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Fusion Protein:PTPN23-SMARCC1 |
Fusion Protein Summary |
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Fusion partner gene information | Fusion gene name: PTPN23-SMARCC1 | FusionPDB ID: 70256 | FusionGDB2.0 ID: 70256 | Hgene | Tgene | Gene symbol | PTPN23 | SMARCC1 | Gene ID | 25930 | 6599 |
Gene name | protein tyrosine phosphatase non-receptor type 23 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1 | |
Synonyms | HD-PTP|HDPTP|PTP-TD14 | BAF155|CRACC1|Rsc8|SRG3|SWI3 | |
Cytomap | 3p21.31 | 3p21.31 | |
Type of gene | protein-coding | protein-coding | |
Description | tyrosine-protein phosphatase non-receptor type 23his domain-containing protein tyrosine phosphataseprotein tyrosine phosphatase TD14 | SWI/SNF complex subunit SMARCC1BRG1-associated factor 155SWI/SNF complex 155 kDa subunitSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1chromatin remodeling complex BAF155 subunitmammalian chromatin remode | |
Modification date | 20200313 | 20200313 | |
UniProtAcc | . | . | |
Ensembl transtripts involved in fusion gene | ENST ids | ENST00000265562, ENST00000431726, | ENST00000425518, ENST00000254480, |
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 11 X 5 X 9=495 | 18 X 18 X 8=2592 |
# samples | 14 | 24 | |
** MAII score | log2(14/495*10)=-1.82200169802201 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(24/2592*10)=-3.43295940727611 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Context (manual curation of fusion genes in FusionPDB) | PubMed: PTPN23 [Title/Abstract] AND SMARCC1 [Title/Abstract] AND fusion [Title/Abstract] | ||
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | PTPN23(47422670)-SMARCC1(47651817), # samples:1 | ||
Anticipated loss of major functional domain due to fusion event. | PTPN23-SMARCC1 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. PTPN23-SMARCC1 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. PTPN23-SMARCC1 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. PTPN23-SMARCC1 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 | SMARCC1 | GO:0006337 | nucleosome disassembly | 8895581 |
Tgene | SMARCC1 | GO:0006338 | chromatin remodeling | 10078207|11018012|11726552 |
Tgene | SMARCC1 | GO:0045893 | positive regulation of transcription, DNA-templated | 11018012 |
![]() * 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 Gene Sample Information |
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![]() * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
ChimerDB4 | GBM | TCGA-06-0878-01A | PTPN23 | chr3 | 47422670 | + | SMARCC1 | chr3 | 47651817 | - |
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Fusion ORF Analysis |
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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) |
ENST00000265562 | PTPN23 | chr3 | 47422670 | + | ENST00000254480 | SMARCC1 | chr3 | 47651817 | - | 3635 | 161 | 5 | 697 | 230 |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000265562 | ENST00000254480 | PTPN23 | chr3 | 47422670 | + | SMARCC1 | chr3 | 47651817 | - | 0.010579869 | 0.9894202 |
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Fusion Amino Acid Sequences |
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>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP >70256_70256_1_PTPN23-SMARCC1_PTPN23_chr3_47422670_ENST00000265562_SMARCC1_chr3_47651817_ENST00000254480_length(amino acids)=230AA_BP=52 MGSWLSQQLQQLREWPGGRRVPAAMEAVPRMPMIWLDLKEAGDFHFQPAVKKLEQQRQQLLTERQNFHMEQLKYAELRARQQMEQQQHGQ NPQQAHQHSGGPGLAPLGAAGHPGMMPHQQPPPYPLMHHQMPPPHPPQPGQIPGPGSMMPGQHMPGRMIPTVAANIHPSGSGPTPPGMPP -------------------------------------------------------------- |
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Fusion Protein Functional Features |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:47422670/chr3:47651817) - 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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Hgene | Tgene |
. | . |
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes. | FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes. |
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- 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 | SMARCC1 | chr3:47422670 | chr3:47651817 | ENST00000254480 | 24 | 28 | 977_1105 | 927.0 | 1106.0 | Compositional bias | Note=Pro-rich |
- Not-retained protein feature among the 13 regional features. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 550_623 | 28.0 | 1637.0 | Coiled coil | Ontology_term=ECO:0000255 |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 1509_1573 | 28.0 | 1637.0 | Compositional bias | Note=Pro-rich |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 716_1108 | 28.0 | 1637.0 | Compositional bias | Note=Pro-rich |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 1192_1452 | 28.0 | 1637.0 | Domain | Tyrosine-protein phosphatase |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 8_394 | 28.0 | 1637.0 | Domain | BRO1 |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 770_1130 | 28.0 | 1637.0 | Region | Note=His |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 953_964 | 28.0 | 1637.0 | Region | Note=6 X 2 AA approximate tandem repeats of P-Q |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 250_283 | 28.0 | 1637.0 | Repeat | Note=TPR 1 |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 374_407 | 28.0 | 1637.0 | Repeat | Note=TPR 2 |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 953_954 | 28.0 | 1637.0 | Repeat | Note=1 |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 955_956 | 28.0 | 1637.0 | Repeat | Note=2 |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 957_958 | 28.0 | 1637.0 | Repeat | Note=3 |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 959_960 | 28.0 | 1637.0 | Repeat | Note=4 |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 961_962 | 28.0 | 1637.0 | Repeat | Note=5 |
Hgene | PTPN23 | chr3:47422670 | chr3:47651817 | ENST00000265562 | + | 1 | 25 | 963_964 | 28.0 | 1637.0 | Repeat | Note=6 |
Tgene | SMARCC1 | chr3:47422670 | chr3:47651817 | ENST00000254480 | 24 | 28 | 914_946 | 927.0 | 1106.0 | Coiled coil | Ontology_term=ECO:0000255 | |
Tgene | SMARCC1 | chr3:47422670 | chr3:47651817 | ENST00000254480 | 24 | 28 | 329_336 | 927.0 | 1106.0 | Compositional bias | Note=Poly-Pro | |
Tgene | SMARCC1 | chr3:47422670 | chr3:47651817 | ENST00000254480 | 24 | 28 | 769_863 | 927.0 | 1106.0 | Compositional bias | Note=Glu-rich | |
Tgene | SMARCC1 | chr3:47422670 | chr3:47651817 | ENST00000254480 | 24 | 28 | 867_878 | 927.0 | 1106.0 | Compositional bias | Note=Poly-Ala | |
Tgene | SMARCC1 | chr3:47422670 | chr3:47651817 | ENST00000254480 | 24 | 28 | 449_546 | 927.0 | 1106.0 | Domain | SWIRM | |
Tgene | SMARCC1 | chr3:47422670 | chr3:47651817 | ENST00000254480 | 24 | 28 | 618_669 | 927.0 | 1106.0 | Domain | SANT |
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Fusion Protein-Protein Interaction |
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Gene | PPI interactors |
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Gene | STRING network |
PTPN23 | |
SMARCC1 |
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Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
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Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs to PTPN23-SMARCC1 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to PTPN23-SMARCC1 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |