeat

Note=HEAT 4

Hgene

NIPBL

chr5:36962376

chr5:37115151

ENST00000282516

2313_2351

203.33333333333334

2805.0

Repeat

Note=HEAT 5

Hgene

NIPBL

chr5:36962376

chr5:37115151

ENST00000448238

1767_1805

203.33333333333334

2698.0

Repeat

Note=HEAT 1

Hgene

NIPBL

chr5:36962376

chr5:37115151

ENST00000448238

1843_1881

203.33333333333334

2698.0

Repeat

Note=HEAT 2

Hgene

NIPBL

chr5:36962376

chr5:37115151

ENST00000448238

1945_1984

203.33333333333334

2698.0

Repeat

Note=HEAT 3

Hgene

NIPBL

chr5:36962376

chr5:37115151

ENST00000448238

2227_2267

203.33333333333334

2698.0

Repeat

Note=HEAT 4

Hgene

NIPBL

chr5:36962376

chr5:37115151

ENST00000448238

2313_2351

203.33333333333334

2698.0

Repeat

Note=HEAT 5

Tgene

C5orf42

chr5:36962376

chr5:37115151

ENST00000425232

2457_2487

3049.3333333333335

3198.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

C5orf42

chr5:36962376

chr5:37115151

ENST00000425232

2691_2724

3049.3333333333335

3198.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

C5orf42

chr5:36962376

chr5:37115151

ENST00000508244

2457_2487

3049.3333333333335

3198.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

C5orf42

chr5:36962376

chr5:37115151

ENST00000508244

2691_2724

3049.3333333333335

3198.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

C5orf42

chr5:36962376

chr5:37115151

ENST00000425232

592_612

3049.3333333333335

3198.0

Transmembrane

Helical

Tgene

C5orf42

chr5:36962376

chr5:37115151

ENST00000425232

631_651

3049.3333333333335

3198.0

Transmembrane

Helical

Tgene

C5orf42

chr5:36962376

chr5:37115151

ENST00000508244

592_612

3049.3333333333335

3198.0

Transmembrane

Helical

Tgene

C5orf42

chr5:36962376

chr5:37115151

ENST00000508244

631_651

3049.3333333333335

3198.0

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 >>>681_NIPBL_36962376_C5orf42_37115151_ranked_0.pdb	NIPBL	36962376	36962376	ENST00000425232	C5orf42	chr5	37115151	-	MNGDMPHVPITTLAGIASLTDLLNQLPLPSPLPATTTKSLLFNARIAEEVNCLLACRDDNLVSQLVHSLNQVSTDHIELKDNLGSDDPEG DIPVLLQAVLARSPNVFREKSMQNRYVQSGMMMSQYKLSQNSMHSSPASSNYQQTTISHSPSSRFVPPQTSSGNRFMPQQNSPVPSPYAP QSPAGYMPYSHPSSYTTHPQMQQGTATFTIQKKAGGAKAAVRKATQSPVTFQKGSNAPCHSLQHTKKHGSAGLAPQTKQVCVEYEREETV	351

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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.

NIPBL_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
NIPBL
C5orf42

- 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 NIPBL-C5orf42

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 NIPBL-C5orf42

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