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Fusion gene ID: 5121 |
FusionGeneSummary for C9orf72_GMCL1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: C9orf72_GMCL1 | Fusion gene ID: 5121 | Hgene | Tgene | Gene symbol | C9orf72 | GMCL1 | Gene ID | 203228 | 64395 |
| Gene name | chromosome 9 open reading frame 72 | germ cell-less, spermatogenesis associated 1 | |
| Synonyms | ALSFTD|DENNL72|FTDALS|FTDALS1 | BTBD13|GCL|GCL1|SPATA29 | |
| Cytomap | 9p21.2 | 2p13.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | guanine nucleotide exchange C9orf72protein C9orf72 | germ cell-less protein-like 1germ cell-less homolog 1spermatogenesis associated 29 | |
| Modification date | 20180527 | 20180522 | |
| UniProtAcc | Q96LT7 | Q96IK5 | |
| Ensembl transtripts involved in fusion gene | ENST00000380003, ENST00000488117, ENST00000379997, | ENST00000282570, ENST00000468386, | |
| Fusion gene scores | * DoF score | 2 X 2 X 1=4 | 1 X 1 X 1=1 |
| # samples | 2 | 1 | |
| ** MAII score | log2(2/4*10)=2.32192809488736 | log2(1/1*10)=3.32192809488736 | |
| Context | PubMed: C9orf72 [Title/Abstract] AND GMCL1 [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 |
| 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 | BF811117 | C9orf72 | chr9 | 27566974 | + | GMCL1 | chr2 | 70067869 | - |
| * 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-intron | ENST00000380003 | ENST00000282570 | C9orf72 | chr9 | 27566974 | + | GMCL1 | chr2 | 70067869 | - |
| intron-intron | ENST00000380003 | ENST00000468386 | C9orf72 | chr9 | 27566974 | + | GMCL1 | chr2 | 70067869 | - |
| intron-intron | ENST00000488117 | ENST00000282570 | C9orf72 | chr9 | 27566974 | + | GMCL1 | chr2 | 70067869 | - |
| intron-intron | ENST00000488117 | ENST00000468386 | C9orf72 | chr9 | 27566974 | + | GMCL1 | chr2 | 70067869 | - |
| intron-intron | ENST00000379997 | ENST00000282570 | C9orf72 | chr9 | 27566974 | + | GMCL1 | chr2 | 70067869 | - |
| intron-intron | ENST00000379997 | ENST00000468386 | C9orf72 | chr9 | 27566974 | + | GMCL1 | chr2 | 70067869 | - |
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FusionProtFeatures for C9orf72_GMCL1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| C9orf72 | GMCL1 |
| Component of the C9orf72-SMCR8 complex, a complex thathas guanine nucleotide exchange factor (GEF) activity andregulates autophagy (PubMed:27193190, PubMed:27103069,PubMed:27617292, PubMed:28195531). In the complex, C9orf72 andSMCR8 probably constitute the catalytic subunits that promote theexchange of GDP to GTP, converting inactive GDP-bound RAB8A andRAB39B into their active GTP-bound form, thereby promotingautophagosome maturation (PubMed:27103069). The C9orf72-SMCR8complex also acts as a regulator of autophagy initiation byinteracting with the ATG1/ULK1 kinase complex and modulating itsprotein kinase activity (PubMed:27617292). Positively regulatesinitiation of autophagy by regulating the RAB1A-dependenttrafficking of the ATG1/ULK1 kinase complex to the phagophorewhich leads to autophagosome formation (PubMed:27334615). Acts asa regulator of mTORC1 signaling by promoting phosphorylation ofmTORC1 substrates (PubMed:27559131). Plays a role in endosomaltrafficking (PubMed:24549040). May be involved in regulating thematuration of phagosomes to lysosomes (By similarity). Regulatesactin dynamics in motor neurons by inhibiting the GTP-bindingactivity of ARF6, leading to ARF6 inactivation (PubMed:27723745).This reduces the activity of the LIMK1 and LIMK2 kinases which areresponsible for phosphorylation and inactivation of cofilin,leading to cofilin activation (PubMed:27723745). Positivelyregulates axon extension and axon growth cone size in spinal motorneurons (PubMed:27723745). Plays a role within the hematopoieticsystem in restricting inflammation and the development ofautoimmunity (By similarity). {ECO:0000250|UniProtKB:Q6DFW0,ECO:0000269|PubMed:24549040, ECO:0000269|PubMed:27103069,ECO:0000269|PubMed:27193190, ECO:0000269|PubMed:27334615,ECO:0000269|PubMed:27559131, ECO:0000269|PubMed:27617292,ECO:0000269|PubMed:27723745, ECO:0000269|PubMed:28195531}. Isoform 1: Regulates stress granule assembly in responseto cellular stress. {ECO:0000269|PubMed:27037575}. Isoform 2: Does not play a role in regulation of stressgranule assembly in response to cellular stress.{ECO:0000269|PubMed:27037575}. | Possible function in spermatogenesis. Enhances thedegradation of MDM2 and increases the amount of p53 probably bymodulating the nucleocytoplasmic transport (By similarity).{ECO:0000250}. |
| 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 C9orf72_GMCL1 |
| 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 C9orf72_GMCL1 |
| 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 C9orf72_GMCL1 |
| 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 C9orf72_GMCL1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | C9orf72 | C0033975 | Psychotic Disorders | 3 | PSYGENET |
| Hgene | C9orf72 | C0349204 | Nonorganic psychosis | 3 | PSYGENET |
| Hgene | C9orf72 | C0036341 | Schizophrenia | 2 | PSYGENET |
| Hgene | C9orf72 | C0005586 | Bipolar Disorder | 1 | PSYGENET |
| Hgene | C9orf72 | C0036337 | Schizoaffective Disorder | 1 | PSYGENET |
| Hgene | C9orf72 | C3495559 | Juvenile arthritis | 1 | CTD_human |
| Hgene | C9orf72 | C3888102 | Frontotemporal Dementia With Motor Neuron Disease | 1 | CTD_human |
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