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Fusion gene ID: 33549 |
FusionGeneSummary for SGCB_SPATA18 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SGCB_SPATA18 | Fusion gene ID: 33549 | Hgene | Tgene | Gene symbol | SGCB | SPATA18 | Gene ID | 6443 | 132671 |
| Gene name | sarcoglycan beta | spermatogenesis associated 18 | |
| Synonyms | A3b|LGMD2E|SGC | Mieap|SPETEX1 | |
| Cytomap | 4q12 | 4q12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | beta-sarcoglycan43 kDa dystrophin-associated glycoprotein43DAGbeta-SGbeta-sarcoglycan(43kD dystrophin-associated glycoprotein)limb girdle muscular dystrophy 2E (non-linked families)sarcoglycan, beta (43kDa dystrophin-associated glycoprotein) | mitochondria-eating proteinspermatogenesis associated 18 homologtestis tissue sperm-binding protein Li 71n | |
| Modification date | 20180519 | 20180523 | |
| UniProtAcc | Q16585 | Q8TC71 | |
| Ensembl transtripts involved in fusion gene | ENST00000381431, ENST00000535450, | ENST00000295213, ENST00000419395, ENST00000506829, | |
| Fusion gene scores | * DoF score | 3 X 3 X 3=27 | 2 X 3 X 2=12 |
| # samples | 3 | 2 | |
| ** MAII score | log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(2/12*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: SGCB [Title/Abstract] AND SPATA18 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * 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 |
| Tgene | SPATA18 | GO:0006974 | cellular response to DNA damage stimulus | 21264221 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * 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. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| TCGA | RV | LUSC | TCGA-66-2787-01A | SGCB | chr4 | 52899597 | - | SPATA18 | chr4 | 52926585 | + |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| In-frame | ENST00000381431 | ENST00000295213 | SGCB | chr4 | 52899597 | - | SPATA18 | chr4 | 52926585 | + |
| In-frame | ENST00000381431 | ENST00000419395 | SGCB | chr4 | 52899597 | - | SPATA18 | chr4 | 52926585 | + |
| 5CDS-intron | ENST00000381431 | ENST00000506829 | SGCB | chr4 | 52899597 | - | SPATA18 | chr4 | 52926585 | + |
| intron-3CDS | ENST00000535450 | ENST00000295213 | SGCB | chr4 | 52899597 | - | SPATA18 | chr4 | 52926585 | + |
| intron-3CDS | ENST00000535450 | ENST00000419395 | SGCB | chr4 | 52899597 | - | SPATA18 | chr4 | 52926585 | + |
| intron-intron | ENST00000535450 | ENST00000506829 | SGCB | chr4 | 52899597 | - | SPATA18 | chr4 | 52926585 | + |
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FusionProtFeatures for SGCB_SPATA18 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SGCB | SPATA18 |
| Component of the sarcoglycan complex, a subcomplex ofthe dystrophin-glycoprotein complex which forms a link between theF-actin cytoskeleton and the extracellular matrix. | Key regulator of mitochondrial quality that mediates therepairing or degradation of unhealthy mitochondria in response tomitochondrial damage. Mediator of mitochondrial protein catabolicprocess (also named MALM) by mediating the degradation of damagedproteins inside mitochondria by promoting the accumulation in themitochondrial matrix of hydrolases that are characteristic of thelysosomal lumen. Also involved in mitochondrion degradation ofdamaged mitochondria by promoting the formation of vacuole-likestructures (named MIV), which engulf and degrade unhealthymitochondria by accumulating lysosomes. The physical interactionof SPATA18/MIEAP, BNIP3 and BNIP3L/NIX at the mitochondrial outermembrane regulates the opening of a pore in the mitochondrialdouble membrane in order to mediate the translocation of lysosomalproteins from the cytoplasm to the mitochondrial matrix.{ECO:0000269|PubMed:21264221, ECO:0000269|PubMed:21264228,ECO:0000269|PubMed:22292033}. |
| 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 . * Minus value of BPloci means that the break pointn is located before the CDS. |
| - In-frame and 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 | SGCB | chr4:52899597 | chr4:52926585 | ENST00000381431 | - | 2 | 6 | 1_65 | 81 | 319 | Topological domain | Cytoplasmic |
| Tgene | >SPATA18 | chr4:52899597 | chr4:52926585 | ENST00000295213 | + | 0 | 13 | 118_187 | 29 | 539 | Coiled coil | Ontology_term=ECO:0000255 |
| Tgene | >SPATA18 | chr4:52899597 | chr4:52926585 | ENST00000295213 | + | 0 | 13 | 219_256 | 29 | 539 | Coiled coil | Ontology_term=ECO:0000255 |
| Tgene | >SPATA18 | chr4:52899597 | chr4:52926585 | ENST00000419395 | + | 0 | 12 | 118_187 | 29 | 507 | Coiled coil | Ontology_term=ECO:0000255 |
| Tgene | >SPATA18 | chr4:52899597 | chr4:52926585 | ENST00000419395 | + | 0 | 12 | 219_256 | 29 | 507 | Coiled coil | Ontology_term=ECO:0000255 |
| Tgene | >SPATA18 | chr4:52899597 | chr4:52926585 | ENST00000295213 | + | 0 | 13 | 257_313 | 29 | 539 | Compositional bias | Note=Ser-rich |
| Tgene | >SPATA18 | chr4:52899597 | chr4:52926585 | ENST00000419395 | + | 0 | 12 | 257_313 | 29 | 507 | Compositional bias | Note=Ser-rich |
| - In-frame and 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 | >SGCB | chr4:52899597 | chr4:52926585 | ENST00000381431 | - | 2 | 6 | 97_314 | 81 | 319 | Compositional bias | Note=Cys-rich |
| Hgene | >SGCB | chr4:52899597 | chr4:52926585 | ENST00000381431 | - | 2 | 6 | 87_318 | 81 | 319 | Topological domain | Extracellular |
| Hgene | >SGCB | chr4:52899597 | chr4:52926585 | ENST00000381431 | - | 2 | 6 | 66_86 | 81 | 319 | Transmembrane | Helical%3B Signal-anchor for type II membrane protein |
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FusionGeneSequence for SGCB_SPATA18 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for SGCB_SPATA18 |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| SGCB | SGCZ, SGCD, ZACN, GLRA2, HTR3A, CHRND, TMED6, TCTN2, TSPAN17 | SPATA18 | PAXIP1, CEP128, ODF2 |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for SGCB_SPATA18 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for SGCB_SPATA18 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | SGCB | C1858593 | Limb-girdle muscular dystrophy, type 2E | 3 | CTD_human;ORPHANET;UNIPROT |
| Hgene | SGCB | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| Hgene | SGCB | C0878544 | Cardiomyopathies | 1 | CTD_human |
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