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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:LAP3-SERPINA1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: LAP3-SERPINA1
	FusionPDB ID: 44039
	FusionGDB2.0 ID: 44039
		Hgene	Tgene
	Gene symbol	LAP3	SERPINA1
	Gene ID	51056	5265
	Gene name	leucine aminopeptidase 3	serpin family A member 1
	Synonyms	HEL-S-106\|LAP\|LAPEP\|PEPS	A1A\|A1AT\|AAT\|PI\|PI1\|PRO2275\|alpha1AT\|nNIF
	Cytomap	4p15.32	14q32.13
	Type of gene	protein-coding	protein-coding
	Description	cytosol aminopeptidaseLAP-3epididymis secretory protein Li 106leucyl aminopeptidasepeptidase Sproline aminopeptidaseprolyl aminopeptidase	alpha-1-antitrypsinalpha-1 antitrypsinalpha-1 protease inhibitoralpha-1-antiproteinasealpha-1-antitrypsin nullalpha-1-antitrypsin short transcript variant 1C4alpha-1-antitrypsin short transcript variant 1C5epididymis secretory sperm binding protein
	Modification date	20200313	20200327
	UniProtAcc	P28838	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000226299, ENST00000606142, ENST00000503467,	ENST00000555289, ENST00000402629, ENST00000355814, ENST00000393087, ENST00000393088, ENST00000404814, ENST00000437397, ENST00000440909, ENST00000448921, ENST00000449399,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	4 X 4 X 3=48	16 X 17 X 6=1632
	# samples	5	18
	** MAII score	log2(5/48*10)=0.0588936890535686 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(18/1632*10)=-3.18057224564182 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: LAP3 [Title/Abstract] AND SERPINA1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	LAP3(17585220)-SERPINA1(94845846), # samples:1
Anticipated loss of major functional domain due to fusion event.	LAP3-SERPINA1 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. LAP3-SERPINA1 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. LAP3-SERPINA1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. LAP3-SERPINA1 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 LAP3 (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 SERPINA1 (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
ChiTaRS5.0	N/A	BG566103	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-

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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)
ENST00000226299	LAP3	chr4	17585220	+	ENST00000440909	SERPINA1	chr14	94845846	-	2638	698	184	708	174
ENST00000226299	LAP3	chr4	17585220	+	ENST00000448921	SERPINA1	chr14	94845846	-	2638	698	184	708	174
ENST00000226299	LAP3	chr4	17585220	+	ENST00000437397	SERPINA1	chr14	94845846	-	2638	698	184	708	174
ENST00000226299	LAP3	chr4	17585220	+	ENST00000355814	SERPINA1	chr14	94845846	-	2638	698	184	708	174
ENST00000226299	LAP3	chr4	17585220	+	ENST00000393087	SERPINA1	chr14	94845846	-	1036	698	184	708	174
ENST00000226299	LAP3	chr4	17585220	+	ENST00000393088	SERPINA1	chr14	94845846	-	1009	698	184	708	174
ENST00000226299	LAP3	chr4	17585220	+	ENST00000404814	SERPINA1	chr14	94845846	-	996	698	184	708	174
ENST00000226299	LAP3	chr4	17585220	+	ENST00000449399	SERPINA1	chr14	94845846	-	936	698	184	708	174
ENST00000606142	LAP3	chr4	17585220	+	ENST00000440909	SERPINA1	chr14	94845846	-	2335	395	1354	1761	135
ENST00000606142	LAP3	chr4	17585220	+	ENST00000448921	SERPINA1	chr14	94845846	-	2335	395	1354	1761	135
ENST00000606142	LAP3	chr4	17585220	+	ENST00000437397	SERPINA1	chr14	94845846	-	2335	395	1354	1761	135
ENST00000606142	LAP3	chr4	17585220	+	ENST00000355814	SERPINA1	chr14	94845846	-	2335	395	1354	1761	135
ENST00000606142	LAP3	chr4	17585220	+	ENST00000393087	SERPINA1	chr14	94845846	-	733	395	19	405	128
ENST00000606142	LAP3	chr4	17585220	+	ENST00000393088	SERPINA1	chr14	94845846	-	706	395	19	405	128
ENST00000606142	LAP3	chr4	17585220	+	ENST00000404814	SERPINA1	chr14	94845846	-	693	395	19	405	128
ENST00000606142	LAP3	chr4	17585220	+	ENST00000449399	SERPINA1	chr14	94845846	-	633	395	19	405	128

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
ENST00000226299	ENST00000440909	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.016752038	0.983248
ENST00000226299	ENST00000448921	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.016752038	0.983248
ENST00000226299	ENST00000437397	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.016752038	0.983248
ENST00000226299	ENST00000355814	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.016752038	0.983248
ENST00000226299	ENST00000393087	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.02092983	0.9790702
ENST00000226299	ENST00000393088	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.022197299	0.97780275
ENST00000226299	ENST00000404814	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.02180666	0.9781934
ENST00000226299	ENST00000449399	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.024312917	0.975687
ENST00000606142	ENST00000440909	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.7843627	0.2156373
ENST00000606142	ENST00000448921	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.7843627	0.2156373
ENST00000606142	ENST00000437397	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.7843627	0.2156373
ENST00000606142	ENST00000355814	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.7843627	0.2156373
ENST00000606142	ENST00000393087	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.025470557	0.97452945
ENST00000606142	ENST00000393088	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.02652986	0.9734701
ENST00000606142	ENST00000404814	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.02601245	0.9739875
ENST00000606142	ENST00000449399	LAP3	chr4	17585220	+	SERPINA1	chr14	94845846	-	0.02540076	0.9745993

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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

>44039_44039_1_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000226299_SERPINA1_chr14_94845846_ENST00000355814_length(amino acids)=174AA_BP=
MRPESPAPRRARPPLSTCSLEGGARGRADKMFLLPLPAAGRVVVRRLAVRRFGSRSLSTADMTKGLVLGIYSKEKEDDVPQFTSAGENFD

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

>44039_44039_2_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000226299_SERPINA1_chr14_94845846_ENST00000393087_length(amino acids)=174AA_BP=
MRPESPAPRRARPPLSTCSLEGGARGRADKMFLLPLPAAGRVVVRRLAVRRFGSRSLSTADMTKGLVLGIYSKEKEDDVPQFTSAGENFD

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

>44039_44039_3_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000226299_SERPINA1_chr14_94845846_ENST00000393088_length(amino acids)=174AA_BP=
MRPESPAPRRARPPLSTCSLEGGARGRADKMFLLPLPAAGRVVVRRLAVRRFGSRSLSTADMTKGLVLGIYSKEKEDDVPQFTSAGENFD

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

>44039_44039_4_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000226299_SERPINA1_chr14_94845846_ENST00000404814_length(amino acids)=174AA_BP=
MRPESPAPRRARPPLSTCSLEGGARGRADKMFLLPLPAAGRVVVRRLAVRRFGSRSLSTADMTKGLVLGIYSKEKEDDVPQFTSAGENFD

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

>44039_44039_5_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000226299_SERPINA1_chr14_94845846_ENST00000437397_length(amino acids)=174AA_BP=
MRPESPAPRRARPPLSTCSLEGGARGRADKMFLLPLPAAGRVVVRRLAVRRFGSRSLSTADMTKGLVLGIYSKEKEDDVPQFTSAGENFD

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

>44039_44039_6_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000226299_SERPINA1_chr14_94845846_ENST00000440909_length(amino acids)=174AA_BP=
MRPESPAPRRARPPLSTCSLEGGARGRADKMFLLPLPAAGRVVVRRLAVRRFGSRSLSTADMTKGLVLGIYSKEKEDDVPQFTSAGENFD

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

>44039_44039_7_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000226299_SERPINA1_chr14_94845846_ENST00000448921_length(amino acids)=174AA_BP=
MRPESPAPRRARPPLSTCSLEGGARGRADKMFLLPLPAAGRVVVRRLAVRRFGSRSLSTADMTKGLVLGIYSKEKEDDVPQFTSAGENFD

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

>44039_44039_8_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000226299_SERPINA1_chr14_94845846_ENST00000449399_length(amino acids)=174AA_BP=
MRPESPAPRRARPPLSTCSLEGGARGRADKMFLLPLPAAGRVVVRRLAVRRFGSRSLSTADMTKGLVLGIYSKEKEDDVPQFTSAGENFD

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

>44039_44039_9_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000606142_SERPINA1_chr14_94845846_ENST00000355814_length(amino acids)=135AA_BP=
MLCFLYLLLRLDQAQQAPEDHYPISLLLPSHMAIGLLMAQEGHCKDSSAMGEEAHHPLTPATPPFPPLSPDWGHMQPDFFVPVAVPAVFR

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

>44039_44039_10_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000606142_SERPINA1_chr14_94845846_ENST00000393087_length(amino acids)=128AA_BP=
MAVRRFGSRSLSTADMTKGLVLGIYSKEKEDDVPQFTSAGENFDKLLAGKLRETLNISGPPLKAGKTRTFYGLHQDFPSVVLVGLGKKAA

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

>44039_44039_11_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000606142_SERPINA1_chr14_94845846_ENST00000393088_length(amino acids)=128AA_BP=
MAVRRFGSRSLSTADMTKGLVLGIYSKEKEDDVPQFTSAGENFDKLLAGKLRETLNISGPPLKAGKTRTFYGLHQDFPSVVLVGLGKKAA

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

>44039_44039_12_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000606142_SERPINA1_chr14_94845846_ENST00000404814_length(amino acids)=128AA_BP=
MAVRRFGSRSLSTADMTKGLVLGIYSKEKEDDVPQFTSAGENFDKLLAGKLRETLNISGPPLKAGKTRTFYGLHQDFPSVVLVGLGKKAA

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

>44039_44039_13_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000606142_SERPINA1_chr14_94845846_ENST00000437397_length(amino acids)=135AA_BP=
MLCFLYLLLRLDQAQQAPEDHYPISLLLPSHMAIGLLMAQEGHCKDSSAMGEEAHHPLTPATPPFPPLSPDWGHMQPDFFVPVAVPAVFR

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

>44039_44039_14_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000606142_SERPINA1_chr14_94845846_ENST00000440909_length(amino acids)=135AA_BP=
MLCFLYLLLRLDQAQQAPEDHYPISLLLPSHMAIGLLMAQEGHCKDSSAMGEEAHHPLTPATPPFPPLSPDWGHMQPDFFVPVAVPAVFR

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

>44039_44039_15_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000606142_SERPINA1_chr14_94845846_ENST00000448921_length(amino acids)=135AA_BP=
MLCFLYLLLRLDQAQQAPEDHYPISLLLPSHMAIGLLMAQEGHCKDSSAMGEEAHHPLTPATPPFPPLSPDWGHMQPDFFVPVAVPAVFR

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

>44039_44039_16_LAP3-SERPINA1_LAP3_chr4_17585220_ENST00000606142_SERPINA1_chr14_94845846_ENST00000449399_length(amino acids)=128AA_BP=
MAVRRFGSRSLSTADMTKGLVLGIYSKEKEDDVPQFTSAGENFDKLLAGKLRETLNISGPPLKAGKTRTFYGLHQDFPSVVLVGLGKKAA

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

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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/chr4:17585220/chr14:94845846)
- 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
LAP3 P28838	.
FUNCTION: Cytolosic metallopeptidase that catalyzes the removal of unsubstituted N-terminal hydrophobic amino acids from various peptides. The presence of Zn(2+) ions is essential for the peptidase activity, and the association with other cofactors can modulate the substrate spectificity of the enzyme. For instance, in the presence of Mn(2+), it displays a specific Cys-Gly hydrolyzing activity of Cys-Gly-S-conjugates. Involved in the metabolism of glutathione and in the degradation of glutathione S-conjugates, which may play a role in the control of the cell redox status. {ECO:0000250\|UniProtKB:P00727}.	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

SERPINA1

chr4:17585220

chr14:94845846

ENST00000355814

368_392

419.0

Region

Note=RCL

Tgene

SERPINA1

chr4:17585220

chr14:94845846

ENST00000393087

368_392

419.0

Region

Note=RCL

Tgene

SERPINA1

chr4:17585220

chr14:94845846

ENST00000393088

368_392

419.0

Region

Note=RCL

Tgene

SERPINA1

chr4:17585220

chr14:94845846

ENST00000402629

368_392

360.0

Region

Note=RCL

Tgene

SERPINA1

chr4:17585220

chr14:94845846

ENST00000404814

368_392

419.0

Region

Note=RCL

Tgene

SERPINA1

chr4:17585220

chr14:94845846

ENST00000437397

368_392

419.0

Region

Note=RCL

Tgene

SERPINA1

chr4:17585220

chr14:94845846

ENST00000440909

368_392

419.0

Region

Note=RCL

Tgene

SERPINA1

chr4:17585220

chr14:94845846

ENST00000448921

368_392

419.0

Region

Note=RCL

Tgene

SERPINA1

chr4:17585220

chr14:94845846

ENST00000449399

368_392

419.0

Region

Note=RCL

- 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

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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
LAP3
SERPINA1

- 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 LAP3-SERPINA1

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 LAP3-SERPINA1

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