![]() |
|||||||
|
Fusion Protein:PKN1-LDLR |
Fusion Gene and Fusion Protein Summary |
![]() |
Fusion partner gene information | Fusion gene name: PKN1-LDLR | FusionPDB ID: 65773 | FusionGDB2.0 ID: 65773 | Hgene | Tgene | Gene symbol | PKN1 | LDLR | Gene ID | 5585 | 3949 |
Gene name | protein kinase N1 | low density lipoprotein receptor | |
Synonyms | DBK|PAK-1|PAK1|PKN|PKN-ALPHA|PRK1|PRKCL1 | FH|FHC|FHCL1|LDLCQ2 | |
Cytomap | 19p13.12 | 19p13.2 | |
Type of gene | protein-coding | protein-coding | |
Description | 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 | low-density lipoprotein receptorLDL receptorlow-density lipoprotein receptor class A domain-containing protein 3 | |
Modification date | 20200329 | 20200322 | |
UniProtAcc | . | Q5SW96 Main function of 5'-partner protein: FUNCTION: Adapter protein (clathrin-associated sorting protein (CLASP)) required for efficient endocytosis of the LDL receptor (LDLR) in polarized cells such as hepatocytes and lymphocytes, but not in non-polarized cells (fibroblasts). May be required for LDL binding and internalization but not for receptor clustering in coated pits. May facilitate the endocytocis of LDLR and LDLR-LDL complexes from coated pits by stabilizing the interaction between the receptor and the structural components of the pits. May also be involved in the internalization of other LDLR family members. Binds to phosphoinositides, which regulate clathrin bud assembly at the cell surface. Required for trafficking of LRP2 to the endocytic recycling compartment which is necessary for LRP2 proteolysis, releasing a tail fragment which translocates to the nucleus and mediates transcriptional repression (By similarity). {ECO:0000250|UniProtKB:D3ZAR1, ECO:0000269|PubMed:15728179}. | |
Ensembl transtripts involved in fusion gene | ENST ids | ENST00000242783, ENST00000342216, ENST00000587429, | ENST00000560628, ENST00000455727, ENST00000535915, ENST00000545707, ENST00000557933, ENST00000558013, ENST00000558518, |
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 10 X 7 X 8=560 | 4 X 6 X 4=96 |
# samples | 12 | 5 | |
** MAII score | log2(12/560*10)=-2.22239242133645 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/96*10)=-0.941106310946431 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Fusion gene context | PubMed: PKN1 [Title/Abstract] AND LDLR [Title/Abstract] AND fusion [Title/Abstract] | ||
Fusion neoantigen context | PubMed: PKN1 [Title/Abstract] AND LDLR [Title/Abstract] AND neoantigen [Title/Abstract] | ||
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | PKN1(14557373)-LDLR(11227535), # samples:2 | ||
Anticipated loss of major functional domain due to fusion event. | PKN1-LDLR 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. PKN1-LDLR 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. PKN1-LDLR 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. PKN1-LDLR 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. PKN1-LDLR seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF. PKN1-LDLR seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. PKN1-LDLR seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF. PKN1-LDLR seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF. PKN1-LDLR seems lost the major protein functional domain in Tgene partner, which is a essential gene 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) |
![]() |
Partner | Gene | GO ID | GO term | PubMed ID |
Hgene | PKN1 | GO:0006357 | regulation of transcription by RNA polymerase II | 12514133 |
Hgene | PKN1 | GO:0006468 | protein phosphorylation | 17332740 |
Hgene | PKN1 | GO:0035407 | histone H3-T11 phosphorylation | 18066052 |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:14557373/chr19:11227535) - 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. |
![]() |
![]() |
![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
![]() |
![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
![]() |
Top |
Fusion Amino Acid Sequences |
![]() |
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) |
ENST00000242783 | PKN1 | chr19 | 14557373 | + | ENST00000558518 | LDLR | chr19 | 11227535 | + | 2500 | 775 | 165 | 1652 | 495 |
ENST00000242783 | PKN1 | chr19 | 14557373 | + | ENST00000557933 | LDLR | chr19 | 11227535 | + | 1924 | 775 | 165 | 1916 | 583 |
ENST00000242783 | PKN1 | chr19 | 14557373 | + | ENST00000455727 | LDLR | chr19 | 11227535 | + | 1821 | 775 | 165 | 1652 | 495 |
ENST00000242783 | PKN1 | chr19 | 14557373 | + | ENST00000535915 | LDLR | chr19 | 11227535 | + | 1875 | 775 | 165 | 1652 | 495 |
ENST00000242783 | PKN1 | chr19 | 14557373 | + | ENST00000545707 | LDLR | chr19 | 11227535 | + | 1794 | 775 | 165 | 1499 | 444 |
ENST00000242783 | PKN1 | chr19 | 14557373 | + | ENST00000558013 | LDLR | chr19 | 11227535 | + | 2143 | 775 | 165 | 1646 | 493 |
ENST00000342216 | PKN1 | chr19 | 14557373 | + | ENST00000558518 | LDLR | chr19 | 11227535 | + | 2384 | 659 | 31 | 1536 | 501 |
ENST00000342216 | PKN1 | chr19 | 14557373 | + | ENST00000557933 | LDLR | chr19 | 11227535 | + | 1808 | 659 | 31 | 1800 | 589 |
ENST00000342216 | PKN1 | chr19 | 14557373 | + | ENST00000455727 | LDLR | chr19 | 11227535 | + | 1705 | 659 | 31 | 1536 | 501 |
ENST00000342216 | PKN1 | chr19 | 14557373 | + | ENST00000535915 | LDLR | chr19 | 11227535 | + | 1759 | 659 | 31 | 1536 | 501 |
ENST00000342216 | PKN1 | chr19 | 14557373 | + | ENST00000545707 | LDLR | chr19 | 11227535 | + | 1678 | 659 | 31 | 1383 | 450 |
ENST00000342216 | PKN1 | chr19 | 14557373 | + | ENST00000558013 | LDLR | chr19 | 11227535 | + | 2027 | 659 | 31 | 1530 | 499 |
![]() |
Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000242783 | ENST00000558518 | PKN1 | chr19 | 14557373 | + | LDLR | chr19 | 11227535 | + | 0.022305634 | 0.9776944 |
ENST00000242783 | ENST00000557933 | PKN1 | chr19 | 14557373 | + | LDLR | chr19 | 11227535 | + | 0.10431041 | 0.8956896 |
ENST00000242783 | ENST00000455727 | PKN1 | chr19 | 14557373 | + | LDLR | chr19 | 11227535 | + | 0.025160855 | 0.97483915 |
ENST00000242783 | ENST00000535915 | PKN1 | chr19 | 14557373 | + | LDLR | chr19 | 11227535 | + | 0.026398083 | 0.97360194 |
ENST00000242783 | ENST00000545707 | PKN1 | chr19 | 14557373 | + | LDLR | chr19 | 11227535 | + | 0.012469866 | 0.9875301 |
ENST00000242783 | ENST00000558013 | PKN1 | chr19 | 14557373 | + | LDLR | chr19 | 11227535 | + | 0.022939015 | 0.977061 |
ENST00000342216 | ENST00000558518 | PKN1 | chr19 | 14557373 | + | LDLR | chr19 | 11227535 | + | 0.04011812 | 0.95988184 |
ENST00000342216 | ENST00000557933 | PKN1 | chr19 | 14557373 | + | LDLR | chr19 | 11227535 | + | 0.11569983 | 0.88430023 |
ENST00000342216 | ENST00000455727 | PKN1 | chr19 | 14557373 | + | LDLR | chr19 | 11227535 | + | 0.038374744 | 0.9616252 |
ENST00000342216 | ENST00000535915 | PKN1 | chr19 | 14557373 | + | LDLR | chr19 | 11227535 | + | 0.04130113 | 0.9586988 |
ENST00000342216 | ENST00000545707 | PKN1 | chr19 | 14557373 | + | LDLR | chr19 | 11227535 | + | 0.021241404 | 0.9787586 |
ENST00000342216 | ENST00000558013 | PKN1 | chr19 | 14557373 | + | LDLR | chr19 | 11227535 | + | 0.033702962 | 0.96629703 |
![]() |
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 |
Top |
Fusion Protein Breakpoint Sequences for PKN1-LDLR |
![]() |
Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
PKN1 | chr19 | 14557373 | LDLR | chr19 | 11227535 | 659 | 209 | GQLENQAAPDDTQDLLSGRLYWVDSK |
PKN1 | chr19 | 14557373 | LDLR | chr19 | 11227535 | 775 | 203 | GQLENQAAPDDTQDLLSGRLYWVDSK |
Top |
Potential FusionNeoAntigen Information of PKN1-LDLR in HLA I |
![]() |
PKN1-LDLR_14557373_11227535.msa |
![]() * 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) |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-A66:01 | DTQDLLSGR | 0.9983 | 0.553 | 10 | 19 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-A26:03 | DTQDLLSGR | 0.9916 | 0.5465 | 10 | 19 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B44:03 | QDLLSGRLY | 0.9399 | 0.8416 | 12 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B35:03 | APDDTQDLL | 0.8432 | 0.9728 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-A68:08 | DTQDLLSGR | 0.8368 | 0.5094 | 10 | 19 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B35:08 | APDDTQDLL | 0.8282 | 0.9659 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B07:05 | APDDTQDLL | 0.8003 | 0.598 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B39:13 | TQDLLSGRL | 0.7098 | 0.915 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B38:01 | TQDLLSGRL | 0.6888 | 0.9518 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B35:02 | APDDTQDLL | 0.5777 | 0.982 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B35:04 | APDDTQDLL | 0.5777 | 0.982 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B13:01 | TQDLLSGRL | 0.4506 | 0.9571 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B81:01 | APDDTQDLL | 0.1975 | 0.6209 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B82:01 | APDDTQDLL | 0.1136 | 0.5119 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B44:02 | QDLLSGRLYW | 0.997 | 0.6148 | 12 | 22 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:01 | TQDLLSGRLY | 0.9955 | 0.5661 | 11 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:25 | TQDLLSGRLY | 0.9786 | 0.6567 | 11 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-A32:13 | QDLLSGRLYW | 0.9371 | 0.903 | 12 | 22 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-A66:01 | DDTQDLLSGR | 0.8788 | 0.6447 | 9 | 19 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-A68:24 | DDTQDLLSGR | 0.8433 | 0.663 | 9 | 19 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-A68:03 | DDTQDLLSGR | 0.8312 | 0.6264 | 9 | 19 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-A68:05 | DDTQDLLSGR | 0.7998 | 0.635 | 9 | 19 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-A32:13 | TQDLLSGRLYW | 0.9941 | 0.9148 | 11 | 22 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B35:04 | QAAPDDTQDLL | 0.9784 | 0.9883 | 5 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B35:02 | QAAPDDTQDLL | 0.9784 | 0.9883 | 5 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B39:10 | APDDTQDL | 0.5343 | 0.9597 | 7 | 15 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C05:09 | TQDLLSGRL | 0.9998 | 0.8881 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C08:15 | TQDLLSGRL | 0.9996 | 0.9763 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C05:09 | APDDTQDLL | 0.9969 | 0.9818 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C04:10 | APDDTQDLL | 0.9962 | 0.8615 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C04:07 | APDDTQDLL | 0.996 | 0.8965 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C08:15 | APDDTQDLL | 0.99 | 0.9853 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C01:17 | AAPDDTQDL | 0.9558 | 0.9817 | 6 | 15 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B39:09 | TQDLLSGRL | 0.8104 | 0.7493 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B07:12 | APDDTQDLL | 0.7826 | 0.7884 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C01:30 | AAPDDTQDL | 0.7662 | 0.9785 | 6 | 15 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B39:08 | TQDLLSGRL | 0.757 | 0.9033 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B39:05 | TQDLLSGRL | 0.6835 | 0.894 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B35:12 | APDDTQDLL | 0.5777 | 0.982 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B39:08 | APDDTQDLL | 0.4786 | 0.9709 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B39:09 | APDDTQDLL | 0.4741 | 0.9161 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B39:10 | APDDTQDLL | 0.469 | 0.971 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C08:03 | APDDTQDLL | 0.4384 | 0.9827 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C04:14 | APDDTQDLL | 0.3972 | 0.8404 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C05:09 | AAPDDTQDLL | 0.9994 | 0.9822 | 6 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C08:15 | AAPDDTQDLL | 0.9981 | 0.9863 | 6 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B44:08 | QDLLSGRLYW | 0.994 | 0.7772 | 12 | 22 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C01:17 | AAPDDTQDLL | 0.9919 | 0.9721 | 6 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:05 | TQDLLSGRLY | 0.9798 | 0.5959 | 11 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-A68:01 | DDTQDLLSGR | 0.8433 | 0.663 | 9 | 19 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-A33:03 | DDTQDLLSGR | 0.7717 | 0.5535 | 9 | 19 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C08:15 | QAAPDDTQDLL | 0.9999 | 0.9793 | 5 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B44:08 | TQDLLSGRLYW | 0.9984 | 0.8235 | 11 | 22 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B35:12 | QAAPDDTQDLL | 0.9784 | 0.9883 | 5 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C04:03 | TQDLLSGRL | 0.9998 | 0.9163 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C05:01 | TQDLLSGRL | 0.9998 | 0.8881 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C08:02 | TQDLLSGRL | 0.9996 | 0.9763 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C05:01 | APDDTQDLL | 0.9969 | 0.9818 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C04:03 | APDDTQDLL | 0.9966 | 0.9272 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C04:01 | APDDTQDLL | 0.996 | 0.8965 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C18:01 | APDDTQDLL | 0.991 | 0.8942 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C08:02 | APDDTQDLL | 0.99 | 0.9853 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C01:03 | AAPDDTQDL | 0.9713 | 0.9797 | 6 | 15 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C01:02 | AAPDDTQDL | 0.9606 | 0.9808 | 6 | 15 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B44:26 | QDLLSGRLY | 0.9399 | 0.8416 | 12 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B44:07 | QDLLSGRLY | 0.9399 | 0.8416 | 12 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B44:13 | QDLLSGRLY | 0.9399 | 0.8416 | 12 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C03:06 | AAPDDTQDL | 0.8964 | 0.9931 | 6 | 15 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B39:02 | TQDLLSGRL | 0.8274 | 0.9073 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B35:13 | APDDTQDLL | 0.7916 | 0.974 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B39:11 | TQDLLSGRL | 0.7074 | 0.8894 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B38:05 | TQDLLSGRL | 0.6888 | 0.9518 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B35:09 | APDDTQDLL | 0.5777 | 0.982 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B67:01 | APDDTQDLL | 0.5011 | 0.9268 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B39:11 | APDDTQDLL | 0.4865 | 0.9299 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C08:01 | APDDTQDLL | 0.4384 | 0.9827 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:09 | TQDLLSGRL | 0.374 | 0.8368 | 11 | 20 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B82:02 | APDDTQDLL | 0.1136 | 0.5119 | 7 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C05:01 | AAPDDTQDLL | 0.9994 | 0.9822 | 6 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C04:03 | AAPDDTQDLL | 0.9993 | 0.925 | 6 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C08:02 | AAPDDTQDLL | 0.9981 | 0.9863 | 6 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C01:03 | AAPDDTQDLL | 0.9981 | 0.9688 | 6 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B44:22 | QDLLSGRLYW | 0.997 | 0.6148 | 12 | 22 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B44:21 | QDLLSGRLYW | 0.9964 | 0.5775 | 12 | 22 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:125 | TQDLLSGRLY | 0.9955 | 0.5661 | 11 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:34 | TQDLLSGRLY | 0.9955 | 0.5661 | 11 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:33 | TQDLLSGRLY | 0.9955 | 0.5661 | 11 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:135 | TQDLLSGRLY | 0.9952 | 0.5869 | 11 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C01:02 | AAPDDTQDLL | 0.9949 | 0.9709 | 6 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:50 | TQDLLSGRLY | 0.9939 | 0.7539 | 11 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:12 | TQDLLSGRLY | 0.9937 | 0.5042 | 11 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:53 | TQDLLSGRLY | 0.9867 | 0.5378 | 11 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:20 | TQDLLSGRLY | 0.9812 | 0.712 | 11 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:39 | TQDLLSGRLY | 0.981 | 0.5088 | 11 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B35:28 | TQDLLSGRLY | 0.9727 | 0.7642 | 11 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-A32:01 | QDLLSGRLYW | 0.9249 | 0.9415 | 12 | 22 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-C08:02 | QAAPDDTQDLL | 0.9999 | 0.9793 | 5 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-A25:01 | DTQDLLSGRLY | 0.9974 | 0.616 | 10 | 21 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B15:24 | TQDLLSGRLYW | 0.9954 | 0.9504 | 11 | 22 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B51:05 | QAAPDDTQDLL | 0.9916 | 0.5825 | 5 | 16 |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 | HLA-B35:09 | QAAPDDTQDLL | 0.9784 | 0.9883 | 5 | 16 |
Top |
Potential FusionNeoAntigen Information of PKN1-LDLR in HLA II |
![]() |
![]() * 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) |
Top |
Fusion breakpoint peptide structures of PKN1-LDLR |
![]() * 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 |
59 | AAPDDTQDLLSGRL | PKN1 | LDLR | chr19 | 14557373 | chr19 | 11227535 | 775 |
Top |
Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PKN1-LDLR |
![]() * 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 | 59 | AAPDDTQDLLSGRL | -7.9953 | -8.11 |
HLA-B14:02 | 3BVN | 59 | AAPDDTQDLLSGRL | -6.76387 | -7.80047 |
HLA-B52:01 | 3W39 | 59 | AAPDDTQDLLSGRL | -6.72115 | -6.83585 |
HLA-B52:01 | 3W39 | 59 | AAPDDTQDLLSGRL | -4.59437 | -5.63097 |
HLA-A24:02 | 5HGA | 59 | AAPDDTQDLLSGRL | -8.73414 | -8.84884 |
HLA-A24:02 | 5HGA | 59 | AAPDDTQDLLSGRL | -6.32039 | -7.35699 |
HLA-B44:05 | 3DX8 | 59 | AAPDDTQDLLSGRL | -5.20472 | -5.31942 |
HLA-B44:05 | 3DX8 | 59 | AAPDDTQDLLSGRL | -4.80907 | -5.84567 |
HLA-A02:01 | 6TDR | 59 | AAPDDTQDLLSGRL | 0.647201 | -0.389399 |
Top |
Vaccine Design for the FusionNeoAntigens of PKN1-LDLR |
![]() |
Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 10 | 19 | DTQDLLSGR | ACACCCAAGATCTCCTCAGTGGCCGCC |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 10 | 21 | DTQDLLSGRLY | ACACCCAAGATCTCCTCAGTGGCCGCCTCTACT |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 11 | 20 | TQDLLSGRL | CCCAAGATCTCCTCAGTGGCCGCCTCT |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 11 | 21 | TQDLLSGRLY | CCCAAGATCTCCTCAGTGGCCGCCTCTACT |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 11 | 22 | TQDLLSGRLYW | CCCAAGATCTCCTCAGTGGCCGCCTCTACTGGG |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 12 | 21 | QDLLSGRLY | AAGATCTCCTCAGTGGCCGCCTCTACT |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 12 | 22 | QDLLSGRLYW | AAGATCTCCTCAGTGGCCGCCTCTACTGGG |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 5 | 16 | QAAPDDTQDLL | AGGCAGCCCCGGATGACACCCAAGATCTCCTCA |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 6 | 15 | AAPDDTQDL | CAGCCCCGGATGACACCCAAGATCTCC |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 6 | 16 | AAPDDTQDLL | CAGCCCCGGATGACACCCAAGATCTCCTCA |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 7 | 15 | APDDTQDL | CCCCGGATGACACCCAAGATCTCC |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 7 | 16 | APDDTQDLL | CCCCGGATGACACCCAAGATCTCCTCA |
PKN1-LDLR | chr19 | 14557373 | chr19 | 11227535 | 9 | 19 | DDTQDLLSGR | ATGACACCCAAGATCTCCTCAGTGGCCGCC |
![]() |
Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
Top |
Information of the samples that have these potential fusion neoantigens of PKN1-LDLR |
![]() |
Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
BRCA | PKN1-LDLR | chr19 | 14557373 | ENST00000242783 | chr19 | 11227535 | ENST00000455727 | TCGA-C8-A26W-01A |
Top |
Potential target of CAR-T therapy development for PKN1-LDLR |
![]() |
![]() * 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 |
Tgene | LDLR | chr19:14557373 | chr19:11227535 | ENST00000455727 | 8 | 16 | 789_810 | 0 | 693.0 | Transmembrane | Helical | |
Tgene | LDLR | chr19:14557373 | chr19:11227535 | ENST00000535915 | 9 | 17 | 789_810 | 0 | 820.0 | Transmembrane | Helical | |
Tgene | LDLR | chr19:14557373 | chr19:11227535 | ENST00000545707 | 9 | 16 | 789_810 | 0 | 683.0 | Transmembrane | Helical | |
Tgene | LDLR | chr19:14557373 | chr19:11227535 | ENST00000558013 | 10 | 18 | 789_810 | 0 | 859.0 | Transmembrane | Helical | |
Tgene | LDLR | chr19:14557373 | chr19:11227535 | ENST00000558518 | 10 | 18 | 789_810 | 0 | 861.0 | Transmembrane | Helical |
![]() * 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 |
Top |
Related Drugs to PKN1-LDLR |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
Top |
Related Diseases to PKN1-LDLR |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |