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Fusion Protein:KLK3-PSMD7

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: KLK3-PSMD7
	FusionPDB ID: 43090
	FusionGDB2.0 ID: 43090
		Hgene	Tgene
	Gene symbol	KLK3	PSMD7
	Gene ID	3818	5713
	Gene name	kallikrein B1	proteasome 26S subunit, non-ATPase 7
	Synonyms	KLK3\|PKK\|PKKD\|PPK	MOV34\|P40\|Rpn8\|S12
	Cytomap	4q35.2	16q23.1
	Type of gene	protein-coding	protein-coding
	Description	plasma kallikreinkallikrein B, plasma (Fletcher factor) 1kininogeninplasma prekallikrein	26S proteasome non-ATPase regulatory subunit 726S proteasome regulatory subunit S1226S proteasome regulatory subunit rpn8Moloney leukemia virus-34 proviral integrationMov34 homologproteasome (prosome, macropain) 26S subunit, non-ATPase, 7 (Mov34 homo
	Modification date	20200320	20200313
	UniProtAcc	P07288 Main function of 5'-partner protein: FUNCTION: Hydrolyzes semenogelin-1 thus leading to the liquefaction of the seminal coagulum.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000326003, ENST00000360617, ENST00000593997, ENST00000595952, ENST00000597483,	ENST00000540379, ENST00000567958, ENST00000568615, ENST00000219313,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	24 X 31 X 2=1488	4 X 3 X 2=24
	# samples	31	4
	** MAII score	log2(31/1488*10)=-2.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/24*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: KLK3 [Title/Abstract] AND PSMD7 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: KLK3 [Title/Abstract] AND PSMD7 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	KLK3(51361508)-PSMD7(74330845), # samples:1
Anticipated loss of major functional domain due to fusion event.	KLK3-PSMD7 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. KLK3-PSMD7 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. KLK3-PSMD7 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. KLK3-PSMD7 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	KLK3	GO:0031639	plasminogen activation	89876
Hgene	KLK3	GO:0051919	positive regulation of fibrinolysis	89876

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:51361508/chr16:74330845)
- 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.

Retention analysis results 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, are available here.

Fusion gene breakpoints across KLK3 (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 PSMD7 (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 Amino Acid Sequences

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)

ENST00000326003

KLK3

chr19

51361508

ENST00000219313

PSMD7

chr16

74330845

1807

310

1251

406

ENST00000597483

KLK3

chr19

51361508

ENST00000219313

PSMD7

chr16

74330845

1792

295

1236

406

ENST00000593997

KLK3

chr19

51361508

ENST00000219313

PSMD7

chr16

74330845

1787

290

1231

406

ENST00000595952

KLK3

chr19

51361508

ENST00000219313

PSMD7

chr16

74330845

1773

276

1217

375

ENST00000360617

KLK3

chr19

51361508

ENST00000219313

PSMD7

chr16

74330845

1766

269

1210

375

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
ENST00000326003	ENST00000219313	KLK3	chr19	51361508	+	PSMD7	chr16	74330845	+	0.001422073	0.99857795
ENST00000597483	ENST00000219313	KLK3	chr19	51361508	+	PSMD7	chr16	74330845	+	0.001280023	0.99872005
ENST00000593997	ENST00000219313	KLK3	chr19	51361508	+	PSMD7	chr16	74330845	+	0.001345193	0.9986547
ENST00000595952	ENST00000219313	KLK3	chr19	51361508	+	PSMD7	chr16	74330845	+	0.001201596	0.9987984
ENST00000360617	ENST00000219313	KLK3	chr19	51361508	+	PSMD7	chr16	74330845	+	0.00128861	0.99871135

Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for KLK3-PSMD7

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
KLK3	chr19	51361508	PSMD7	chr16	74330845	269	62	ATPQAGAALNQRSHPLVLLSVVDHFN
KLK3	chr19	51361508	PSMD7	chr16	74330845	276	62	ATPQAGAALNQRSHPLVLLSVVDHFN
KLK3	chr19	51361508	PSMD7	chr16	74330845	290	93	ATPQAGAALNQRSHPLVLLSVVDHFN
KLK3	chr19	51361508	PSMD7	chr16	74330845	295	93	ATPQAGAALNQRSHPLVLLSVVDHFN
KLK3	chr19	51361508	PSMD7	chr16	74330845	310	93	ATPQAGAALNQRSHPLVLLSVVDHFN

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Potential FusionNeoAntigen Information of KLK3-PSMD7 in HLA I

Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

KLK3-PSMD7_51361508_74330845.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:24	QRSHPLVL	0.9997	0.741	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B14:01	QRSHPLVL	0.9993	0.8415	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B14:02	QRSHPLVL	0.9993	0.8415	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B07:10	QRSHPLVL	0.7065	0.5257	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B27:05	QRSHPLVLL	0.9998	0.5259	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B27:04	QRSHPLVLL	0.9998	0.5796	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B27:07	QRSHPLVLL	0.9998	0.5527	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:24	QRSHPLVLL	0.9995	0.7037	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:01	QRSHPLVLL	0.9993	0.8984	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B14:01	QRSHPLVLL	0.9992	0.8091	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B14:02	QRSHPLVLL	0.9992	0.8091	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:06	QRSHPLVLL	0.999	0.8226	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:06	SHPLVLLSV	0.999	0.8811	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:24	SHPLVLLSV	0.9989	0.6743	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B38:01	QRSHPLVLL	0.9987	0.9533	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B08:01	ALNQRSHPL	0.9986	0.5706	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B38:02	QRSHPLVLL	0.9986	0.9549	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B14:02	SHPLVLLSV	0.9982	0.8749	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B14:01	SHPLVLLSV	0.9982	0.8749	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:01	SHPLVLLSV	0.9981	0.9088	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B38:01	SHPLVLLSV	0.9979	0.9764	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B14:01	NQRSHPLVL	0.9978	0.8339	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B14:02	NQRSHPLVL	0.9978	0.8339	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B08:09	ALNQRSHPL	0.9977	0.7068	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B38:02	SHPLVLLSV	0.9976	0.9783	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:01	NQRSHPLVL	0.9973	0.6248	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-A30:08	RSHPLVLLS	0.9911	0.8466	11	20
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:10	SHPLVLLSV	0.9848	0.682	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:06	NQRSHPLVL	0.9829	0.7421	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:01	NQRSHPLVL	0.9808	0.8613	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-A02:13	ALNQRSHPL	0.9795	0.5893	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-A02:38	ALNQRSHPL	0.9695	0.6054	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B48:01	QRSHPLVLL	0.9669	0.671	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:37	SHPLVLLSV	0.9654	0.7596	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B38:02	NQRSHPLVL	0.9482	0.9068	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:13	NQRSHPLVL	0.9481	0.8724	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:37	QRSHPLVLL	0.8345	0.5296	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:25	NQRSHPLVL	0.6766	0.7077	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B13:02	NQRSHPLVL	0.5993	0.5356	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B13:01	NQRSHPLVL	0.4957	0.777	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B07:10	QRSHPLVLL	0.1168	0.5549	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B52:01	NQRSHPLVL	0.0881	0.7156	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-A30:08	RSHPLVLLSV	0.9976	0.8442	11	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B48:01	NQRSHPLVLL	0.9836	0.5221	9	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B48:01	ALNQRSHPLVL	0.8366	0.7131	7	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C15:06	RSHPLVLL	1	0.9422	11	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:05	QRSHPLVL	0.9996	0.9575	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:95	QRSHPLVL	0.9995	0.6975	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:12	QRSHPLVL	0.9993	0.9125	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:27	QRSHPLVL	0.9993	0.9427	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C12:16	QRSHPLVL	0.9842	0.9453	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B14:03	QRSHPLVL	0.9723	0.828	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B27:14	QRSHPLVLL	0.9998	0.5477	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:09	QRSHPLVLL	0.9993	0.7841	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:95	QRSHPLVLL	0.9992	0.6531	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:05	QRSHPLVLL	0.999	0.9505	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:12	QRSHPLVLL	0.999	0.8985	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B42:02	ALNQRSHPL	0.9989	0.5618	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:05	QRSHPLVLL	0.9985	0.8942	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:09	SHPLVLLSV	0.9984	0.7528	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:46	QRSHPLVLL	0.9982	0.9155	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:12	SHPLVLLSV	0.998	0.9164	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:27	QRSHPLVLL	0.9975	0.9358	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:05	SHPLVLLSV	0.9974	0.8924	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:19	QRSHPLVLL	0.997	0.8053	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:13	QRSHPLVLL	0.996	0.9466	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:29	QRSHPLVLL	0.9958	0.9058	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:80	QRSHPLVLL	0.9956	0.9472	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:67	QRSHPLVLL	0.9956	0.9472	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:03	NQRSHPLVL	0.9953	0.987	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C12:12	NQRSHPLVL	0.9943	0.8827	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B27:03	QRSHPLVLL	0.9939	0.5702	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:10	QRSHPLVLL	0.9909	0.9668	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:09	NQRSHPLVL	0.9836	0.6063	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:12	NQRSHPLVL	0.9799	0.861	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:04	NQRSHPLVL	0.9714	0.6595	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B73:01	QRSHPLVLL	0.9617	0.7571	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:13	NQRSHPLVL	0.9488	0.9094	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:05	NQRSHPLVL	0.9462	0.8331	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:05	NQRSHPLVL	0.9219	0.894	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:08	NQRSHPLVL	0.9099	0.8238	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C12:16	NQRSHPLVL	0.9098	0.9103	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:29	NQRSHPLVL	0.8894	0.8179	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C03:14	NQRSHPLVL	0.8614	0.9585	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:10	NQRSHPLVL	0.8537	0.9364	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:46	NQRSHPLVL	0.8471	0.8264	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:95	NQRSHPLVL	0.8357	0.6025	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:80	NQRSHPLVL	0.833	0.9141	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:67	NQRSHPLVL	0.833	0.9141	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B14:03	ALNQRSHPL	0.8275	0.8264	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:19	NQRSHPLVL	0.8051	0.709	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:27	NQRSHPLVL	0.8	0.8847	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:13	SHPLVLLSV	0.7629	0.9346	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B14:03	NQRSHPLVL	0.7583	0.834	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:29	SHPLVLLSV	0.7353	0.9325	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:21	NQRSHPLVL	0.6602	0.6685	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B14:03	QRSHPLVLL	0.6142	0.7828	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B14:03	SHPLVLLSV	0.6129	0.8702	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C12:16	QRSHPLVLL	0.577	0.944	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C01:30	ALNQRSHPL	0.4047	0.9476	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B51:07	NQRSHPLVL	0.0759	0.563	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:04	LNQRSHPLVL	0.813	0.7265	8	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C15:05	RSHPLVLL	1	0.972	11	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C15:02	RSHPLVLL	1	0.9469	11	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C16:02	RSHPLVLL	0.9998	0.9963	11	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:22	QRSHPLVL	0.9997	0.7093	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:01	QRSHPLVL	0.9997	0.7024	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:31	QRSHPLVL	0.9994	0.9095	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:08	QRSHPLVL	0.9991	0.9853	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:17	QRSHPLVL	0.9872	0.9876	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:02	QRSHPLVL	0.9872	0.9876	10	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B27:10	QRSHPLVLL	0.9998	0.6827	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B27:06	QRSHPLVLL	0.9998	0.6208	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B27:09	QRSHPLVLL	0.9998	0.5364	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:01	QRSHPLVLL	0.9993	0.6643	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:31	QRSHPLVLL	0.9992	0.8972	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B38:05	QRSHPLVLL	0.9987	0.9533	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B08:18	ALNQRSHPL	0.9986	0.5706	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:31	SHPLVLLSV	0.9983	0.9116	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:17	QRSHPLVLL	0.9982	0.9465	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B38:05	SHPLVLLSV	0.9979	0.9764	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:135	NQRSHPLVL	0.9976	0.6241	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:125	NQRSHPLVL	0.9973	0.6248	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:33	NQRSHPLVL	0.9973	0.6248	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:34	NQRSHPLVL	0.9973	0.6248	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:27	NQRSHPLVL	0.9971	0.6867	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:02	QRSHPLVLL	0.9956	0.9472	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C12:03	NQRSHPLVL	0.9944	0.9535	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:17	NQRSHPLVL	0.9936	0.9848	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:08	QRSHPLVLL	0.9936	0.9823	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:02	NQRSHPLVL	0.9936	0.9848	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-A30:01	RSHPLVLLS	0.9923	0.9415	11	20
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-A02:03	ALNQRSHPL	0.992	0.5504	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:04	QRSHPLVLL	0.9906	0.9504	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:53	NQRSHPLVL	0.9868	0.5917	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:31	NQRSHPLVL	0.9867	0.8609	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:73	NQRSHPLVL	0.9831	0.7225	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:50	NQRSHPLVL	0.9808	0.7762	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:02	NQRSHPLVL	0.9805	0.8737	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:22	QRSHPLVLL	0.9793	0.6963	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:08	NQRSHPLVL	0.9764	0.9752	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B08:12	NQRSHPLVL	0.9631	0.5404	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:04	NQRSHPLVL	0.9606	0.9197	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C03:05	NQRSHPLVL	0.9597	0.8491	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:35	NQRSHPLVL	0.9588	0.631	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:54	NQRSHPLVL	0.9554	0.5587	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:09	QRSHPLVLL	0.9504	0.7083	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C03:67	NQRSHPLVL	0.9375	0.903	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:73	ALNQRSHPL	0.9347	0.5754	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:06	NQRSHPLVL	0.933	0.9804	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C12:02	NQRSHPLVL	0.9263	0.9279	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:09	SHPLVLLSV	0.9259	0.7147	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B08:12	ALNQRSHPL	0.9226	0.7644	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:30	NQRSHPLVL	0.9172	0.6323	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:11	NQRSHPLVL	0.9074	0.7527	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:17	NQRSHPLVL	0.9042	0.908	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:22	NQRSHPLVL	0.8781	0.6142	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:02	NQRSHPLVL	0.833	0.9141	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:04	ALNQRSHPL	0.8318	0.8888	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:30	ALNQRSHPL	0.8226	0.5985	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:01	NQRSHPLVL	0.8174	0.5564	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:06	QRSHPLVLL	0.7999	0.9866	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:12	NQRSHPLVL	0.7734	0.642	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B48:02	NQRSHPLVL	0.7601	0.5442	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:17	SHPLVLLSV	0.7459	0.9562	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C01:02	ALNQRSHPL	0.7421	0.935	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C01:03	ALNQRSHPL	0.7224	0.9102	7	16
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C07:04	SHPLVLLSV	0.7173	0.9631	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:39	NQRSHPLVL	0.6954	0.5633	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B39:11	SHPLVLLSV	0.693	0.8687	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:17	QRSHPLVLL	0.6421	0.9862	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:02	QRSHPLVLL	0.6421	0.9862	10	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B07:13	NQRSHPLVL	0.5774	0.8193	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:06	SHPLVLLSV	0.395	0.9908	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B35:28	NQRSHPLVL	0.2595	0.5763	9	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:17	SHPLVLLSV	0.1619	0.9936	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C06:02	SHPLVLLSV	0.1619	0.9936	12	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-C15:02	RSHPLVLLSV	0.9997	0.9326	11	21
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:73	NQRSHPLVLL	0.9933	0.7163	9	19
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:73	LNQRSHPLVL	0.8244	0.7771	8	18
KLK3-PSMD7	chr19	51361508	chr16	74330845	310	HLA-B15:73	ALNQRSHPLVL	0.9892	0.7884	7	18

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Potential FusionNeoAntigen Information of KLK3-PSMD7 in HLA II

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA II

FusionNeoAntigen peptide

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of KLK3-PSMD7

3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
47	AALNQRSHPLVLLS	KLK3	PSMD7	chr19	51361508	chr16	74330845	310

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of KLK3-PSMD7

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	47	AALNQRSHPLVLLS	-7.9962	-8.1096
HLA-B14:02	3BVN	47	AALNQRSHPLVLLS	-5.70842	-6.74372
HLA-B52:01	3W39	47	AALNQRSHPLVLLS	-6.83737	-6.95077
HLA-B52:01	3W39	47	AALNQRSHPLVLLS	-4.4836	-5.5189
HLA-A11:01	4UQ2	47	AALNQRSHPLVLLS	-10.0067	-10.1201
HLA-A11:01	4UQ2	47	AALNQRSHPLVLLS	-9.03915	-10.0745
HLA-A24:02	5HGA	47	AALNQRSHPLVLLS	-6.56204	-6.67544
HLA-A24:02	5HGA	47	AALNQRSHPLVLLS	-5.42271	-6.45801
HLA-B44:05	3DX8	47	AALNQRSHPLVLLS	-7.85648	-8.89178
HLA-B44:05	3DX8	47	AALNQRSHPLVLLS	-5.3978	-5.5112
HLA-A02:01	6TDR	47	AALNQRSHPLVLLS	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of KLK3-PSMD7

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
KLK3-PSMD7	chr19	51361508	chr16	74330845	10	18	QRSHPLVL	CAGAGGAGTCACCCCCTGGTGCTG
KLK3-PSMD7	chr19	51361508	chr16	74330845	10	19	QRSHPLVLL	CAGAGGAGTCACCCCCTGGTGCTGCTC
KLK3-PSMD7	chr19	51361508	chr16	74330845	11	19	RSHPLVLL	AGGAGTCACCCCCTGGTGCTGCTC
KLK3-PSMD7	chr19	51361508	chr16	74330845	11	20	RSHPLVLLS	AGGAGTCACCCCCTGGTGCTGCTCAGT
KLK3-PSMD7	chr19	51361508	chr16	74330845	11	21	RSHPLVLLSV	AGGAGTCACCCCCTGGTGCTGCTCAGTGTG
KLK3-PSMD7	chr19	51361508	chr16	74330845	12	21	SHPLVLLSV	AGTCACCCCCTGGTGCTGCTCAGTGTG
KLK3-PSMD7	chr19	51361508	chr16	74330845	7	16	ALNQRSHPL	GCATTGAACCAGAGGAGTCACCCCCTG
KLK3-PSMD7	chr19	51361508	chr16	74330845	7	18	ALNQRSHPLVL	GCATTGAACCAGAGGAGTCACCCCCTGGTGCTG
KLK3-PSMD7	chr19	51361508	chr16	74330845	8	18	LNQRSHPLVL	TTGAACCAGAGGAGTCACCCCCTGGTGCTG
KLK3-PSMD7	chr19	51361508	chr16	74330845	9	18	NQRSHPLVL	AACCAGAGGAGTCACCCCCTGGTGCTG
KLK3-PSMD7	chr19	51361508	chr16	74330845	9	19	NQRSHPLVLL	AACCAGAGGAGTCACCCCCTGGTGCTGCTC

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide

FusionNEoAntigen RNA sequence

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Information of the samples that have these potential fusion neoantigens of KLK3-PSMD7

These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.

Cancer type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
N/A	KLK3-PSMD7	chr19	51361508	ENST00000326003	chr16	74330845	ENST00000219313	BF858256

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Potential target of CAR-T therapy development for KLK3-PSMD7

Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to KLK3-PSMD7

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 KLK3-PSMD7

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

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)