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Fusion gene ID: 36107 |
FusionGeneSummary for SS18_NPC1 |
Fusion gene summary |
Fusion gene information | Fusion gene name: SS18_NPC1 | Fusion gene ID: 36107 | Hgene | Tgene | Gene symbol | SS18 | NPC1 | Gene ID | 6760 | 4864 |
Gene name | SS18, nBAF chromatin remodeling complex subunit | NPC intracellular cholesterol transporter 1 | |
Synonyms | SSXT|SYT | NPC|POGZ|SLC65A1 | |
Cytomap | 18q11.2 | 18q11.2 | |
Type of gene | protein-coding | protein-coding | |
Description | protein SSXTsynovial sarcoma translocated to X chromosome proteinsynovial sarcoma translocation, chromosome 18synovial sarcoma, translocated to X chromosome | NPC intracellular cholesterol transporter 1Niemann-Pick C1 proteintruncated Niemann-Pick C1 | |
Modification date | 20180523 | 20180519 | |
UniProtAcc | Q15532 | O15118 | |
Ensembl transtripts involved in fusion gene | ENST00000415083, ENST00000542420, ENST00000542743, ENST00000539849, ENST00000269137, ENST00000545952, ENST00000585241, | ENST00000269228, ENST00000412552, ENST00000540608, | |
Fusion gene scores | * DoF score | 13 X 16 X 6=1248 | 6 X 5 X 4=120 |
# samples | 37 | 6 | |
** MAII score | log2(37/1248*10)=-1.75402075834594 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(6/120*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Context | PubMed: SS18 [Title/Abstract] AND NPC1 [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 | SS18 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 15919756 |
Tgene | NPC1 | GO:0006486 | protein glycosylation | 10821832 |
Tgene | NPC1 | GO:0030301 | cholesterol transport | 18772377 |
Tgene | NPC1 | GO:0033344 | cholesterol efflux | 16141411 |
Tgene | NPC1 | GO:0042632 | cholesterol homeostasis | 12719428 |
Tgene | NPC1 | GO:0090150 | establishment of protein localization to membrane | 23360953 |
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 | LD | PAAD | TCGA-XN-A8T3-01A | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
* 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 |
5CDS-intron | ENST00000415083 | ENST00000269228 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000415083 | ENST00000412552 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000415083 | ENST00000540608 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000542420 | ENST00000269228 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000542420 | ENST00000412552 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000542420 | ENST00000540608 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000542743 | ENST00000269228 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000542743 | ENST00000412552 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000542743 | ENST00000540608 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
intron-intron | ENST00000539849 | ENST00000269228 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
intron-intron | ENST00000539849 | ENST00000412552 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
intron-intron | ENST00000539849 | ENST00000540608 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000269137 | ENST00000269228 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000269137 | ENST00000412552 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000269137 | ENST00000540608 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000545952 | ENST00000269228 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000545952 | ENST00000412552 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5CDS-intron | ENST00000545952 | ENST00000540608 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5UTR-intron | ENST00000585241 | ENST00000269228 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5UTR-intron | ENST00000585241 | ENST00000412552 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
5UTR-intron | ENST00000585241 | ENST00000540608 | SS18 | chr18 | 23658040 | - | NPC1 | chr18 | 21086606 | - |
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FusionProtFeatures for SS18_NPC1 |
Main function of each fusion partner protein. (from UniProt) |
Hgene | Tgene |
SS18 | NPC1 |
Appears to function synergistically with RBM14 as atranscriptional coactivator. Isoform 1 and isoform 2 function innuclear receptor coactivation. Isoform 1 and isoform 2 function ingeneral transcriptional coactivation.{ECO:0000269|PubMed:15919756}. | Intracellular cholesterol transporter which acts inconcert with NPC2 and plays an important role in the egress ofcholesterol from the endosomal/lysosomal compartment. Both NPC1and NPC2 function as the cellular 'tag team duo' (TTD) to catalyzethe mobilization of cholesterol within the multivesicularenvironment of the late endosome (LE) to effect egress through thelimiting bilayer of the LE. NPC2 binds unesterified cholesterolthat has been released from LDLs in the lumen of the lateendosomes/lysosomes and transfers it to the cholesterol-bindingpocket of the N-terminal domain of NPC1. Cholesterol binds to NPC1with the hydroxyl group buried in the binding pocket and isexported from the limiting membrane of late endosomes/ lysosomesto the ER and plasma membrane by an unknown mechanism. Bindsoxysterol with higher affinity than cholesterol. May play a rolein vesicular trafficking in glia, a process that may be crucialfor maintaining the structural and functional integrity of nerveterminals. {ECO:0000269|PubMed:12554680,ECO:0000269|PubMed:18772377, ECO:0000269|PubMed:19563754}. (Microbial infection) Acts as an endosomal entryreceptor for ebolavirus. {ECO:0000269|PubMed:21866103,ECO:0000269|PubMed:25855742}. |
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 SS18_NPC1 |
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 SS18_NPC1 |
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 |
SS18 | SMARCA2, SMARCB1, EP300, MLLT10, GRB2, SMARCD1, RBM14, YWHAG, ELAVL1, CUL3, CST11, ATF2, TLE1, SMARCA5, HDAC1, HDAC2, EED, SUZ12, EZH2, SS18, NFKBID, DPF3, DPF2, SMARCE1, ARID1B, ARID1A, PHF10, SMARCC2, SMARCC1, GLTSCR1, SMARCD3, SMARCD2, SMARCA4, ARID2, DPF1, ACTL6A, ACTL6B, BCL7A, BCL7C, BCL7B, BRD9, CDKN1A, NEFM, RAB5C, SYNCRIP | NPC1 | VPS4A, OSBPL5, LRP6, TMEM173, UNC93B1, FBXO6, MRPS28, TMOD3, LGR4, LGALS8, PTPRK, IL17RC, TPRA1 |
- 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 SS18_NPC1 |
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 SS18_NPC1 |
Diseases associated with fusion partners. (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Hgene | SS18 | C0039101 | synovial sarcoma | 1 | CTD_human;ORPHANET |
Tgene | NPC1 | C3179455 | Niemann-Pick Disease, Type C1 | 16 | UNIPROT |
Tgene | NPC1 | C0220756 | Niemann-Pick Disease, Type C | 2 | CTD_human |
Tgene | NPC1 | C0004134 | Ataxia | 1 | CTD_human |
Tgene | NPC1 | C0004153 | Atherosclerosis | 1 | CTD_human |
Tgene | NPC1 | C0006309 | Brucellosis | 1 | CTD_human |
Tgene | NPC1 | C0013362 | Dysarthria | 1 | CTD_human;HPO |
Tgene | NPC1 | C0023890 | Liver Cirrhosis | 1 | CTD_human |
Tgene | NPC1 | C0023895 | Liver diseases | 1 | CTD_human |
Tgene | NPC1 | C0028754 | Obesity | 1 | CTD_human |
Tgene | NPC1 | C0029089 | Ophthalmoplegia | 1 | CTD_human |