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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:C9orf85-FXN

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: C9orf85-FXN
	FusionPDB ID: 12149
	FusionGDB2.0 ID: 12149
		Hgene	Tgene
	Gene symbol	C9orf85	FXN
	Gene ID	138241	2395
	Gene name	chromosome 9 open reading frame 85	frataxin
	Synonyms	-	CyaY\|FA\|FARR\|FRDA\|X25
	Cytomap	9q21.13	9q21.11
	Type of gene	protein-coding	protein-coding
	Description	uncharacterized protein C9orf85	frataxin, mitochondrialFriedreich ataxia protein
	Modification date	20200313	20200315
	UniProtAcc	Q96MD7	Q16595
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000334731, ENST00000377031, ENST00000486911,	ENST00000377270, ENST00000396364, ENST00000396366, ENST00000498653,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 5 X 3=105	8 X 8 X 7=448
	# samples	7	10
	** MAII score	log2(7/105*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/448*10)=-2.16349873228288 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: C9orf85 [Title/Abstract] AND FXN [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	C9orf85(74526752)-FXN(71679854), # samples:2
Anticipated loss of major functional domain due to fusion event.	C9orf85-FXN 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. C9orf85-FXN 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	FXN	GO:0010722	regulation of ferrochelatase activity	15123683
Tgene	FXN	GO:0016226	iron-sulfur cluster assembly	29491838
Tgene	FXN	GO:0016540	protein autoprocessing	12785837
Tgene	FXN	GO:0018283	iron incorporation into metallo-sulfur cluster	12785837
Tgene	FXN	GO:0051349	positive regulation of lyase activity	20053667
Tgene	FXN	GO:0070301	cellular response to hydrogen peroxide	15641778

Fusion gene breakpoints across C9orf85 (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 FXN (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	SKCM	TCGA-FS-A1ZP-06A	C9orf85	chr9	74526752	+	FXN	chr9	71679854	+

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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)
ENST00000334731	C9orf85	chr9	74526752	+	ENST00000396364	FXN	chr9	71679854	+	668	292	285	1	95
ENST00000334731	C9orf85	chr9	74526752	+	ENST00000377270	FXN	chr9	71679854	+	1992	292	178	540	120
ENST00000334731	C9orf85	chr9	74526752	+	ENST00000396366	FXN	chr9	71679854	+	809	292	178	498	106
ENST00000334731	C9orf85	chr9	74526752	+	ENST00000498653	FXN	chr9	71679854	+	884	292	178	540	120
ENST00000377031	C9orf85	chr9	74526752	+	ENST00000396364	FXN	chr9	71679854	+	668	292	285	1	95
ENST00000377031	C9orf85	chr9	74526752	+	ENST00000377270	FXN	chr9	71679854	+	1992	292	178	540	120
ENST00000377031	C9orf85	chr9	74526752	+	ENST00000396366	FXN	chr9	71679854	+	809	292	178	498	106
ENST00000377031	C9orf85	chr9	74526752	+	ENST00000498653	FXN	chr9	71679854	+	884	292	178	540	120
ENST00000486911	C9orf85	chr9	74526752	+	ENST00000396364	FXN	chr9	71679854	+	552	176	62	307	81
ENST00000486911	C9orf85	chr9	74526752	+	ENST00000377270	FXN	chr9	71679854	+	1876	176	62	424	120
ENST00000486911	C9orf85	chr9	74526752	+	ENST00000396366	FXN	chr9	71679854	+	693	176	62	382	106
ENST00000486911	C9orf85	chr9	74526752	+	ENST00000498653	FXN	chr9	71679854	+	768	176	62	424	120

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
ENST00000334731	ENST00000396364	C9orf85	chr9	74526752	+	FXN	chr9	71679854	+	0.5241358	0.47586417
ENST00000334731	ENST00000377270	C9orf85	chr9	74526752	+	FXN	chr9	71679854	+	0.0530824	0.94691765
ENST00000334731	ENST00000396366	C9orf85	chr9	74526752	+	FXN	chr9	71679854	+	0.08747691	0.91252315
ENST00000334731	ENST00000498653	C9orf85	chr9	74526752	+	FXN	chr9	71679854	+	0.023234805	0.9767652
ENST00000377031	ENST00000396364	C9orf85	chr9	74526752	+	FXN	chr9	71679854	+	0.5241358	0.47586417
ENST00000377031	ENST00000377270	C9orf85	chr9	74526752	+	FXN	chr9	71679854	+	0.0530824	0.94691765
ENST00000377031	ENST00000396366	C9orf85	chr9	74526752	+	FXN	chr9	71679854	+	0.08747691	0.91252315
ENST00000377031	ENST00000498653	C9orf85	chr9	74526752	+	FXN	chr9	71679854	+	0.023234805	0.9767652
ENST00000486911	ENST00000396364	C9orf85	chr9	74526752	+	FXN	chr9	71679854	+	0.23994747	0.76005256
ENST00000486911	ENST00000377270	C9orf85	chr9	74526752	+	FXN	chr9	71679854	+	0.028759072	0.97124094
ENST00000486911	ENST00000396366	C9orf85	chr9	74526752	+	FXN	chr9	71679854	+	0.054709453	0.9452906
ENST00000486911	ENST00000498653	C9orf85	chr9	74526752	+	FXN	chr9	71679854	+	0.015120322	0.9848797

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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

>12149_12149_1_C9orf85-FXN_C9orf85_chr9_74526752_ENST00000334731_FXN_chr9_71679854_ENST00000377270_length(amino acids)=120AA_BP=38
MISAMSSQKGNVARSRPQKHQNTFSFKNDKFDKSVQTKSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGV

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

>12149_12149_2_C9orf85-FXN_C9orf85_chr9_74526752_ENST00000334731_FXN_chr9_71679854_ENST00000396364_length(amino acids)=95AA_BP=
MHTFIELVIFEAKRILVLLRSGTSHVAFLGAHRRNQSHPSPGAGKRMRGKKTNELLPGIDASVNDPEETNAAFPPRLWVSPRDSSGRSKS

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

>12149_12149_3_C9orf85-FXN_C9orf85_chr9_74526752_ENST00000334731_FXN_chr9_71679854_ENST00000396366_length(amino acids)=106AA_BP=38
MISAMSSQKGNVARSRPQKHQNTFSFKNDKFDKSVQTKSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSRYVVDLSVMTGLGKTGCTPT

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

>12149_12149_4_C9orf85-FXN_C9orf85_chr9_74526752_ENST00000334731_FXN_chr9_71679854_ENST00000498653_length(amino acids)=120AA_BP=38
MISAMSSQKGNVARSRPQKHQNTFSFKNDKFDKSVQTKSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGV

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

>12149_12149_5_C9orf85-FXN_C9orf85_chr9_74526752_ENST00000377031_FXN_chr9_71679854_ENST00000377270_length(amino acids)=120AA_BP=38
MISAMSSQKGNVARSRPQKHQNTFSFKNDKFDKSVQTKSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGV

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

>12149_12149_6_C9orf85-FXN_C9orf85_chr9_74526752_ENST00000377031_FXN_chr9_71679854_ENST00000396364_length(amino acids)=95AA_BP=
MHTFIELVIFEAKRILVLLRSGTSHVAFLGAHRRNQSHPSPGAGKRMRGKKTNELLPGIDASVNDPEETNAAFPPRLWVSPRDSSGRSKS

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

>12149_12149_7_C9orf85-FXN_C9orf85_chr9_74526752_ENST00000377031_FXN_chr9_71679854_ENST00000396366_length(amino acids)=106AA_BP=38
MISAMSSQKGNVARSRPQKHQNTFSFKNDKFDKSVQTKSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSRYVVDLSVMTGLGKTGCTPT

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

>12149_12149_8_C9orf85-FXN_C9orf85_chr9_74526752_ENST00000377031_FXN_chr9_71679854_ENST00000498653_length(amino acids)=120AA_BP=38
MISAMSSQKGNVARSRPQKHQNTFSFKNDKFDKSVQTKSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGV

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

>12149_12149_9_C9orf85-FXN_C9orf85_chr9_74526752_ENST00000486911_FXN_chr9_71679854_ENST00000377270_length(amino acids)=120AA_BP=38
MISAMSSQKGNVARSRPQKHQNTFSFKNDKFDKSVQTKSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGV

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

>12149_12149_10_C9orf85-FXN_C9orf85_chr9_74526752_ENST00000486911_FXN_chr9_71679854_ENST00000396364_length(amino acids)=81AA_BP=38

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

>12149_12149_11_C9orf85-FXN_C9orf85_chr9_74526752_ENST00000486911_FXN_chr9_71679854_ENST00000396366_length(amino acids)=106AA_BP=38
MISAMSSQKGNVARSRPQKHQNTFSFKNDKFDKSVQTKSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSRYVVDLSVMTGLGKTGCTPT

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

>12149_12149_12_C9orf85-FXN_C9orf85_chr9_74526752_ENST00000486911_FXN_chr9_71679854_ENST00000498653_length(amino acids)=120AA_BP=38
MISAMSSQKGNVARSRPQKHQNTFSFKNDKFDKSVQTKSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGV

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

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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/chr9:74526752/chr9:71679854)
- 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
C9orf85 Q96MD7	FXN Q16595
	FUNCTION: Promotes the biosynthesis of heme and assembly and repair of iron-sulfur clusters by delivering Fe(2+) to proteins involved in these pathways. May play a role in the protection against iron-catalyzed oxidative stress through its ability to catalyze the oxidation of Fe(2+) to Fe(3+); the oligomeric form but not the monomeric form has in vitro ferroxidase activity. May be able to store large amounts of iron in the form of a ferrihydrite mineral by oligomerization; however, the physiological relevance is unsure as reports are conflicting and the function has only been shown using heterologous overexpression systems. Modulates the RNA-binding activity of ACO1. {ECO:0000269\|PubMed:12785837, ECO:0000269\|PubMed:15247478, ECO:0000269\|PubMed:15641778, ECO:0000269\|PubMed:16239244, ECO:0000269\|PubMed:16608849, ECO:0000269\|PubMed:20053667}.

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

C9orf85

chr9:74526752

chr9:71679854

ENST00000334731

23_79

34.0

158.0

Compositional bias

Note=Lys-rich

Hgene

C9orf85

chr9:74526752

chr9:71679854

ENST00000377031

23_79

34.0

180.0

Compositional bias

Note=Lys-rich

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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
C9orf85
FXN

- 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 C9orf85-FXN

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 C9orf85-FXN

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