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Fusion gene ID: 97 |
FusionGeneSummary for ABCA1_LAS1L |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: ABCA1_LAS1L | Fusion gene ID: 97 | Hgene | Tgene | Gene symbol | ABCA1 | LAS1L | Gene ID | 19 | 81887 |
| Gene name | ATP binding cassette subfamily A member 1 | LAS1 like, ribosome biogenesis factor | |
| Synonyms | ABC-1|ABC1|CERP|HDLDT1|TGD | Las1-like|WTS|dJ475B7.2 | |
| Cytomap | 9q31.1 | Xq12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | ATP-binding cassette sub-family A member 1ATP-binding cassette transporter A1ATP-binding cassette, sub-family A (ABC1), member 1cholesterol efflux regulatory proteinmembrane-bound | ribosomal biogenesis protein LAS1Lprotein LAS1 homolog | |
| Modification date | 20180527 | 20180523 | |
| UniProtAcc | O95477 | Q9Y4W2 | |
| Ensembl transtripts involved in fusion gene | ENST00000374736, ENST00000494467, ENST00000423487, ENST00000374733, | ENST00000374807, ENST00000374811, ENST00000374804, ENST00000312391, | |
| Fusion gene scores | * DoF score | 11 X 7 X 7=539 | 2 X 2 X 1=4 |
| # samples | 10 | 2 | |
| ** MAII score | log2(10/539*10)=-2.43028527297778 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(2/4*10)=2.32192809488736 | |
| Context | PubMed: ABCA1 [Title/Abstract] AND LAS1L [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 |
| Hgene | ABCA1 | GO:0007040 | lysosome organization | 15163665 |
| Hgene | ABCA1 | GO:0008203 | cholesterol metabolic process | 14747463 |
| Hgene | ABCA1 | GO:0016197 | endosomal transport | 14747463 |
| Hgene | ABCA1 | GO:0033344 | cholesterol efflux | 10431236|11162594|23931754 |
| Hgene | ABCA1 | GO:0033700 | phospholipid efflux | 10431236|11162594 |
| Hgene | ABCA1 | GO:0042632 | cholesterol homeostasis | 10431236 |
| Hgene | ABCA1 | GO:0045332 | phospholipid translocation | 24097981 |
| 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 |
| ChiTaRS3.1 | AK130814 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| * 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 |
| intron-3CDS | ENST00000374736 | ENST00000374807 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3CDS | ENST00000374736 | ENST00000374811 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3CDS | ENST00000374736 | ENST00000374804 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3UTR | ENST00000374736 | ENST00000312391 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3CDS | ENST00000494467 | ENST00000374807 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3CDS | ENST00000494467 | ENST00000374811 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3CDS | ENST00000494467 | ENST00000374804 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3UTR | ENST00000494467 | ENST00000312391 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3CDS | ENST00000423487 | ENST00000374807 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3CDS | ENST00000423487 | ENST00000374811 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3CDS | ENST00000423487 | ENST00000374804 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3UTR | ENST00000423487 | ENST00000312391 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3CDS | ENST00000374733 | ENST00000374807 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3CDS | ENST00000374733 | ENST00000374811 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3CDS | ENST00000374733 | ENST00000374804 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
| intron-3UTR | ENST00000374733 | ENST00000312391 | ABCA1 | chr9 | 107576733 | - | LAS1L | chrX | 64737950 | - |
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FusionProtFeatures for ABCA1_LAS1L |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| ABCA1 | LAS1L |
| Involved in the biogenesis of the 60S ribosomal subunit.Required for maturation of the 28S rRNA. Functions as a componentof the Five Friends of Methylated CHTOP (5FMC) complex; the 5FMCcomplex is recruited to ZNF148 by methylated CHTOP, leading todesumoylation of ZNF148 and subsequent transactivation of ZNF148target genes. {ECO:0000269|PubMed:20647540,ECO:0000269|PubMed:22872859}. |
| 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 |
| - 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 |
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FusionGeneSequence for ABCA1_LAS1L |
| 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 ABCA1_LAS1L |
| 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 |
| - 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 ABCA1_LAS1L |
| 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 |
| Hgene | ABCA1 | O95477 | DB01016 | Glyburide | ATP-binding cassette sub-family A member 1 | small molecule | approved |
| Hgene | ABCA1 | O95477 | DB01599 | Probucol | ATP-binding cassette sub-family A member 1 | small molecule | approved|investigational |
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RelatedDiseases for ABCA1_LAS1L |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | ABCA1 | C0039292 | Tangier Disease | 19 | CTD_human;ORPHANET;UNIPROT |
| Hgene | ABCA1 | C1704429 | Hypoalphalipoproteinemia, Familial | 4 | ORPHANET;UNIPROT |
| Hgene | ABCA1 | C2931838 | Familial HDL deficiency | 2 | CTD_human |
| Hgene | ABCA1 | C0004153 | Atherosclerosis | 1 | CTD_human |
| Hgene | ABCA1 | C0009404 | Colorectal Neoplasms | 1 | CTD_human |
| Hgene | ABCA1 | C0020443 | Hypercholesterolemia | 1 | CTD_human |
| Hgene | ABCA1 | C0020445 | Hypercholesterolemia, Familial | 1 | CTD_human |
| Hgene | ABCA1 | C0022661 | Kidney Failure, Chronic | 1 | CTD_human |
| Hgene | ABCA1 | C0031117 | Peripheral Neuropathy | 1 | CTD_human |
| Hgene | ABCA1 | C0036341 | Schizophrenia | 1 | PSYGENET |
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