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Fusion Protein:AP3S1-MITF |
Fusion Gene and Fusion Protein Summary |
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Fusion partner gene information | Fusion gene name: AP3S1-MITF | FusionPDB ID: 5299 | FusionGDB2.0 ID: 5299 | Hgene | Tgene | Gene symbol | AP3S1 | MITF | Gene ID | 1176 | 4286 |
Gene name | adaptor related protein complex 3 subunit sigma 1 | melanocyte inducing transcription factor | |
Synonyms | CLAPS3|Sigma3A | CMM8|COMMAD|MI|WS2|WS2A|bHLHe32 | |
Cytomap | 5q22.3-q23.1 | 3p13 | |
Type of gene | protein-coding | protein-coding | |
Description | AP-3 complex subunit sigma-1adapter-related protein complex 3 subunit sigma-1adaptor related protein complex 3 sigma 1 subunitclathrin adaptor complex AP3, sigma-3A subunitclathrin-associated/assembly/adapter protein, small 3clathrin-associated/assem | microphthalmia-associated transcription factorclass E basic helix-loop-helix protein 32melanogenesis associated transcription factormicrophtalmia-associated transcription factor | |
Modification date | 20200320 | 20200329 | |
UniProtAcc | Q92572 Main function of 5'-partner protein: FUNCTION: Part of the AP-3 complex, an adaptor-related complex which is not clathrin-associated. The complex is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. In concert with the BLOC-1 complex, AP-3 is required to target cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals. | O75030 Main function of 5'-partner protein: FUNCTION: Transcription factor that regulates the expression of genes with essential roles in cell differentiation, proliferation and survival. Binds to M-boxes (5'-TCATGTG-3') and symmetrical DNA sequences (E-boxes) (5'-CACGTG-3') found in the promoters of target genes, such as BCL2 and tyrosinase (TYR). Plays an important role in melanocyte development by regulating the expression of tyrosinase (TYR) and tyrosinase-related protein 1 (TYRP1). Plays a critical role in the differentiation of various cell types, such as neural crest-derived melanocytes, mast cells, osteoclasts and optic cup-derived retinal pigment epithelium. {ECO:0000269|PubMed:10587587, ECO:0000269|PubMed:22647378, ECO:0000269|PubMed:27889061, ECO:0000269|PubMed:9647758}. | |
Ensembl transtripts involved in fusion gene | ENST ids | ENST00000316788, ENST00000505423, | ENST00000394348, ENST00000314557, ENST00000314589, ENST00000328528, ENST00000352241, ENST00000394351, ENST00000394355, ENST00000448226, ENST00000472437, ENST00000531774, |
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 9 X 5 X 6=270 | 10 X 9 X 7=630 |
# samples | 9 | 10 | |
** MAII score | log2(9/270*10)=-1.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(10/630*10)=-2.65535182861255 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Fusion gene context | PubMed: AP3S1 [Title/Abstract] AND MITF [Title/Abstract] AND fusion [Title/Abstract] | ||
Fusion neoantigen context | PubMed: AP3S1 [Title/Abstract] AND MITF [Title/Abstract] AND neoantigen [Title/Abstract] | ||
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | AP3S1(115205825)-MITF(69986973), # samples:1 | ||
Anticipated loss of major functional domain due to fusion event. | AP3S1-MITF 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. AP3S1-MITF 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) |
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Partner | Gene | GO ID | GO term | PubMed ID |
Tgene | MITF | GO:0010628 | positive regulation of gene expression | 22234890 |
Tgene | MITF | GO:0045893 | positive regulation of transcription, DNA-templated | 9647758 |
Tgene | MITF | GO:0045944 | positive regulation of transcription by RNA polymerase II | 20530484|21209915 |
Tgene | MITF | GO:0065003 | protein-containing complex assembly | 20530484 |
Tgene | MITF | GO:2000144 | positive regulation of DNA-templated transcription, initiation | 8995290|12204775 |
Tgene | MITF | GO:2001141 | regulation of RNA biosynthetic process | 16411896 |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:115205825/chr3:69986973) - 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. |
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![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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![]() * 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 |
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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) |
ENST00000316788 | AP3S1 | chr5 | 115205825 | + | ENST00000352241 | MITF | chr3 | 69986973 | + | 5127 | 830 | 257 | 2038 | 593 |
ENST00000316788 | AP3S1 | chr5 | 115205825 | + | ENST00000448226 | MITF | chr3 | 69986973 | + | 2838 | 830 | 257 | 2056 | 599 |
ENST00000316788 | AP3S1 | chr5 | 115205825 | + | ENST00000472437 | MITF | chr3 | 69986973 | + | 2438 | 830 | 257 | 2038 | 593 |
ENST00000316788 | AP3S1 | chr5 | 115205825 | + | ENST00000328528 | MITF | chr3 | 69986973 | + | 5128 | 830 | 257 | 2038 | 593 |
ENST00000316788 | AP3S1 | chr5 | 115205825 | + | ENST00000314589 | MITF | chr3 | 69986973 | + | 2438 | 830 | 257 | 2038 | 593 |
ENST00000316788 | AP3S1 | chr5 | 115205825 | + | ENST00000394355 | MITF | chr3 | 69986973 | + | 5124 | 830 | 257 | 2038 | 593 |
ENST00000316788 | AP3S1 | chr5 | 115205825 | + | ENST00000314557 | MITF | chr3 | 69986973 | + | 2459 | 830 | 257 | 2038 | 593 |
ENST00000316788 | AP3S1 | chr5 | 115205825 | + | ENST00000394351 | MITF | chr3 | 69986973 | + | 2633 | 830 | 257 | 2056 | 599 |
ENST00000316788 | AP3S1 | chr5 | 115205825 | + | ENST00000531774 | MITF | chr3 | 69986973 | + | 1871 | 830 | 257 | 1870 | 538 |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000316788 | ENST00000352241 | AP3S1 | chr5 | 115205825 | + | MITF | chr3 | 69986973 | + | 0.000863559 | 0.9991365 |
ENST00000316788 | ENST00000448226 | AP3S1 | chr5 | 115205825 | + | MITF | chr3 | 69986973 | + | 0.005037619 | 0.99496233 |
ENST00000316788 | ENST00000472437 | AP3S1 | chr5 | 115205825 | + | MITF | chr3 | 69986973 | + | 0.011610089 | 0.98838997 |
ENST00000316788 | ENST00000328528 | AP3S1 | chr5 | 115205825 | + | MITF | chr3 | 69986973 | + | 0.000861224 | 0.9991387 |
ENST00000316788 | ENST00000314589 | AP3S1 | chr5 | 115205825 | + | MITF | chr3 | 69986973 | + | 0.011610089 | 0.98838997 |
ENST00000316788 | ENST00000394355 | AP3S1 | chr5 | 115205825 | + | MITF | chr3 | 69986973 | + | 0.000864954 | 0.9991351 |
ENST00000316788 | ENST00000314557 | AP3S1 | chr5 | 115205825 | + | MITF | chr3 | 69986973 | + | 0.011086946 | 0.988913 |
ENST00000316788 | ENST00000394351 | AP3S1 | chr5 | 115205825 | + | MITF | chr3 | 69986973 | + | 0.006687081 | 0.9933129 |
ENST00000316788 | ENST00000531774 | AP3S1 | chr5 | 115205825 | + | MITF | chr3 | 69986973 | + | 0.023082968 | 0.976917 |
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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 AP3S1-MITF |
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Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
AP3S1 | chr5 | 115205825 | MITF | chr3 | 69986973 | 830 | 190 | DSSESELGILDLIQVQTHLENPTKYH |
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Potential FusionNeoAntigen Information of AP3S1-MITF in HLA I |
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AP3S1-MITF_115205825_69986973.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) |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 830 | HLA-A02:07 | ILDLIQVQT | 0.9618 | 0.8377 | 8 | 17 |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 830 | HLA-B51:07 | DLIQVQTHL | 0.8111 | 0.8459 | 10 | 19 |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 830 | HLA-C05:09 | ILDLIQVQTHL | 1 | 0.9786 | 8 | 19 |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 830 | HLA-A02:07 | ILDLIQVQTHL | 0.9915 | 0.7583 | 8 | 19 |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 830 | HLA-A25:01 | DLIQVQTHL | 0.9897 | 0.9556 | 10 | 19 |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 830 | HLA-A69:01 | DLIQVQTHL | 0.7904 | 0.7778 | 10 | 19 |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 830 | HLA-B08:12 | DLIQVQTHL | 0.6253 | 0.9103 | 10 | 19 |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 830 | HLA-C05:01 | ILDLIQVQTHL | 1 | 0.9786 | 8 | 19 |
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Potential FusionNeoAntigen Information of AP3S1-MITF in HLA II |
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AP3S1-MITF_115205825_69986973.msa |
![]() * 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) |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 830 | DRB1-0411 | ILDLIQVQTHLENPT | 8 | 23 |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 830 | DRB1-0491 | ILDLIQVQTHLENPT | 8 | 23 |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 830 | DRB1-1457 | ILDLIQVQTHLENPT | 8 | 23 |
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Fusion breakpoint peptide structures of AP3S1-MITF |
![]() * 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 |
5003 | LGILDLIQVQTHLE | AP3S1 | MITF | chr5 | 115205825 | chr3 | 69986973 | 830 |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of AP3S1-MITF |
![]() * 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 | 5003 | LGILDLIQVQTHLE | -7.9962 | -8.1096 |
HLA-B14:02 | 3BVN | 5003 | LGILDLIQVQTHLE | -5.70842 | -6.74372 |
HLA-B52:01 | 3W39 | 5003 | LGILDLIQVQTHLE | -6.83737 | -6.95077 |
HLA-B52:01 | 3W39 | 5003 | LGILDLIQVQTHLE | -4.4836 | -5.5189 |
HLA-A11:01 | 4UQ2 | 5003 | LGILDLIQVQTHLE | -10.0067 | -10.1201 |
HLA-A11:01 | 4UQ2 | 5003 | LGILDLIQVQTHLE | -9.03915 | -10.0745 |
HLA-A24:02 | 5HGA | 5003 | LGILDLIQVQTHLE | -6.56204 | -6.67544 |
HLA-A24:02 | 5HGA | 5003 | LGILDLIQVQTHLE | -5.42271 | -6.45801 |
HLA-B44:05 | 3DX8 | 5003 | LGILDLIQVQTHLE | -7.85648 | -8.89178 |
HLA-B44:05 | 3DX8 | 5003 | LGILDLIQVQTHLE | -5.3978 | -5.5112 |
HLA-A02:01 | 6TDR | 5003 | LGILDLIQVQTHLE | -3.37154 | -4.40684 |
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Vaccine Design for the FusionNeoAntigens of AP3S1-MITF |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 10 | 19 | DLIQVQTHL | CTAATTCAAGTGCAGACCCACCTCGAA |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 8 | 17 | ILDLIQVQT | TTAGATCTAATTCAAGTGCAGACCCAC |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 8 | 19 | ILDLIQVQTHL | TTAGATCTAATTCAAGTGCAGACCCACCTCGAA |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
AP3S1-MITF | chr5 | 115205825 | chr3 | 69986973 | 8 | 23 | ILDLIQVQTHLENPT | TTAGATCTAATTCAAGTGCAGACCCACCTCGAAAACCCCACCAAG |
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Information of the samples that have these potential fusion neoantigens of AP3S1-MITF |
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Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
KIRC | AP3S1-MITF | chr5 | 115205825 | ENST00000316788 | chr3 | 69986973 | ENST00000314557 | TCGA-A3-3376-01A |
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Potential target of CAR-T therapy development for AP3S1-MITF |
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![]() * 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 |
![]() * 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 AP3S1-MITF |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to AP3S1-MITF |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Hgene | AP3S1 | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
Tgene | MITF | C2700265 | Waardenburg Syndrome Type 2 | 11 | CLINGEN;CTD_human;ORPHANET |
Tgene | MITF | C1860339 | WAARDENBURG SYNDROME, TYPE IIA | 5 | CTD_human;GENOMICS_ENGLAND;UNIPROT |
Tgene | MITF | C3152204 | MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 8 | 4 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
Tgene | MITF | C4310625 | COLOBOMA, OSTEOPETROSIS, MICROPHTHALMIA, MACROCEPHALY, ALBINISM, AND DEAFNESS | 3 | CTD_human;GENOMICS_ENGLAND;UNIPROT |
Tgene | MITF | C0391816 | Tietz syndrome | 2 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
Tgene | MITF | C1863198 | ALBINISM, OCULAR, WITH SENSORINEURAL DEAFNESS (disorder) | 2 | GENOMICS_ENGLAND;ORPHANET |
Tgene | MITF | C3266898 | Waardenburg Syndrome | 2 | GENOMICS_ENGLAND;ORPHANET |
Tgene | MITF | C0007134 | Renal Cell Carcinoma | 1 | CTD_human |
Tgene | MITF | C0007621 | Neoplastic Cell Transformation | 1 | CTD_human |
Tgene | MITF | C0011052 | Prelingual Deafness | 1 | CTD_human |
Tgene | MITF | C0011053 | Deafness | 1 | CTD_human |
Tgene | MITF | C0022283 | Incontinentia Pigmenti Achromians | 1 | CTD_human |
Tgene | MITF | C0025202 | melanoma | 1 | CGI;CTD_human |
Tgene | MITF | C0036305 | Schamberg Disease | 1 | CTD_human |
Tgene | MITF | C0078918 | Albinism, Oculocutaneous | 1 | CTD_human |
Tgene | MITF | C0078921 | Albinism, Tyrosinase-Negative | 1 | CTD_human |
Tgene | MITF | C0078922 | Albinism, Tyrosinase-Positive | 1 | CTD_human |
Tgene | MITF | C0078923 | Albinism, Yellow-Mutant | 1 | CTD_human |
Tgene | MITF | C0086395 | Hearing Loss, Extreme | 1 | CTD_human |
Tgene | MITF | C0151779 | Cutaneous Melanoma | 1 | CGI;CTD_human |
Tgene | MITF | C0279702 | Conventional (Clear Cell) Renal Cell Carcinoma | 1 | CTD_human |
Tgene | MITF | C0549567 | Pigmentation Disorders | 1 | CTD_human |
Tgene | MITF | C0581883 | Complete Hearing Loss | 1 | CTD_human |
Tgene | MITF | C0751068 | Deafness, Acquired | 1 | CTD_human |
Tgene | MITF | C1266042 | Chromophobe Renal Cell Carcinoma | 1 | CTD_human |
Tgene | MITF | C1266043 | Sarcomatoid Renal Cell Carcinoma | 1 | CTD_human |
Tgene | MITF | C1266044 | Collecting Duct Carcinoma of the Kidney | 1 | CTD_human |
Tgene | MITF | C1306837 | Papillary Renal Cell Carcinoma | 1 | CTD_human;ORPHANET |
Tgene | MITF | C1708353 | Hereditary Paraganglioma-Pheochromocytoma Syndrome | 1 | CLINGEN |
Tgene | MITF | C1848519 | WAARDENBURG SYNDROME, TYPE 4A | 1 | ORPHANET |
Tgene | MITF | C2314896 | Familial Atypical Mole Melanoma Syndrome | 1 | ORPHANET |
Tgene | MITF | C2700405 | WAARDENBURG SYNDROME, TYPE IIE | 1 | CTD_human |
Tgene | MITF | C3665473 | Bilateral Deafness | 1 | CTD_human |
Tgene | MITF | C4082305 | Deaf Mutism | 1 | CTD_human |
Tgene | MITF | C4518333 | Clear cell papillary renal cell carcinoma | 1 | ORPHANET |
Tgene | MITF | C4750999 | Ocular albinism with congenital sensorineural deafness | 1 | GENOMICS_ENGLAND |