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Fusion gene ID: 41660 |
FusionGeneSummary for VRK1_SAMD4A |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: VRK1_SAMD4A | Fusion gene ID: 41660 | Hgene | Tgene | Gene symbol | VRK1 | SAMD4A | Gene ID | 7443 | 23034 |
| Gene name | vaccinia related kinase 1 | sterile alpha motif domain containing 4A | |
| Synonyms | PCH1|PCH1A | SAMD4|SMAUG|SMAUG1|SMG|SMGA | |
| Cytomap | 14q32.2 | 14q22.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | serine/threonine-protein kinase VRK1vaccinia virus B1R-related kinase 1 | protein Smaug homolog 1SAM domain-containing protein 4A | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | Q99986 | Q9UPU9 | |
| Ensembl transtripts involved in fusion gene | ENST00000216639, ENST00000555067, | ENST00000554335, ENST00000251091, ENST00000555112, ENST00000392067, ENST00000357634, ENST00000555192, | |
| Fusion gene scores | * DoF score | 4 X 3 X 4=48 | 5 X 5 X 3=75 |
| # samples | 4 | 7 | |
| ** MAII score | log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(7/75*10)=-0.0995356735509144 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: VRK1 [Title/Abstract] AND SAMD4A [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 | VRK1 | GO:0006468 | protein phosphorylation | 22194607 |
| Hgene | VRK1 | GO:0043987 | histone H3-S10 phosphorylation | 22194607 |
| Hgene | VRK1 | GO:0046777 | protein autophosphorylation | 21543316|22194607 |
| Hgene | VRK1 | GO:0072355 | histone H3-T3 phosphorylation | 22194607 |
| Hgene | VRK1 | GO:0090166 | Golgi disassembly | 19103756 |
| Tgene | SAMD4A | GO:0045727 | positive regulation of translation | 16221671 |
| 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 | HNSC | TCGA-HD-7753-01A | VRK1 | chr14 | 97327072 | + | SAMD4A | chr14 | 55168780 | + |
| * 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 | ENST00000216639 | ENST00000554335 | VRK1 | chr14 | 97327072 | + | SAMD4A | chr14 | 55168780 | + |
| Frame-shift | ENST00000216639 | ENST00000251091 | VRK1 | chr14 | 97327072 | + | SAMD4A | chr14 | 55168780 | + |
| 5CDS-3UTR | ENST00000216639 | ENST00000555112 | VRK1 | chr14 | 97327072 | + | SAMD4A | chr14 | 55168780 | + |
| 5CDS-3UTR | ENST00000216639 | ENST00000392067 | VRK1 | chr14 | 97327072 | + | SAMD4A | chr14 | 55168780 | + |
| 5CDS-3UTR | ENST00000216639 | ENST00000357634 | VRK1 | chr14 | 97327072 | + | SAMD4A | chr14 | 55168780 | + |
| 5CDS-intron | ENST00000216639 | ENST00000555192 | VRK1 | chr14 | 97327072 | + | SAMD4A | chr14 | 55168780 | + |
| 3UTR-3CDS | ENST00000555067 | ENST00000554335 | VRK1 | chr14 | 97327072 | + | SAMD4A | chr14 | 55168780 | + |
| 3UTR-3CDS | ENST00000555067 | ENST00000251091 | VRK1 | chr14 | 97327072 | + | SAMD4A | chr14 | 55168780 | + |
| 3UTR-3UTR | ENST00000555067 | ENST00000555112 | VRK1 | chr14 | 97327072 | + | SAMD4A | chr14 | 55168780 | + |
| 3UTR-3UTR | ENST00000555067 | ENST00000392067 | VRK1 | chr14 | 97327072 | + | SAMD4A | chr14 | 55168780 | + |
| 3UTR-3UTR | ENST00000555067 | ENST00000357634 | VRK1 | chr14 | 97327072 | + | SAMD4A | chr14 | 55168780 | + |
| 3UTR-intron | ENST00000555067 | ENST00000555192 | VRK1 | chr14 | 97327072 | + | SAMD4A | chr14 | 55168780 | + |
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FusionProtFeatures for VRK1_SAMD4A |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| VRK1 | SAMD4A |
| Serine/threonine kinase involved in Golgi disassemblyduring the cell cycle: following phosphorylation by PLK3 duringmitosis, required to induce Golgi fragmentation. Acts by mediatingphosphorylation of downstream target protein. Phosphorylates 'Thr-18' of p53/TP53 and may thereby prevent the interaction betweenp53/TP53 and MDM2. Phosphorylates casein and histone H3.Phosphorylates BANF1: disrupts its ability to bind DNA, reducesits binding to LEM domain-containing proteins and causes itsrelocalization from the nucleus to the cytoplasm. PhosphorylatesATF2 which activates its transcriptional activity.{ECO:0000269|PubMed:10951572, ECO:0000269|PubMed:14645249,ECO:0000269|PubMed:15105425, ECO:0000269|PubMed:16495336,ECO:0000269|PubMed:18617507, ECO:0000269|PubMed:19103756}. | Acts as a translational repressor of SRE-containingmessengers. {ECO:0000269|PubMed:16221671}. |
| 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 VRK1_SAMD4A |
| 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 VRK1_SAMD4A |
| 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 |
| VRK1 | VRK1, TP53, HIST2H3C, HIST2H2BE, TFAP4, TRMT1L, FEN1, WIBG, RBM25, SF3B5, VPS52, SRPK2, EGFR, SERPINB5, CYP1A1, RACGAP1, COIL, HIST3H3, HIST1H2BG, HIST1H3A, NBN, RNF8, SNW1, ZBTB42, GTF2E2, SNRNP27, FGB, USP47, HSD3B2, SLC38A7, SMIM12, FOXA1, TRIM25 | SAMD4A | YWHAG, YWHAB, GOLGA2, NUTM1, XPO1, SAMD4B, INPPL1, TNIP1, YWHAZ, YWHAE, DDB2, YWHAH, CSDE1, GAN, PDP1, TRIM25 |
| - 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 VRK1_SAMD4A |
| 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 VRK1_SAMD4A |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | VRK1 | C3714756 | Intellectual Disability | 1 | CTD_human;HPO |
| Tgene | SAMD4A | C0236969 | Substance-Related Disorders | 1 | CTD_human |
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