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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:COL2A1-CLIC4 (FusionGDB2 ID:HG1280TG25932) |
Fusion Gene Summary for COL2A1-CLIC4 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: COL2A1-CLIC4 | Fusion gene ID: hg1280tg25932 | Hgene | Tgene | Gene symbol | COL2A1 | CLIC4 | Gene ID | 1280 | 25932 |
| Gene name | collagen type II alpha 1 chain | chloride intracellular channel 4 | |
| Synonyms | ANFH|AOM|COL11A3|SEDC|STL1 | CLIC4L|H1|MTCLIC|huH1|p64H1 | |
| Cytomap | ('COL2A1')('CLIC4') 12q13.11 | 1p36.11 | |
| Type of gene | protein-coding | protein-coding | |
| Description | collagen alpha-1(II) chainalpha-1 type II collagenarthroophthalmopathy, progressive (Stickler syndrome)cartilage collagenchondrocalcincollagen II, alpha-1 polypeptidecollagen, type II, alpha 1 | chloride intracellular channel protein 4chloride intracellular channel 4 likeepididymis secretory sperm binding proteinintracellular chloride ion channel protein p64H1 | |
| Modification date | 20200328 | 20200313 | |
| UniProtAcc | P02458 | Q9Y696 | |
| Ensembl transtripts involved in fusion gene | ENST00000337299, ENST00000380518, ENST00000493991, | ||
| Fusion gene scores | * DoF score | 5 X 6 X 2=60 | 12 X 10 X 5=600 |
| # samples | 6 | 12 | |
| ** MAII score | log2(6/60*10)=0 | log2(12/600*10)=-2.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: COL2A1 [Title/Abstract] AND CLIC4 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | COL2A1(48367016)-CLIC4(25168268), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | |||
| * 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 |
| Tgene | CLIC4 | GO:0030336 | negative regulation of cell migration | 12163372 |
| Fusion gene information * 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
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Fusion Gene ORF analysis for COL2A1-CLIC4 |
| 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 |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
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Fusion Genomic Features for COL2A1-CLIC4 |
| FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
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Fusion Protein Features for COL2A1-CLIC4 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:48367016/:25168268) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| COL2A1 | CLIC4 |
| FUNCTION: Type II collagen is specific for cartilaginous tissues. It is essential for the normal embryonic development of the skeleton, for linear growth and for the ability of cartilage to resist compressive forces. | FUNCTION: Can insert into membranes and form poorly selective ion channels that may also transport chloride ions. Channel activity depends on the pH. Membrane insertion seems to be redox-regulated and may occur only under oxydizing conditions. Promotes cell-surface expression of HRH3. Has alternate cellular functions like a potential role in angiogenesis or in maintaining apical-basolateral membrane polarity during mitosis and cytokinesis. Could also promote endothelial cell proliferation and regulate endothelial morphogenesis (tubulogenesis). {ECO:0000269|PubMed:12163372, ECO:0000269|PubMed:14569596, ECO:0000269|PubMed:16176272, ECO:0000269|PubMed:16239224, ECO:0000269|PubMed:18302930, ECO:0000269|PubMed:19247789}. |
| 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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Fusion Gene Sequence for COL2A1-CLIC4 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
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Fusion Gene PPI Analysis for COL2A1-CLIC4 |
| 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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Related Drugs for COL2A1-CLIC4 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Hgene | COL2A1 | P02458 | DB00048 | Collagenase clostridium histolyticum | Binder | Biotech | Approved|Investigational |
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Related Diseases for COL2A1-CLIC4 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | COL2A1 | C0220685 | Achondrogenesis type 2 | 13 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Hgene | COL2A1 | C2745959 | Spondyloepiphyseal dysplasia, congenita | 12 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Hgene | COL2A1 | C0003865 | Arthritis, Adjuvant-Induced | 9 | CTD_human |
| Hgene | COL2A1 | C0265279 | Kniest dysplasia | 9 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Hgene | COL2A1 | C0971858 | Arthritis, Collagen-Induced | 9 | CTD_human |
| Hgene | COL2A1 | C0993582 | Arthritis, Experimental | 9 | CTD_human |
| Hgene | COL2A1 | C1836080 | Stickler Syndrome, Type I, Nonsyndromic Ocular | 8 | CTD_human;GENOMICS_ENGLAND;UNIPROT |
| Hgene | COL2A1 | C1835437 | Platyspondylic Lethal Skeletal Dysplasia, Torrance Type | 6 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Hgene | COL2A1 | C1836683 | Czech dysplasia, metatarsal type | 6 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Hgene | COL2A1 | C2020284 | Stickler syndrome, type 1 | 6 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Hgene | COL2A1 | C0432214 | Namaqualand hip dysplasia | 5 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Hgene | COL2A1 | C0700635 | Strudwick syndrome | 5 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Hgene | COL2A1 | C4225273 | SPONDYLOEPIPHYSEAL DYSPLASIA, STANESCU TYPE | 5 | CLINGEN;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Hgene | COL2A1 | C0013604 | Edema | 4 | CTD_human |
| Hgene | COL2A1 | C0151603 | Anasarca | 4 | CTD_human |
| Hgene | COL2A1 | C0796173 | Spondyloperipheral dysplasia short ulna | 4 | CTD_human;GENOMICS_ENGLAND;ORPHANET |
| Hgene | COL2A1 | C4551562 | AVASCULAR NECROSIS OF FEMORAL HEAD, PRIMARY, 1 | 4 | GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Hgene | COL2A1 | C0003864 | Arthritis | 3 | CTD_human |
| Hgene | COL2A1 | C0023234 | Legg-Calve-Perthes Disease | 3 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Hgene | COL2A1 | C0162323 | Polyarthritis | 3 | CTD_human |
| Hgene | COL2A1 | C1851536 | Epiphyseal Dysplasia, Multiple, with Myopia and Conductive Deafness | 3 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Hgene | COL2A1 | C0003873 | Rheumatoid Arthritis | 2 | CTD_human |
| Hgene | COL2A1 | C0008925 | Cleft Palate | 2 | CTD_human;GENOMICS_ENGLAND |
| Hgene | COL2A1 | C0021368 | Inflammation | 2 | CTD_human |
| Hgene | COL2A1 | C0029408 | Degenerative polyarthritis | 2 | CTD_human |
| Hgene | COL2A1 | C0041834 | Erythema | 2 | CTD_human |
| Hgene | COL2A1 | C0086743 | Osteoarthrosis Deformans | 2 | CTD_human |
| Hgene | COL2A1 | C0376634 | Craniofacial Abnormalities | 2 | CTD_human |
| Hgene | COL2A1 | C1262477 | Weight decreased | 2 | CTD_human |
| Hgene | COL2A1 | C1852989 | Vitreoretinopathy with Phalangeal Epiphyseal Dysplasia | 2 | GENOMICS_ENGLAND |
| Hgene | COL2A1 | C1861481 | Stickler syndrome, type 3 | 2 | ORPHANET |
| Hgene | COL2A1 | C4302548 | Dysspondyloenchondromatosis | 2 | ORPHANET |
| Hgene | COL2A1 | C4520892 | Otospondylomegaepiphyseal dysplasia | 2 | CTD_human;GENOMICS_ENGLAND |
| Hgene | COL2A1 | C0005974 | Bone Resorption | 1 | CTD_human |
| Hgene | COL2A1 | C0007302 | Cartilage Diseases | 1 | CTD_human |
| Hgene | COL2A1 | C0008479 | Chondrosarcoma | 1 | CTD_human |
| Hgene | COL2A1 | C0013366 | Dyschondroplasias | 1 | CTD_human |
| Hgene | COL2A1 | C0015397 | Disorder of eye | 1 | GENOMICS_ENGLAND |
| Hgene | COL2A1 | C0018784 | Sensorineural Hearing Loss (disorder) | 1 | CTD_human |
| Hgene | COL2A1 | C0020507 | Hyperplasia | 1 | CTD_human |
| Hgene | COL2A1 | C0025202 | melanoma | 1 | CTD_human |
| Hgene | COL2A1 | C0025237 | Melnick-Needles Syndrome | 1 | CTD_human |
| Hgene | COL2A1 | C0026760 | Multiple Epiphyseal Dysplasia | 1 | CTD_human |
| Hgene | COL2A1 | C0027092 | Myopia | 1 | CTD_human |
| Hgene | COL2A1 | C0029422 | Osteochondrodysplasias | 1 | CTD_human |
| Hgene | COL2A1 | C0035305 | Retinal Detachment | 1 | CTD_human |
| Hgene | COL2A1 | C0036391 | Schwartz-Jampel Syndrome | 1 | CTD_human |
| Hgene | COL2A1 | C0038015 | Spondyloepiphyseal Dysplasia | 1 | CTD_human |
| Hgene | COL2A1 | C0039103 | Synovitis | 1 | CTD_human |
| Hgene | COL2A1 | C0085700 | Chondromalacia | 1 | CTD_human |
| Hgene | COL2A1 | C0086543 | Cataract | 1 | CTD_human |
| Hgene | COL2A1 | C0339546 | Retinal Pigment Epithelial Detachment | 1 | CTD_human |
| Hgene | COL2A1 | C0410480 | Avascular Necrosis of Femur Head | 1 | CTD_human;GENOMICS_ENGLAND;ORPHANET |
| Hgene | COL2A1 | C0410574 | Synovial Hypertrophy | 1 | CTD_human |
| Hgene | COL2A1 | C0432221 | Spondylometaphyseal dysplasia, 'corner fracture' type | 1 | ORPHANET |
| Hgene | COL2A1 | C0432272 | Van Buchem disease | 1 | CTD_human |
| Hgene | COL2A1 | C0524524 | Pseudoaphakia | 1 | CTD_human |
| Hgene | COL2A1 | C0542428 | Hypochondrogenesis | 1 | ORPHANET |
| Hgene | COL2A1 | C1510497 | Lens Opacities | 1 | CTD_human |
| Hgene | COL2A1 | C1691779 | Sensory hearing loss | 1 | CTD_human |
| Hgene | COL2A1 | C1836081 | RHEGMATOGENOUS RETINAL DETACHMENT, AUTOSOMAL DOMINANT | 1 | ORPHANET |
| Hgene | COL2A1 | C1837218 | Cleft palate, isolated | 1 | CTD_human |
| Hgene | COL2A1 | C1840452 | Hyaloideoretinal degeneration of Wagner | 1 | CTD_human |
| Hgene | COL2A1 | C1855310 | Megaepiphyseal dwarfism | 1 | CTD_human |
| Hgene | COL2A1 | C1866688 | Spondylometaphyseal dysplasia, Algerian type | 1 | ORPHANET |
| Hgene | COL2A1 | C3541456 | Spondyloepiphyseal Dysplasia Tarda, X-Linked | 1 | CTD_human |
| Hgene | COL2A1 | C4479260 | AVASCULAR NECROSIS OF FEMORAL HEAD, PRIMARY, 2 | 1 | ORPHANET |
| Hgene | COL2A1 | C4551479 | Schwartz-Jampel Syndrome, Type 1 | 1 | CTD_human |
| Tgene | C0029408 | Degenerative polyarthritis | 1 | CTD_human | |
| Tgene | C0033578 | Prostatic Neoplasms | 1 | CTD_human | |
| Tgene | C0043094 | Weight Gain | 1 | CTD_human | |
| Tgene | C0086743 | Osteoarthrosis Deformans | 1 | CTD_human | |
| Tgene | C0376358 | Malignant neoplasm of prostate | 1 | CTD_human |
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