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Fusion gene ID: 15943 |
FusionGeneSummary for HDAC4_SNX18 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: HDAC4_SNX18 | Fusion gene ID: 15943 | Hgene | Tgene | Gene symbol | HDAC4 | SNX18 | Gene ID | 9759 | 112574 |
| Gene name | histone deacetylase 4 | sorting nexin 18 | |
| Synonyms | AHO3|BDMR|HA6116|HD4|HDAC-4|HDAC-A|HDACA | SH3PX2|SH3PXD3B|SNAG1 | |
| Cytomap | 2q37.3 | 5q11.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | histone deacetylase 4histone deacetylase A | sorting nexin-18SH3 and PX domain-containing protein 3Bsorting nexin associated golgi protein 1sorting nexin-associated Golgi protein 1 | |
| Modification date | 20180522 | 20180522 | |
| UniProtAcc | P56524 | Q96RF0 | |
| Ensembl transtripts involved in fusion gene | ENST00000345617, ENST00000543185, ENST00000541256, ENST00000553145, | ENST00000343017, ENST00000326277, ENST00000381410, | |
| Fusion gene scores | * DoF score | 8 X 5 X 7=280 | 2 X 3 X 2=12 |
| # samples | 8 | 5 | |
| ** MAII score | log2(8/280*10)=-1.8073549220576 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/12*10)=2.05889368905357 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: HDAC4 [Title/Abstract] AND SNX18 [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 | HDAC4 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 10869435|16236793 |
| Hgene | HDAC4 | GO:0006338 | chromatin remodeling | 18850004 |
| Hgene | HDAC4 | GO:0006476 | protein deacetylation | 27708256 |
| Hgene | HDAC4 | GO:0016575 | histone deacetylation | 10869435 |
| Hgene | HDAC4 | GO:0033235 | positive regulation of protein sumoylation | 17696781 |
| Hgene | HDAC4 | GO:0034983 | peptidyl-lysine deacetylation | 18614528 |
| Hgene | HDAC4 | GO:0045892 | negative regulation of transcription, DNA-templated | 10869435 |
| Hgene | HDAC4 | GO:0070932 | histone H3 deacetylation | 12590135 |
| Hgene | HDAC4 | GO:0070933 | histone H4 deacetylation | 12590135 |
| Tgene | SNX18 | GO:0006897 | endocytosis | 20427313 |
| Tgene | SNX18 | GO:0043547 | positive regulation of GTPase activity | 20427313 |
| 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 | LUAD | TCGA-78-7536-01A | HDAC4 | chr2 | 240158289 | - | SNX18 | chr5 | 53839009 | + |
| * 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 |
| Frame-shift | ENST00000345617 | ENST00000343017 | HDAC4 | chr2 | 240158289 | - | SNX18 | chr5 | 53839009 | + |
| 5CDS-intron | ENST00000345617 | ENST00000326277 | HDAC4 | chr2 | 240158289 | - | SNX18 | chr5 | 53839009 | + |
| 5CDS-intron | ENST00000345617 | ENST00000381410 | HDAC4 | chr2 | 240158289 | - | SNX18 | chr5 | 53839009 | + |
| intron-3CDS | ENST00000543185 | ENST00000343017 | HDAC4 | chr2 | 240158289 | - | SNX18 | chr5 | 53839009 | + |
| intron-intron | ENST00000543185 | ENST00000326277 | HDAC4 | chr2 | 240158289 | - | SNX18 | chr5 | 53839009 | + |
| intron-intron | ENST00000543185 | ENST00000381410 | HDAC4 | chr2 | 240158289 | - | SNX18 | chr5 | 53839009 | + |
| intron-3CDS | ENST00000541256 | ENST00000343017 | HDAC4 | chr2 | 240158289 | - | SNX18 | chr5 | 53839009 | + |
| intron-intron | ENST00000541256 | ENST00000326277 | HDAC4 | chr2 | 240158289 | - | SNX18 | chr5 | 53839009 | + |
| intron-intron | ENST00000541256 | ENST00000381410 | HDAC4 | chr2 | 240158289 | - | SNX18 | chr5 | 53839009 | + |
| intron-3CDS | ENST00000553145 | ENST00000343017 | HDAC4 | chr2 | 240158289 | - | SNX18 | chr5 | 53839009 | + |
| intron-intron | ENST00000553145 | ENST00000326277 | HDAC4 | chr2 | 240158289 | - | SNX18 | chr5 | 53839009 | + |
| intron-intron | ENST00000553145 | ENST00000381410 | HDAC4 | chr2 | 240158289 | - | SNX18 | chr5 | 53839009 | + |
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FusionProtFeatures for HDAC4_SNX18 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| HDAC4 | SNX18 |
| Responsible for the deacetylation of lysine residues onthe N-terminal part of the core histones (H2A, H2B, H3 and H4).Histone deacetylation gives a tag for epigenetic repression andplays an important role in transcriptional regulation, cell cycleprogression and developmental events. Histone deacetylases act viathe formation of large multiprotein complexes. Involved in musclematuration via its interaction with the myocyte enhancer factorssuch as MEF2A, MEF2C and MEF2D. Involved in the MTA1-mediatedepigenetic regulation of ESR1 expression in breast cancer.Deacetylates HSPA1A and HSPA1B at 'Lys-77' leading to theirpreferential binding to co-chaperone STUB1 (PubMed:27708256).{ECO:0000269|PubMed:10523670, ECO:0000269|PubMed:24413532,ECO:0000269|PubMed:27708256}. | Involved in endocytosis and intracellular vesicletrafficking, both during interphase and at the end of mitosis.Required for efficient progress through mitosis and cytokinesis.Required for normal formation of the cleavage furrow at the end ofmitosis. Plays a role in endocytosis via clathrin-coated pits, butalso clathrin-independent, actin-dependent fluid-phaseendocytosis. Plays a role in macropinocytosis. Binds to membranesenriched in phosphatidylinositol 4,5-bisphosphate and promotesmembrane tubulation. Stimulates the GTPase activity of DNM2.Promotes DNM2 location at the plasma membrane.{ECO:0000269|PubMed:18411244, ECO:0000269|PubMed:20427313,ECO:0000269|PubMed:21048941, ECO:0000269|PubMed:22718350}. |
| 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 HDAC4_SNX18 |
| 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 HDAC4_SNX18 |
| 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 |
| HDAC4 | ZBTB16, SFN, CTBP1, GATA1, RARA, RXRA, NR2C1, NR2C2, AR, PPARD, PPARG, IKZF2, ZNF354A, HDAC9, MEF2A, MEF2C, MEF2D, HDAC4, RBBP4, HDAC3, NCOR1, NCOR2, YWHAE, YWHAG, YWHAZ, BCL6, BCOR, IKZF1, IKZF3, IKZF4, YWHAB, MECOM, SUV39H1, UBE2I, MAPK3, MAPK1, FOXP3, DNAJB6, DNAJB8, ATF2, MORC2, RUNX2, SENP1, CDK5, PARK2, NR1H2, SIN3A, HIF1A, CAMK2D, ESR1, YY1, LZTR1, SS18L1, SP1, REST, MARK3, GATA3, CAMK1, GCM1, NUP214, DNAJB5, SYK, ESCO2, GNB1, CTNNB1, TP53BP1, SRF, SIRT1, LCOR, HNF4A, CDKN1A, RANBP2, SMAD3, YWHAQ, ANKRA2, ATRX, REV3L, MAP1S, RFXANK, CIITA, RFX5, RFXAP, IFRD1, PPP2CA, NFKBIA, NFKBIE, HDAC5, CAMK4, CSRP3, HDAC7, PPP2R4, AHRR, CEBPD, BCORL1, NUP155, ACTA1, NPPB, CACNA1C, ATXN1, HIC1, NFKB1, SF1, KDM5B, ELAVL1, PPP2R1A, STAT1, ZEB2, NFATC1, BRMS1, NACC1, JDP2, ATF3, APP, ZBTB7B, YWHAH, TBL1XR1, MIF4GD, GSK3B, CDR2, GOLGA2, KRT31, KRT38, PNMA1, MTUS2, LDOC1, EFEMP2, RINT1, CCDC136, KRT40, CUL7, KCTD3, KIF13B, ZBTB21, KSR1, GIGYF1, LRFN1, CGN, DENND1A, SH3PXD2A, SRGAP2, RTKN, EIF4E2, MAST3, SIPA1L1, PPM1H, DENND4C, LIMA1, MAGI1, TESK2, DCLK1, ZNF638, SRSF12, SYDE1, MAPKAP1, NF1, AGAP1, CBY1, CDC25B, CDK16, NADK, CDC25C, FAM110B, USP21, GIGYF2, CAMSAP2, FAM53C, ANKRD34A, LPIN3, TIAM1, KIAA1804, RASAL2, PHLDB2, RALGPS2, FAM110A, PLEKHA7, KIF1C, GAB2, NAV1, MELK, SH3RF3, PTPN14, STARD13, DENND4A, OSBPL6, INPP5E, NR1H3 | SNX18 | ITCH, CUL1, FASLG, CBL, GRB2, ANKRD28, GRAP2, AURKA, UBR2, EWSR1, XPO1, DNM2, RELL1, CD44, SDC2, ZNF764, CDC16, RNGTT |
| - 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 HDAC4_SNX18 |
| 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 | HDAC4 | P56524 | DB01593 | Zinc | Histone deacetylase 4 | small molecule | approved|investigational |
| Hgene | HDAC4 | P56524 | DB06176 | Romidepsin | Histone deacetylase 4 | small molecule | approved|investigational |
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RelatedDiseases for HDAC4_SNX18 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | HDAC4 | C0036341 | Schizophrenia | 2 | PSYGENET |
| Hgene | HDAC4 | C0005695 | Bladder Neoplasm | 1 | CTD_human |
| Hgene | HDAC4 | C0011570 | Mental Depression | 1 | PSYGENET |
| Hgene | HDAC4 | C0011616 | Contact Dermatitis | 1 | CTD_human |
| Hgene | HDAC4 | C0221357 | Brachydactyly | 1 | CTD_human;HPO |
| Hgene | HDAC4 | C0236736 | Cocaine-Related Disorders | 1 | CTD_human |
| Hgene | HDAC4 | C0340543 | Familial primary pulmonary hypertension | 1 | CTD_human |
| Hgene | HDAC4 | C0345967 | Malignant mesothelioma | 1 | CTD_human |
| Hgene | HDAC4 | C0525045 | Mood Disorders | 1 | PSYGENET |
| Hgene | HDAC4 | C1862102 | BRACHYDACTYLY, TYPE E1 | 1 | CTD_human |
| Hgene | HDAC4 | C2931817 | Chromosome 2q37 deletion syndrome | 1 | CTD_human;ORPHANET |
| Hgene | HDAC4 | C3714756 | Intellectual Disability | 1 | CTD_human;HPO |
| Tgene | SNX18 | C4277682 | Chemical and Drug Induced Liver Injury | 1 | CTD_human |
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