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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:ARHGEF38-PPA2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ARHGEF38-PPA2
	FusionPDB ID: 6303
	FusionGDB2.0 ID: 6303
		Hgene	Tgene
	Gene symbol	ARHGEF38	PPA2
	Gene ID	54848	27068
	Gene name	Rho guanine nucleotide exchange factor 38	inorganic pyrophosphatase 2
	Synonyms	-	HSPC124\|SCFAI\|SCFI\|SID6-306
	Cytomap	4q24	4q24
	Type of gene	protein-coding	protein-coding
	Description	rho guanine nucleotide exchange factor 38Rho guanine nucleotide exchange factor (GEF) 38	inorganic pyrophosphatase 2, mitochondrialPPase 2pyrophosphatase (inorganic) 2pyrophosphatase SID6-306pyrophosphate phospho-hydrolase 2
	Modification date	20200313	20200313
	UniProtAcc	Q9NXL2	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000265154, ENST00000420470, ENST00000508036,	ENST00000509426, ENST00000310267, ENST00000341695, ENST00000348706, ENST00000354147, ENST00000357415, ENST00000380004, ENST00000432483,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 5 X 3=90	17 X 10 X 8=1360
	# samples	6	18
	** MAII score	log2(6/90*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(18/1360*10)=-2.91753783980803 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: ARHGEF38 [Title/Abstract] AND PPA2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ARHGEF38(106474118)-PPA2(106320321), # samples:3
Anticipated loss of major functional domain due to fusion event.	ARHGEF38-PPA2 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. ARHGEF38-PPA2 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

Fusion gene breakpoints across ARHGEF38 (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 PPA2 (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-AO-A0JM-01A	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-
ChimerDB4	COAD	TCGA-CM-5868-01A	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-
ChimerDB4	READ	TCGA-DC-6154	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-

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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)
ENST00000420470	ARHGEF38	chr4	106474118	+	ENST00000341695	PPA2	chr4	106320321	-	1338	340	84	689	201
ENST00000420470	ARHGEF38	chr4	106474118	+	ENST00000348706	PPA2	chr4	106320321	-	1172	340	84	689	201
ENST00000420470	ARHGEF38	chr4	106474118	+	ENST00000432483	PPA2	chr4	106320321	-	850	340	84	689	201
ENST00000420470	ARHGEF38	chr4	106474118	+	ENST00000354147	PPA2	chr4	106320321	-	850	340	84	689	201
ENST00000420470	ARHGEF38	chr4	106474118	+	ENST00000380004	PPA2	chr4	106320321	-	847	340	84	689	201
ENST00000420470	ARHGEF38	chr4	106474118	+	ENST00000357415	PPA2	chr4	106320321	-	847	340	84	689	201
ENST00000265154	ARHGEF38	chr4	106474118	+	ENST00000341695	PPA2	chr4	106320321	-	1340	342	86	691	201
ENST00000265154	ARHGEF38	chr4	106474118	+	ENST00000348706	PPA2	chr4	106320321	-	1174	342	86	691	201
ENST00000265154	ARHGEF38	chr4	106474118	+	ENST00000432483	PPA2	chr4	106320321	-	852	342	86	691	201
ENST00000265154	ARHGEF38	chr4	106474118	+	ENST00000354147	PPA2	chr4	106320321	-	852	342	86	691	201
ENST00000265154	ARHGEF38	chr4	106474118	+	ENST00000380004	PPA2	chr4	106320321	-	849	342	86	691	201
ENST00000265154	ARHGEF38	chr4	106474118	+	ENST00000357415	PPA2	chr4	106320321	-	849	342	86	691	201

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
ENST00000420470	ENST00000341695	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-	0.007444457	0.99255556
ENST00000420470	ENST00000348706	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-	0.008682669	0.9913174
ENST00000420470	ENST00000432483	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-	0.006568579	0.9934314
ENST00000420470	ENST00000354147	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-	0.006568579	0.9934314
ENST00000420470	ENST00000380004	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-	0.006646204	0.99335384
ENST00000420470	ENST00000357415	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-	0.006646204	0.99335384
ENST00000265154	ENST00000341695	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-	0.007325979	0.99267405
ENST00000265154	ENST00000348706	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-	0.008343753	0.9916563
ENST00000265154	ENST00000432483	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-	0.00611144	0.9938885
ENST00000265154	ENST00000354147	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-	0.00611144	0.9938885
ENST00000265154	ENST00000380004	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-	0.006210312	0.99378973
ENST00000265154	ENST00000357415	ARHGEF38	chr4	106474118	+	PPA2	chr4	106320321	-	0.006210312	0.99378973

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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

>6303_6303_1_ARHGEF38-PPA2_ARHGEF38_chr4_106474118_ENST00000265154_PPA2_chr4_106320321_ENST00000341695_length(amino acids)=201AA_BP=85
MRHLSNQPLPASLQSLSLPNMEPKEATGKENMVTKKKNLAFLRSRLYMLERRKTDTVVESSVSGDHSGTLRRSQSDRTEYNQKLQDIDDV
KKFKPGYLEATLNWFRLYKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPFRCTQEEARSLVES

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

>6303_6303_2_ARHGEF38-PPA2_ARHGEF38_chr4_106474118_ENST00000265154_PPA2_chr4_106320321_ENST00000348706_length(amino acids)=201AA_BP=85
MRHLSNQPLPASLQSLSLPNMEPKEATGKENMVTKKKNLAFLRSRLYMLERRKTDTVVESSVSGDHSGTLRRSQSDRTEYNQKLQDIDDV
KKFKPGYLEATLNWFRLYKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPFRCTQEEARSLVES

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

>6303_6303_3_ARHGEF38-PPA2_ARHGEF38_chr4_106474118_ENST00000265154_PPA2_chr4_106320321_ENST00000354147_length(amino acids)=201AA_BP=85
MRHLSNQPLPASLQSLSLPNMEPKEATGKENMVTKKKNLAFLRSRLYMLERRKTDTVVESSVSGDHSGTLRRSQSDRTEYNQKLQDIDDV
KKFKPGYLEATLNWFRLYKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPFRCTQEEARSLVES

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

>6303_6303_4_ARHGEF38-PPA2_ARHGEF38_chr4_106474118_ENST00000265154_PPA2_chr4_106320321_ENST00000357415_length(amino acids)=201AA_BP=85
MRHLSNQPLPASLQSLSLPNMEPKEATGKENMVTKKKNLAFLRSRLYMLERRKTDTVVESSVSGDHSGTLRRSQSDRTEYNQKLQDIDDV
KKFKPGYLEATLNWFRLYKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPFRCTQEEARSLVES

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

>6303_6303_5_ARHGEF38-PPA2_ARHGEF38_chr4_106474118_ENST00000265154_PPA2_chr4_106320321_ENST00000380004_length(amino acids)=201AA_BP=85
MRHLSNQPLPASLQSLSLPNMEPKEATGKENMVTKKKNLAFLRSRLYMLERRKTDTVVESSVSGDHSGTLRRSQSDRTEYNQKLQDIDDV
KKFKPGYLEATLNWFRLYKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPFRCTQEEARSLVES

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

>6303_6303_6_ARHGEF38-PPA2_ARHGEF38_chr4_106474118_ENST00000265154_PPA2_chr4_106320321_ENST00000432483_length(amino acids)=201AA_BP=85
MRHLSNQPLPASLQSLSLPNMEPKEATGKENMVTKKKNLAFLRSRLYMLERRKTDTVVESSVSGDHSGTLRRSQSDRTEYNQKLQDIDDV
KKFKPGYLEATLNWFRLYKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPFRCTQEEARSLVES

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

>6303_6303_7_ARHGEF38-PPA2_ARHGEF38_chr4_106474118_ENST00000420470_PPA2_chr4_106320321_ENST00000341695_length(amino acids)=201AA_BP=85
MRHLSNQPLPASLQSLSLPNMEPKEATGKENMVTKKKNLAFLRSRLYMLERRKTDTVVESSVSGDHSGTLRRSQSDRTEYNQKLQDIDDV
KKFKPGYLEATLNWFRLYKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPFRCTQEEARSLVES

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

>6303_6303_8_ARHGEF38-PPA2_ARHGEF38_chr4_106474118_ENST00000420470_PPA2_chr4_106320321_ENST00000348706_length(amino acids)=201AA_BP=85
MRHLSNQPLPASLQSLSLPNMEPKEATGKENMVTKKKNLAFLRSRLYMLERRKTDTVVESSVSGDHSGTLRRSQSDRTEYNQKLQDIDDV
KKFKPGYLEATLNWFRLYKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPFRCTQEEARSLVES

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

>6303_6303_9_ARHGEF38-PPA2_ARHGEF38_chr4_106474118_ENST00000420470_PPA2_chr4_106320321_ENST00000354147_length(amino acids)=201AA_BP=85
MRHLSNQPLPASLQSLSLPNMEPKEATGKENMVTKKKNLAFLRSRLYMLERRKTDTVVESSVSGDHSGTLRRSQSDRTEYNQKLQDIDDV
KKFKPGYLEATLNWFRLYKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPFRCTQEEARSLVES

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

>6303_6303_10_ARHGEF38-PPA2_ARHGEF38_chr4_106474118_ENST00000420470_PPA2_chr4_106320321_ENST00000357415_length(amino acids)=201AA_BP=85
MRHLSNQPLPASLQSLSLPNMEPKEATGKENMVTKKKNLAFLRSRLYMLERRKTDTVVESSVSGDHSGTLRRSQSDRTEYNQKLQDIDDV
KKFKPGYLEATLNWFRLYKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPFRCTQEEARSLVES

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

>6303_6303_11_ARHGEF38-PPA2_ARHGEF38_chr4_106474118_ENST00000420470_PPA2_chr4_106320321_ENST00000380004_length(amino acids)=201AA_BP=85
MRHLSNQPLPASLQSLSLPNMEPKEATGKENMVTKKKNLAFLRSRLYMLERRKTDTVVESSVSGDHSGTLRRSQSDRTEYNQKLQDIDDV
KKFKPGYLEATLNWFRLYKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPFRCTQEEARSLVES

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

>6303_6303_12_ARHGEF38-PPA2_ARHGEF38_chr4_106474118_ENST00000420470_PPA2_chr4_106320321_ENST00000432483_length(amino acids)=201AA_BP=85
MRHLSNQPLPASLQSLSLPNMEPKEATGKENMVTKKKNLAFLRSRLYMLERRKTDTVVESSVSGDHSGTLRRSQSDRTEYNQKLQDIDDV
KKFKPGYLEATLNWFRLYKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPFRCTQEEARSLVES

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

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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/chr4:106474118/chr4:106320321)
- 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
ARHGEF38 Q9NXL2	.
FUNCTION: May act as a guanine-nucleotide releasing factor. {ECO:0000250}.	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

ARHGEF38

chr4:106474118

chr4:106320321

ENST00000265154

689_694

65.33333333333333

220.0

Compositional bias

Note=Poly-Ser

Hgene

ARHGEF38

chr4:106474118

chr4:106320321

ENST00000420470

689_694

65.33333333333333

778.0

Compositional bias

Note=Poly-Ser

Hgene

ARHGEF38

chr4:106474118

chr4:106320321

ENST00000265154

327_536

65.33333333333333

220.0

Domain

BAR

Hgene

ARHGEF38

chr4:106474118

chr4:106320321

ENST00000265154

582_645

65.33333333333333

220.0

Domain

SH3 1

Hgene

ARHGEF38

chr4:106474118

chr4:106320321

ENST00000265154

713_776

65.33333333333333

220.0

Domain

SH3 2

Hgene

ARHGEF38

chr4:106474118

chr4:106320321

ENST00000265154

94_285

65.33333333333333

220.0

Domain

Hgene

ARHGEF38

chr4:106474118

chr4:106320321

ENST00000420470

327_536

65.33333333333333

778.0

Domain

BAR

Hgene

ARHGEF38

chr4:106474118

chr4:106320321

ENST00000420470

582_645

65.33333333333333

778.0

Domain

SH3 1

Hgene

ARHGEF38

chr4:106474118

chr4:106320321

ENST00000420470

713_776

65.33333333333333

778.0

Domain

SH3 2

Hgene

ARHGEF38

chr4:106474118

chr4:106320321

ENST00000420470

94_285

65.33333333333333

778.0

Domain

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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 >>>268_ARHGEF38_106474118_PPA2_106320321_ranked_0.pdb	ARHGEF38	106474118	106474118	ENST00000357415	PPA2	chr4	106320321	-	MRHLSNQPLPASLQSLSLPNMEPKEATGKENMVTKKKNLAFLRSRLYMLERRKTDTVVESSVSGDHSGTLRRSQSDRTEYNQKLQDIDDV KKFKPGYLEATLNWFRLYKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPFRCTQEEARSLVES	201

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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.

ARHGEF38_pLDDT.png

PPA2_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
ARHGEF38
PPA2

- 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 ARHGEF38-PPA2

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 ARHGEF38-PPA2

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