|
||||||
|
 | |
| |
| |
| |
| |
|
Fusion gene ID: 12544 |
FusionGeneSummary for FAM129B_SHMT1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: FAM129B_SHMT1 | Fusion gene ID: 12544 | Hgene | Tgene | Gene symbol | FAM129B | SHMT1 | Gene ID | 64855 | 6470 |
| Gene name | family with sequence similarity 129 member B | serine hydroxymethyltransferase 1 | |
| Synonyms | C9orf88|MEG-3|MINERVA|OC58|bA356B19.6 | CSHMT|SHMT | |
| Cytomap | 9q34.11 | 17p11.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | niban-like protein 1melanoma invasion by ERK | serine hydroxymethyltransferase, cytosoliccytoplasmic serine hydroxymethyltransferaseglycine hydroxymethyltransferaseserine hydroxymethyltransferase 1 (soluble)serine methylase | |
| Modification date | 20180522 | 20180519 | |
| UniProtAcc | Q96TA1 | P34896 | |
| Ensembl transtripts involved in fusion gene | ENST00000373314, ENST00000373312, ENST00000468379, | ENST00000316694, ENST00000352886, ENST00000539052, ENST00000354098, | |
| Fusion gene scores | * DoF score | 14 X 9 X 9=1134 | 3 X 2 X 3=18 |
| # samples | 13 | 4 | |
| ** MAII score | log2(13/1134*10)=-3.12483711191377 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(4/18*10)=1.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: FAM129B [Title/Abstract] AND SHMT1 [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 | FAM129B | GO:0008285 | negative regulation of cell proliferation | 14602737|17569660|20032057|20179190 |
| Hgene | FAM129B | GO:0045892 | negative regulation of transcription, DNA-templated | 17569660 |
| Hgene | FAM129B | GO:0045893 | positive regulation of transcription, DNA-templated | 17569660|20032057|20179190 |
| Hgene | FAM129B | GO:2000279 | negative regulation of DNA biosynthetic process | 14602737|17569660|20032057 |
| Hgene | FAM129B | GO:2000679 | positive regulation of transcription regulatory region DNA binding | 17569660 |
| Tgene | SHMT1 | GO:0006544 | glycine metabolic process | 24698160 |
| Tgene | SHMT1 | GO:0006563 | L-serine metabolic process | 24698160 |
| Tgene | SHMT1 | GO:0006565 | L-serine catabolic process | 17482557 |
| Tgene | SHMT1 | GO:0009113 | purine nucleobase biosynthetic process | 11516159 |
| Tgene | SHMT1 | GO:0017148 | negative regulation of translation | 10995219 |
| Tgene | SHMT1 | GO:0035999 | tetrahydrofolate interconversion | 24698160 |
| Tgene | SHMT1 | GO:0046653 | tetrahydrofolate metabolic process | 24698160 |
| Tgene | SHMT1 | GO:0046655 | folic acid metabolic process | 11278996 |
| Tgene | SHMT1 | GO:0051262 | protein tetramerization | 9753690 |
| Tgene | SHMT1 | GO:0051289 | protein homotetramerization | 24698160 |
| Tgene | SHMT1 | GO:1904482 | cellular response to tetrahydrofolate | 24698160 |
| 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 | CESC | TCGA-DS-A1OC-01A | FAM129B | chr9 | 130293927 | - | SHMT1 | chr17 | 18259314 | - |
| * 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-5UTR | ENST00000373314 | ENST00000316694 | FAM129B | chr9 | 130293927 | - | SHMT1 | chr17 | 18259314 | - |
| 5CDS-5UTR | ENST00000373314 | ENST00000352886 | FAM129B | chr9 | 130293927 | - | SHMT1 | chr17 | 18259314 | - |
| 5CDS-5UTR | ENST00000373314 | ENST00000539052 | FAM129B | chr9 | 130293927 | - | SHMT1 | chr17 | 18259314 | - |
| 5CDS-5UTR | ENST00000373314 | ENST00000354098 | FAM129B | chr9 | 130293927 | - | SHMT1 | chr17 | 18259314 | - |
| 5CDS-5UTR | ENST00000373312 | ENST00000316694 | FAM129B | chr9 | 130293927 | - | SHMT1 | chr17 | 18259314 | - |
| 5CDS-5UTR | ENST00000373312 | ENST00000352886 | FAM129B | chr9 | 130293927 | - | SHMT1 | chr17 | 18259314 | - |
| 5CDS-5UTR | ENST00000373312 | ENST00000539052 | FAM129B | chr9 | 130293927 | - | SHMT1 | chr17 | 18259314 | - |
| 5CDS-5UTR | ENST00000373312 | ENST00000354098 | FAM129B | chr9 | 130293927 | - | SHMT1 | chr17 | 18259314 | - |
| 5UTR-5UTR | ENST00000468379 | ENST00000316694 | FAM129B | chr9 | 130293927 | - | SHMT1 | chr17 | 18259314 | - |
| 5UTR-5UTR | ENST00000468379 | ENST00000352886 | FAM129B | chr9 | 130293927 | - | SHMT1 | chr17 | 18259314 | - |
| 5UTR-5UTR | ENST00000468379 | ENST00000539052 | FAM129B | chr9 | 130293927 | - | SHMT1 | chr17 | 18259314 | - |
| 5UTR-5UTR | ENST00000468379 | ENST00000354098 | FAM129B | chr9 | 130293927 | - | SHMT1 | chr17 | 18259314 | - |
Top |
FusionProtFeatures for FAM129B_SHMT1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| FAM129B | SHMT1 |
| May play a role in apoptosis suppression. May promotemelanoma cell invasion in vitro. {ECO:0000269|PubMed:19362540,ECO:0000269|PubMed:21148485}. | Interconversion of serine and glycine (PubMed:8505317,PubMed:24698160). {ECO:0000269|PubMed:24698160,ECO:0000269|PubMed:8505317}. |
| 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 |
Top |
FusionGeneSequence for FAM129B_SHMT1 |
| 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). |
Top |
FusionGenePPI for FAM129B_SHMT1 |
| 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 |
| FAM129B | KEAP1, HTATSF1, ZNF512B, DDI2, CORO1C, DNM1L, GLUL, PAWR, PUF60, SHMT1, TARS, VPS26A, VPS29, VPS35, ZYX, GTF2A1, H3F3A, NUDC, PAPOLA, SNX2, SNX6, TSN, NTRK1, TMEM17, SNW1, CDC5L, EGFR, HRAS, KRAS, CDH1, CTDSPL, PTPRG, CDK15, PDE4DIP, TRIM25 | SHMT1 | PRSS23, DLEU1, PIM1, ZC3H4, MCAT, HSPA1L, DEDD, APEH, CTTN, CARS, FAM129B, GARS, GSPT2, HARS, HIST1H4A, IDE, PAWR, ATP6V1C1, C18orf25, PBDC1, GTF2F2, TSN, TTC1, XPO5, SHMT2, SNX2, SNX6, STAT1, VPS29, MAPK9, SHMT1, SULT1A3, ARFIP1, ATIC, HSPE1, ITPA, PGK2, PAICS, PPAT, PRRC1, SMAD4, STXBP1, DPYSL5, ARNT, C7orf60 |
| - 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 |
Top |
RelatedDrugs for FAM129B_SHMT1 |
| 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 |
| Tgene | SHMT1 | P34896 | DB00114 | Pyridoxal Phosphate | Serine hydroxymethyltransferase, cytosolic | small molecule | approved|investigational|nutraceutical |
| Tgene | SHMT1 | P34896 | DB00145 | Glycine | Serine hydroxymethyltransferase, cytosolic | small molecule | approved|nutraceutical|vet_approved |
Top |
RelatedDiseases for FAM129B_SHMT1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | SHMT1 | C0024305 | Lymphoma, Non-Hodgkin | 1 | CTD_human |
| Tgene | SHMT1 | C0027765 | nervous system disorder | 1 | CTD_human |
| Tgene | SHMT1 | C0036341 | Schizophrenia | 1 | PSYGENET |
| Tgene | SHMT1 | C0041755 | Adverse reaction to drug | 1 | CTD_human |
| Tgene | SHMT1 | C1458155 | Mammary Neoplasms | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|