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Fusion Protein:CDK12-FAM20A |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: CDK12-FAM20A | FusionPDB ID: 15132 | FusionGDB2.0 ID: 15132 | Hgene | Tgene | Gene symbol | CDK12 | FAM20A | Gene ID | 51755 | 54757 |
| Gene name | cyclin dependent kinase 12 | FAM20A golgi associated secretory pathway pseudokinase | |
| Synonyms | CRK7|CRKR|CRKRS | AI1G|AIGFS|FP2747 | |
| Cytomap | 17q12 | 17q24.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cyclin-dependent kinase 12CDC2-related protein kinase 7Cdc2-related kinase, arginine/serine-richcell division cycle 2-related protein kinase 7cell division protein kinase 12 | pseudokinase FAM20Afamily with sequence similarity 20, member Aprotein FAM20A | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | Q9NYV4 | Q96MK3 | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000430627, ENST00000447079, ENST00000559545, | ENST00000226094, ENST00000592554, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 29 X 13 X 13=4901 | 6 X 5 X 2=60 |
| # samples | 31 | 4 | |
| ** MAII score | log2(31/4901*10)=-3.98273602613552 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(4/60*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: CDK12 [Title/Abstract] AND FAM20A [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | CDK12(37628016)-FAM20A(66551884), # samples:3 | ||
| Anticipated loss of major functional domain due to fusion event. | CDK12-FAM20A seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. CDK12-FAM20A seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. CDK12-FAM20A seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. CDK12-FAM20A seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. | ||
| * 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 | CDK12 | GO:0046777 | protein autophosphorylation | 11683387 |
| Tgene | FAM20A | GO:0001934 | positive regulation of protein phosphorylation | 25789606 |
| Fusion gene breakpoints across CDK12 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| Fusion gene breakpoints across FAM20A (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Gene Sample Information |
| Fusion gene information from FusionGDB2.0. |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * 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 |
| ChimerDB4 | BRCA | TCGA-3C-AALI-01A | CDK12 | chr17 | 37628016 | - | FAM20A | chr17 | 66551884 | - |
| ChimerDB4 | BRCA | TCGA-3C-AALI-01A | CDK12 | chr17 | 37628016 | + | FAM20A | chr17 | 66551884 | - |
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Fusion ORF Analysis |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| 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) |
| ENST00000430627 | CDK12 | chr17 | 37628016 | + | ENST00000592554 | FAM20A | chr17 | 66551884 | - | 4070 | 2242 | 185 | 3463 | 1092 |
| ENST00000447079 | CDK12 | chr17 | 37628016 | + | ENST00000592554 | FAM20A | chr17 | 66551884 | - | 3792 | 1964 | 33 | 3185 | 1050 |
| 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 |
| ENST00000430627 | ENST00000592554 | CDK12 | chr17 | 37628016 | + | FAM20A | chr17 | 66551884 | - | 0.000525886 | 0.9994741 |
| ENST00000447079 | ENST00000592554 | CDK12 | chr17 | 37628016 | + | FAM20A | chr17 | 66551884 | - | 0.000441316 | 0.9995586 |
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Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP >15132_15132_1_CDK12-FAM20A_CDK12_chr17_37628016_ENST00000430627_FAM20A_chr17_66551884_ENST00000592554_length(amino acids)=1092AA_BP=431 MPSPPPSRGALVGVELGLGGWVGVAFWSAGELFSLLQVRGKGMPNSERHGGKKDGSGGASGTLQPSSGGGSSNSRERHRLVSKHKRHKSK HSKDMGLVTPEAASLGTVIKPLVEYDDISSDSDTFSDDMAFKLDRRENDERRGSDRSDRLHKHRHHQHRRSRDLLKAKQTEKEKSQEVSS KSGSMKDRISGSSKRSNEETDDYGKAQVAKSSSKESRSSKLHKEKTRKERELKSGHKDRSKSHRKRETPKSYKTVDSPKRRSRSPHRKWS DSSKQDDSPSGASYGQDYDLSPSRSHTSSNYDSYKKSPGSTSRRQSVSPPYKEPSAYQSSTRSPSPYSRRQRSVSPYSRRRSSSYERSGS YSGRSPSPYGRRRSSSPFLSKRSLSRSPLPSRKSMKSRSRSPAYSRHSSSHSKKKRSSSRSRHSSISPVRLPLNSSLGAELSRKKKERAA AAAAAKMDGKESKGSPVFLPRKENSSVEAKDSGLESKKLPRSVKLEKSAPDTELVNVTHLNTEVKNSSDTGKVKLDENSEKHLVKDLKAQ GTRDSKPIALKEEIVTPKETETSEKETPPPLPTIASPPPPLPTTTPPPQTPPLPPLPPIPALPQQPPLPPSQPAFSQVPASSTSTLPPST HSKTSAVSSQANSQPPVQVSVKTQVSVTAAIPHLKTSTLPPLPLPPLLPGDDDMDRRHKMYREQMNLTSLDPPLQLRLEASWVQFHLGIN RHGLYSRSSPVVSKLLQDMRHFPTISADYSQDEKALLGACDCTQIVKPSGVHLKLVLRFSDFGKAMFKPMRQQRDEETPVDFFYFIDFQR HNAEIAAFHLDRILDFRRVPPTVGRIVNVTKEILEVTKNEILQSVFFVSPASNVCFFAKCPYMCKTEYAVCGNPHLLEGSLSAFLPSLNL APRLSVPNPWIRSYTLAGKEEWEVNPLYCDTVKQIYPYNNSQRLLNVIDMAIFDFLIGNMDRHHYEMFTKFGDDGFLIHLDNARGFGRHS HDEISILSPLSQCCMIKKKTLLHLQLLAQADYRLSDVMRESLLEDQLSPVLTEPHLLALDRRLQTILRTVEGCIVAHGQQSVIVDGPVEQ -------------------------------------------------------------- >15132_15132_2_CDK12-FAM20A_CDK12_chr17_37628016_ENST00000447079_FAM20A_chr17_66551884_ENST00000592554_length(amino acids)=1050AA_BP=389 MPNSERHGGKKDGSGGASGTLQPSSGGGSSNSRERHRLVSKHKRHKSKHSKDMGLVTPEAASLGTVIKPLVEYDDISSDSDTFSDDMAFK LDRRENDERRGSDRSDRLHKHRHHQHRRSRDLLKAKQTEKEKSQEVSSKSGSMKDRISGSSKRSNEETDDYGKAQVAKSSSKESRSSKLH KEKTRKERELKSGHKDRSKSHRKRETPKSYKTVDSPKRRSRSPHRKWSDSSKQDDSPSGASYGQDYDLSPSRSHTSSNYDSYKKSPGSTS RRQSVSPPYKEPSAYQSSTRSPSPYSRRQRSVSPYSRRRSSSYERSGSYSGRSPSPYGRRRSSSPFLSKRSLSRSPLPSRKSMKSRSRSP AYSRHSSSHSKKKRSSSRSRHSSISPVRLPLNSSLGAELSRKKKERAAAAAAAKMDGKESKGSPVFLPRKENSSVEAKDSGLESKKLPRS VKLEKSAPDTELVNVTHLNTEVKNSSDTGKVKLDENSEKHLVKDLKAQGTRDSKPIALKEEIVTPKETETSEKETPPPLPTIASPPPPLP TTTPPPQTPPLPPLPPIPALPQQPPLPPSQPAFSQVPASSTSTLPPSTHSKTSAVSSQANSQPPVQVSVKTQVSVTAAIPHLKTSTLPPL PLPPLLPGDDDMDRRHKMYREQMNLTSLDPPLQLRLEASWVQFHLGINRHGLYSRSSPVVSKLLQDMRHFPTISADYSQDEKALLGACDC TQIVKPSGVHLKLVLRFSDFGKAMFKPMRQQRDEETPVDFFYFIDFQRHNAEIAAFHLDRILDFRRVPPTVGRIVNVTKEILEVTKNEIL QSVFFVSPASNVCFFAKCPYMCKTEYAVCGNPHLLEGSLSAFLPSLNLAPRLSVPNPWIRSYTLAGKEEWEVNPLYCDTVKQIYPYNNSQ RLLNVIDMAIFDFLIGNMDRHHYEMFTKFGDDGFLIHLDNARGFGRHSHDEISILSPLSQCCMIKKKTLLHLQLLAQADYRLSDVMRESL -------------------------------------------------------------- |
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Fusion Protein Functional Features |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:37628016/chr17:66551884) - 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 |
| CDK12 | FAM20A |
| FUNCTION: Cyclin-dependent kinase that phosphorylates the C-terminal domain (CTD) of the large subunit of RNA polymerase II (POLR2A), thereby acting as a key regulator of transcription elongation. Regulates the expression of genes involved in DNA repair and is required for the maintenance of genomic stability. Preferentially phosphorylates 'Ser-5' in CTD repeats that are already phosphorylated at 'Ser-7', but can also phosphorylate 'Ser-2'. Required for RNA splicing, possibly by phosphorylating SRSF1/SF2. Involved in regulation of MAP kinase activity, possibly leading to affect the response to estrogen inhibitors. {ECO:0000269|PubMed:11683387, ECO:0000269|PubMed:19651820, ECO:0000269|PubMed:20952539, ECO:0000269|PubMed:22012619, ECO:0000269|PubMed:24662513}. | FUNCTION: Pseudokinase that acts as an allosteric activator of the Golgi serine/threonine protein kinase FAM20C and is involved in biomineralization of teeth. Forms a complex with FAM20C and increases the ability of FAM20C to phosphorylate the proteins that form the 'matrix' that guides the deposition of the enamel minerals. {ECO:0000269|PubMed:25789606}. |
| 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. |
| - 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 |
| Hgene | CDK12 | chr17:37628016 | chr17:66551884 | ENST00000430627 | + | 2 | 14 | 407_413 | 643.6666666666666 | 1482.0 | Compositional bias | Note=Poly-Ala |
| Hgene | CDK12 | chr17:37628016 | chr17:66551884 | ENST00000430627 | + | 2 | 14 | 535_540 | 643.6666666666666 | 1482.0 | Compositional bias | Note=Poly-Pro |
| Hgene | CDK12 | chr17:37628016 | chr17:66551884 | ENST00000447079 | + | 2 | 14 | 407_413 | 643.6666666666666 | 1491.0 | Compositional bias | Note=Poly-Ala |
| Hgene | CDK12 | chr17:37628016 | chr17:66551884 | ENST00000447079 | + | 2 | 14 | 535_540 | 643.6666666666666 | 1491.0 | Compositional bias | Note=Poly-Pro |
| - 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 |
| Hgene | CDK12 | chr17:37628016 | chr17:66551884 | ENST00000430627 | + | 2 | 14 | 1266_1280 | 643.6666666666666 | 1482.0 | Compositional bias | Note=Poly-Pro |
| Hgene | CDK12 | chr17:37628016 | chr17:66551884 | ENST00000447079 | + | 2 | 14 | 1266_1280 | 643.6666666666666 | 1491.0 | Compositional bias | Note=Poly-Pro |
| Hgene | CDK12 | chr17:37628016 | chr17:66551884 | ENST00000430627 | + | 2 | 14 | 727_1020 | 643.6666666666666 | 1482.0 | Domain | Protein kinase |
| Hgene | CDK12 | chr17:37628016 | chr17:66551884 | ENST00000447079 | + | 2 | 14 | 727_1020 | 643.6666666666666 | 1491.0 | Domain | Protein kinase |
| Hgene | CDK12 | chr17:37628016 | chr17:66551884 | ENST00000430627 | + | 2 | 14 | 733_741 | 643.6666666666666 | 1482.0 | Nucleotide binding | Note=ATP |
| Hgene | CDK12 | chr17:37628016 | chr17:66551884 | ENST00000430627 | + | 2 | 14 | 814_819 | 643.6666666666666 | 1482.0 | Nucleotide binding | Note=ATP |
| Hgene | CDK12 | chr17:37628016 | chr17:66551884 | ENST00000447079 | + | 2 | 14 | 733_741 | 643.6666666666666 | 1491.0 | Nucleotide binding | Note=ATP |
| Hgene | CDK12 | chr17:37628016 | chr17:66551884 | ENST00000447079 | + | 2 | 14 | 814_819 | 643.6666666666666 | 1491.0 | Nucleotide binding | Note=ATP |
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Fusion Protein-Protein Interaction |
| 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 from validated records (BIOGRID-3.4.160) |
| Gene | PPI interactors |
| Protein-protein interactors based on sequence similarity (STRING) |
| Gene | STRING network |
| CDK12 | |
| FAM20A |
| - Retained interactions in fusion protein (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost interactions due to fusion (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs to CDK12-FAM20A |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to CDK12-FAM20A |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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