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Fusion Protein:CDK12-FAM20A |
Fusion Gene and Fusion Protein Summary |
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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 Main function of 5'-partner protein: 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}. | Q96MK3 Main function of 5'-partner protein: 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}. | |
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 | |
Fusion gene context | PubMed: CDK12 [Title/Abstract] AND FAM20A [Title/Abstract] AND fusion [Title/Abstract] | ||
Fusion neoantigen context | PubMed: CDK12 [Title/Abstract] AND FAM20A [Title/Abstract] AND neoantigen [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) |
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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 |
![]() 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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![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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![]() * 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 Amino Acid Sequences |
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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 |
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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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Get the fusion protein sequences from here. |
Fusion protein sequence information is available in the fasta format. >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP |
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Fusion Protein Breakpoint Sequences for CDK12-FAM20A |
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Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
CDK12 | chr17 | 37628016 | FAM20A | chr17 | 66551884 | 1964 | 389 | SRSRHSSISPVRLPLNSSLGAELSRK |
CDK12 | chr17 | 37628016 | FAM20A | chr17 | 66551884 | 2242 | 431 | SRSRHSSISPVRLPLNSSLGAELSRK |
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Potential FusionNeoAntigen Information of CDK12-FAM20A in HLA I |
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CDK12-FAM20A_37628016_66551884.msa |
![]() * We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5) |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA I | FusionNeoAntigen peptide | Binding score | Immunogenic score | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-A30:08 | SISPVRLPL | 0.8639 | 0.7543 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B27:04 | SPVRLPLNSSL | 0.9943 | 0.7008 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B27:05 | SPVRLPLNSSL | 0.9927 | 0.7508 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B35:03 | SPVRLPLNSSL | 0.9582 | 0.775 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B35:04 | SPVRLPLNSSL | 0.8946 | 0.7651 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B35:02 | SPVRLPLNSSL | 0.8946 | 0.7651 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C01:17 | ISPVRLPL | 0.9973 | 0.8666 | 7 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C01:30 | ISPVRLPL | 0.9929 | 0.9307 | 7 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C03:07 | SISPVRLPL | 0.9993 | 0.9315 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C03:08 | SISPVRLPL | 0.9992 | 0.8292 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C15:06 | SISPVRLPL | 0.9992 | 0.8214 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C03:19 | SISPVRLPL | 0.999 | 0.9579 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C02:06 | SISPVRLPL | 0.9938 | 0.8751 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B07:12 | SISPVRLPL | 0.9864 | 0.5011 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C03:14 | SISPVRLPL | 0.9643 | 0.9298 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C01:30 | SISPVRLPL | 0.7015 | 0.9112 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C01:17 | SISPVRLPL | 0.6749 | 0.8671 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C15:06 | SSISPVRLPL | 0.9996 | 0.8231 | 5 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B07:12 | SPVRLPLNSSL | 0.9997 | 0.6748 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B39:10 | SPVRLPLNSSL | 0.9288 | 0.8194 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B35:12 | SPVRLPLNSSL | 0.8946 | 0.7651 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B27:03 | SPVRLPLNSSL | 0.8339 | 0.7923 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C01:03 | ISPVRLPL | 0.997 | 0.819 | 7 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C01:02 | ISPVRLPL | 0.997 | 0.8676 | 7 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C03:04 | SISPVRLPL | 0.9992 | 0.9729 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C03:03 | SISPVRLPL | 0.9992 | 0.9729 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C15:05 | SISPVRLPL | 0.9989 | 0.8559 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C03:05 | SISPVRLPL | 0.9987 | 0.8902 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C15:02 | SISPVRLPL | 0.9984 | 0.8013 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C03:17 | SISPVRLPL | 0.9984 | 0.9152 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B07:13 | SISPVRLPL | 0.996 | 0.6991 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C03:06 | SISPVRLPL | 0.995 | 0.9565 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B15:73 | SISPVRLPL | 0.9883 | 0.8193 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B15:30 | SISPVRLPL | 0.9691 | 0.6628 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-A32:01 | SISPVRLPL | 0.9637 | 0.8501 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C01:02 | SISPVRLPL | 0.6972 | 0.8682 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-C17:01 | SISPVRLPL | 0.6904 | 0.716 | 6 | 15 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B27:06 | SPVRLPLNSSL | 0.9952 | 0.6804 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B27:10 | SPVRLPLNSSL | 0.9947 | 0.8341 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B27:08 | SPVRLPLNSSL | 0.9924 | 0.6316 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B27:09 | SPVRLPLNSSL | 0.9914 | 0.7094 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B35:13 | SPVRLPLNSSL | 0.9525 | 0.7797 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B67:01 | SPVRLPLNSSL | 0.9197 | 0.5769 | 8 | 19 |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 | HLA-B35:09 | SPVRLPLNSSL | 0.8946 | 0.7651 | 8 | 19 |
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Potential FusionNeoAntigen Information of CDK12-FAM20A in HLA II |
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![]() * We used NetMHCIIpan v4.1 (%rank<0.5). |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA II | FusionNeoAntigen peptide | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Fusion breakpoint peptide structures of CDK12-FAM20A |
![]() * The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA. |
File name | BPseq | Hgene | Tgene | Hchr | Hbp | Tchr | Tbp | AAlen |
8672 | SISPVRLPLNSSLG | CDK12 | FAM20A | chr17 | 37628016 | chr17 | 66551884 | 2242 |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CDK12-FAM20A |
![]() * We used Glide to predict the interaction between HLAs and neoantigens. |
HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
HLA-B14:02 | 3BVN | 8672 | SISPVRLPLNSSLG | -7.9962 | -8.1096 |
HLA-B14:02 | 3BVN | 8672 | SISPVRLPLNSSLG | -5.70842 | -6.74372 |
HLA-B52:01 | 3W39 | 8672 | SISPVRLPLNSSLG | -6.83737 | -6.95077 |
HLA-B52:01 | 3W39 | 8672 | SISPVRLPLNSSLG | -4.4836 | -5.5189 |
HLA-A11:01 | 4UQ2 | 8672 | SISPVRLPLNSSLG | -10.0067 | -10.1201 |
HLA-A11:01 | 4UQ2 | 8672 | SISPVRLPLNSSLG | -9.03915 | -10.0745 |
HLA-A24:02 | 5HGA | 8672 | SISPVRLPLNSSLG | -6.56204 | -6.67544 |
HLA-A24:02 | 5HGA | 8672 | SISPVRLPLNSSLG | -5.42271 | -6.45801 |
HLA-B44:05 | 3DX8 | 8672 | SISPVRLPLNSSLG | -7.85648 | -8.89178 |
HLA-B44:05 | 3DX8 | 8672 | SISPVRLPLNSSLG | -5.3978 | -5.5112 |
HLA-A02:01 | 6TDR | 8672 | SISPVRLPLNSSLG | -3.37154 | -4.40684 |
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Vaccine Design for the FusionNeoAntigens of CDK12-FAM20A |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 5 | 15 | SSISPVRLPL | ACCTGGAGATGATGACATGGATAGGCGACA |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 6 | 15 | SISPVRLPL | TGGAGATGATGACATGGATAGGCGACA |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 7 | 15 | ISPVRLPL | AGATGATGACATGGATAGGCGACA |
CDK12-FAM20A | chr17 | 37628016 | chr17 | 66551884 | 8 | 19 | SPVRLPLNSSL | TGATGACATGGATAGGCGACACAAGATGTACAG |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
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Information of the samples that have these potential fusion neoantigens of CDK12-FAM20A |
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Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
BRCA | CDK12-FAM20A | chr17 | 37628016 | ENST00000430627 | chr17 | 66551884 | ENST00000592554 | TCGA-3C-AALI-01A |
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Potential target of CAR-T therapy development for CDK12-FAM20A |
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![]() * Minus value of BPloci means that the break point is located before the CDS. |
- In-frame and retained 'Transmembrane'. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
![]() * We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image. |
Hgene | Hchr | Hbp | Henst | Tgene | Tchr | Tbp | Tenst | DeepLoc result |
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Related Drugs to CDK12-FAM20A |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to CDK12-FAM20A |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |