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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:SPINT2-PAK1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SPINT2-PAK1
	FusionPDB ID: 85850
	FusionGDB2.0 ID: 85850
		Hgene	Tgene
	Gene symbol	SPINT2	PAK1
	Gene ID	10653	5585
	Gene name	serine peptidase inhibitor, Kunitz type 2	protein kinase N1
	Synonyms	DIAR3\|HAI-2\|HAI2\|Kop\|PB	DBK\|PAK-1\|PAK1\|PKN\|PKN-ALPHA\|PRK1\|PRKCL1
	Cytomap	19q13.2	19p13.12
	Type of gene	protein-coding	protein-coding
	Description	kunitz-type protease inhibitor 2hepatocyte growth factor activator inhibitor type 2serine protease inhibitor, Kunitz type, 2testicular tissue protein Li 183	serine/threonine-protein kinase N1protease-activated kinase 1protein kinase C-like 1protein kinase C-like PKNprotein kinase C-related kinase 1protein kinase PKN-alphaserine-threonine kinase Nserine/threonine protein kinase N
	Modification date	20200315	20200329
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000301244, ENST00000454580, ENST00000587090,	ENST00000525542, ENST00000278568, ENST00000356341, ENST00000528203, ENST00000530617,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	16 X 8 X 9=1152	22 X 17 X 10=3740
	# samples	21	26
	** MAII score	log2(21/1152*10)=-2.45567948377619 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(26/3740*10)=-3.84645474174655 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: SPINT2 [Title/Abstract] AND PAK1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SPINT2(38755638)-PAK1(77085410), # samples:2
Anticipated loss of major functional domain due to fusion event.	SPINT2-PAK1 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. SPINT2-PAK1 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. SPINT2-PAK1 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. SPINT2-PAK1 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
Hgene	SPINT2	GO:0022408	negative regulation of cell-cell adhesion	19592578
Hgene	SPINT2	GO:2000146	negative regulation of cell motility	19592578
Tgene	PAK1	GO:0006357	regulation of transcription by RNA polymerase II	12514133
Tgene	PAK1	GO:0006468	protein phosphorylation	17332740
Tgene	PAK1	GO:0035407	histone H3-T11 phosphorylation	18066052

Fusion gene breakpoints across SPINT2 (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 PAK1 (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-A1-A0SQ-01A	SPINT2	chr19	38755638	+	PAK1	chr11	77085410	-

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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)
ENST00000301244	SPINT2	chr19	38755638	+	ENST00000356341	PAK1	chr11	77085410	-	3307	541	411	1739	442
ENST00000301244	SPINT2	chr19	38755638	+	ENST00000530617	PAK1	chr11	77085410	-	2791	541	411	1670	419
ENST00000301244	SPINT2	chr19	38755638	+	ENST00000278568	PAK1	chr11	77085410	-	2115	541	411	1763	450
ENST00000301244	SPINT2	chr19	38755638	+	ENST00000528203	PAK1	chr11	77085410	-	2039	541	411	1763	450
ENST00000454580	SPINT2	chr19	38755638	+	ENST00000356341	PAK1	chr11	77085410	-	3189	423	293	1621	442
ENST00000454580	SPINT2	chr19	38755638	+	ENST00000530617	PAK1	chr11	77085410	-	2673	423	293	1552	419
ENST00000454580	SPINT2	chr19	38755638	+	ENST00000278568	PAK1	chr11	77085410	-	1997	423	293	1645	450
ENST00000454580	SPINT2	chr19	38755638	+	ENST00000528203	PAK1	chr11	77085410	-	1921	423	293	1645	450

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
ENST00000301244	ENST00000356341	SPINT2	chr19	38755638	+	PAK1	chr11	77085410	-	0.001450718	0.9985493
ENST00000301244	ENST00000530617	SPINT2	chr19	38755638	+	PAK1	chr11	77085410	-	0.001415633	0.9985844
ENST00000301244	ENST00000278568	SPINT2	chr19	38755638	+	PAK1	chr11	77085410	-	0.003208948	0.99679106
ENST00000301244	ENST00000528203	SPINT2	chr19	38755638	+	PAK1	chr11	77085410	-	0.004325493	0.99567455
ENST00000454580	ENST00000356341	SPINT2	chr19	38755638	+	PAK1	chr11	77085410	-	0.001260012	0.99874
ENST00000454580	ENST00000530617	SPINT2	chr19	38755638	+	PAK1	chr11	77085410	-	0.001206399	0.9987936
ENST00000454580	ENST00000278568	SPINT2	chr19	38755638	+	PAK1	chr11	77085410	-	0.002617713	0.9973822
ENST00000454580	ENST00000528203	SPINT2	chr19	38755638	+	PAK1	chr11	77085410	-	0.003690855	0.9963091

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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

>85850_85850_1_SPINT2-PAK1_SPINT2_chr19_38755638_ENST00000301244_PAK1_chr11_77085410_ENST00000278568_length(amino acids)=450AA_BP=43
MRVSAELAMAQLCGLRRSRAFLALLGSLLLSGVLAADRERSIHDKSAEDYNSSNALNVKAVSETPAVPPVSEDEDDDDDDATPPPVIAPR
PEHTKSVYTRSVIEPLPVTPTRDVATSPISPTENNTTPPDALTRNTEKQKKKPKMSDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGT
VYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCREC
LQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPP
YLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQVRKLRFQVFSNFSMIAASIPEDCQAPLQPHSTDCCS

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

>85850_85850_2_SPINT2-PAK1_SPINT2_chr19_38755638_ENST00000301244_PAK1_chr11_77085410_ENST00000356341_length(amino acids)=442AA_BP=43
MRVSAELAMAQLCGLRRSRAFLALLGSLLLSGVLAADRERSIHDKSAEDYNSSNALNVKAVSETPAVPPVSEDEDDDDDDATPPPVIAPR
PEHTKSVYTRSVIEPLPVTPTRDVATSPISPTENNTTPPDALTRNTEKQKKKPKMSDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGT
VYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCREC
LQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPP

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

>85850_85850_3_SPINT2-PAK1_SPINT2_chr19_38755638_ENST00000301244_PAK1_chr11_77085410_ENST00000528203_length(amino acids)=450AA_BP=43
MRVSAELAMAQLCGLRRSRAFLALLGSLLLSGVLAADRERSIHDKSAEDYNSSNALNVKAVSETPAVPPVSEDEDDDDDDATPPPVIAPR
PEHTKSVYTRSVIEPLPVTPTRDVATSPISPTENNTTPPDALTRNTEKQKKKPKMSDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGT
VYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCREC
LQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPP
YLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQVRKLRFQVFSNFSMIAASIPEDCQAPLQPHSTDCCS

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

>85850_85850_4_SPINT2-PAK1_SPINT2_chr19_38755638_ENST00000301244_PAK1_chr11_77085410_ENST00000530617_length(amino acids)=419AA_BP=43
MRVSAELAMAQLCGLRRSRAFLALLGSLLLSGVLAADRERSIHDKSAEDYNSSNALNVKAVSETPAVPPVSEDEDDDDDDATPPPVIAPR
PEHTKSVYTRSVIEPLPVTPTRDVATSPISPTENNTTPPDALTRNTEKQKKKPKMSDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGT
VYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCREC
LQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPP

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

>85850_85850_5_SPINT2-PAK1_SPINT2_chr19_38755638_ENST00000454580_PAK1_chr11_77085410_ENST00000278568_length(amino acids)=450AA_BP=43
MRVSAELAMAQLCGLRRSRAFLALLGSLLLSGVLAADRERSIHDKSAEDYNSSNALNVKAVSETPAVPPVSEDEDDDDDDATPPPVIAPR
PEHTKSVYTRSVIEPLPVTPTRDVATSPISPTENNTTPPDALTRNTEKQKKKPKMSDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGT
VYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCREC
LQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPP
YLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQVRKLRFQVFSNFSMIAASIPEDCQAPLQPHSTDCCS

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

>85850_85850_6_SPINT2-PAK1_SPINT2_chr19_38755638_ENST00000454580_PAK1_chr11_77085410_ENST00000356341_length(amino acids)=442AA_BP=43
MRVSAELAMAQLCGLRRSRAFLALLGSLLLSGVLAADRERSIHDKSAEDYNSSNALNVKAVSETPAVPPVSEDEDDDDDDATPPPVIAPR
PEHTKSVYTRSVIEPLPVTPTRDVATSPISPTENNTTPPDALTRNTEKQKKKPKMSDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGT
VYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCREC
LQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPP

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

>85850_85850_7_SPINT2-PAK1_SPINT2_chr19_38755638_ENST00000454580_PAK1_chr11_77085410_ENST00000528203_length(amino acids)=450AA_BP=43
MRVSAELAMAQLCGLRRSRAFLALLGSLLLSGVLAADRERSIHDKSAEDYNSSNALNVKAVSETPAVPPVSEDEDDDDDDATPPPVIAPR
PEHTKSVYTRSVIEPLPVTPTRDVATSPISPTENNTTPPDALTRNTEKQKKKPKMSDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGT
VYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCREC
LQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPP
YLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQVRKLRFQVFSNFSMIAASIPEDCQAPLQPHSTDCCS

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

>85850_85850_8_SPINT2-PAK1_SPINT2_chr19_38755638_ENST00000454580_PAK1_chr11_77085410_ENST00000530617_length(amino acids)=419AA_BP=43
MRVSAELAMAQLCGLRRSRAFLALLGSLLLSGVLAADRERSIHDKSAEDYNSSNALNVKAVSETPAVPPVSEDEDDDDDDATPPPVIAPR
PEHTKSVYTRSVIEPLPVTPTRDVATSPISPTENNTTPPDALTRNTEKQKKKPKMSDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGT
VYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCREC
LQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPP

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

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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/chr19:38755638/chr11:77085410)
- 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

PAK1

chr19:38755638

chr11:77085410

ENST00000278568

270_521

146.33333333333334

554.0

Domain

Protein kinase

Tgene

PAK1

chr19:38755638

chr11:77085410

ENST00000356341

270_521

146.33333333333334

546.0

Domain

Protein kinase

Tgene

PAK1

chr19:38755638

chr11:77085410

ENST00000278568

276_284

146.33333333333334

554.0

Nucleotide binding

Note=ATP

Tgene

PAK1

chr19:38755638

chr11:77085410

ENST00000278568

345_347

146.33333333333334

554.0

Nucleotide binding

Note=ATP

Tgene

PAK1

chr19:38755638

chr11:77085410

ENST00000356341

276_284

146.33333333333334

546.0

Nucleotide binding

Note=ATP

Tgene

PAK1

chr19:38755638

chr11:77085410

ENST00000356341

345_347

146.33333333333334

546.0

Nucleotide binding

Note=ATP

- 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

SPINT2

chr19:38755638

chr11:77085410

ENST00000301244

219_252

35.333333333333336

253.0

Topological domain

Cytoplasmic

Hgene

SPINT2

chr19:38755638

chr11:77085410

ENST00000301244

28_197

35.333333333333336

253.0

Topological domain

Extracellular

Hgene

SPINT2

chr19:38755638

chr11:77085410

ENST00000454580

219_252

35.333333333333336

196.0

Topological domain

Cytoplasmic

Hgene

SPINT2

chr19:38755638

chr11:77085410

ENST00000454580

28_197

35.333333333333336

196.0

Topological domain

Extracellular

Hgene

SPINT2

chr19:38755638

chr11:77085410

ENST00000301244

198_218

35.333333333333336

253.0

Transmembrane

Helical

Hgene

SPINT2

chr19:38755638

chr11:77085410

ENST00000454580

198_218

35.333333333333336

196.0

Transmembrane

Helical

Tgene

PAK1

chr19:38755638

chr11:77085410

ENST00000278568

75_88

146.33333333333334

554.0

Domain

CRIB

Tgene

PAK1

chr19:38755638

chr11:77085410

ENST00000356341

75_88

146.33333333333334

546.0

Domain

CRIB

Tgene

PAK1

chr19:38755638

chr11:77085410

ENST00000278568

70_140

146.33333333333334

554.0

Region

Note=Autoregulatory region

Tgene

PAK1

chr19:38755638

chr11:77085410

ENST00000278568

75_105

146.33333333333334

554.0

Region

Note=GTPase-binding

Tgene

PAK1

chr19:38755638

chr11:77085410

ENST00000356341

70_140

146.33333333333334

546.0

Region

Note=Autoregulatory region

Tgene

PAK1

chr19:38755638

chr11:77085410

ENST00000356341

75_105

146.33333333333334

546.0

Region

Note=GTPase-binding

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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
SPINT2
PAK1

- 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
Tgene	PAK1	chr19:38755638	chr11:77085410	ENST00000278568		3	16	132_270	146.33333333333334	554.0	CRIPAK
Tgene	PAK1	chr19:38755638	chr11:77085410	ENST00000356341		3	15	132_270	146.33333333333334	546.0	CRIPAK

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Related Drugs to SPINT2-PAK1

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 SPINT2-PAK1

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