FusionNeoAntigen Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use

Center for Computational Systems Medicine
leaf

Fusion Gene and Fusion Protein Summary

leaf

Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

leaf

Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

leaf

Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

leaf

Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

leaf

Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

leaf

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

leaf

Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

leaf

Potential target of CAR-T therapy development

leaf

Information on the samples that have these potential fusion neoantigens

leaf

Fusion Protein Targeting Drugs - (Manual Curation)

leaf

Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:CDK12-FAM20A

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CDK12-FAM20A
FusionPDB ID: 15132
FusionGDB2.0 ID: 15132
HgeneTgene
Gene symbol

CDK12

FAM20A

Gene ID

51755

54757

Gene namecyclin dependent kinase 12FAM20A golgi associated secretory pathway pseudokinase
SynonymsCRK7|CRKR|CRKRSAI1G|AIGFS|FP2747
Cytomap

17q12

17q24.2

Type of geneprotein-codingprotein-coding
Descriptioncyclin-dependent kinase 12CDC2-related protein kinase 7Cdc2-related kinase, arginine/serine-richcell division cycle 2-related protein kinase 7cell division protein kinase 12pseudokinase FAM20Afamily with sequence similarity 20, member Aprotein FAM20A
Modification date2020031320200313
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 geneENST idsENST00000430627, ENST00000447079, 
ENST00000559545, 
ENST00000226094, 
ENST00000592554, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score29 X 13 X 13=49016 X 5 X 2=60
# samples 314
** MAII scorelog2(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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneCDK12

GO:0046777

protein autophosphorylation

11683387

TgeneFAM20A

GO:0001934

positive regulation of protein phosphorylation

25789606



check button 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.
FGviewer

check buttonRetention analysis results 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, are available here.

check buttonFusion 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.
all structure

check buttonFusion 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.
all structure


Top

Fusion Amino Acid Sequences


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000430627CDK12chr1737628016+ENST00000592554FAM20Achr1766551884-4070224218534631092
ENST00000447079CDK12chr1737628016+ENST00000592554FAM20Achr1766551884-379219643331851050

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000430627ENST00000592554CDK12chr1737628016+FAM20Achr1766551884-0.0005258860.9994741
ENST00000447079ENST00000592554CDK12chr1737628016+FAM20Achr1766551884-0.0004413160.9995586

check button Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

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

Top

Fusion Protein Breakpoint Sequences for CDK12-FAM20A

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
CDK12chr1737628016FAM20Achr17665518841964389SRSRHSSISPVRLPLNSSLGAELSRK
CDK12chr1737628016FAM20Achr17665518842242431SRSRHSSISPVRLPLNSSLGAELSRK

Top

Potential FusionNeoAntigen Information of CDK12-FAM20A in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
CDK12-FAM20A_37628016_66551884.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)
CDK12-FAM20Achr1737628016chr17665518842242HLA-A30:08SISPVRLPL0.86390.7543615
CDK12-FAM20Achr1737628016chr17665518842242HLA-B27:04SPVRLPLNSSL0.99430.7008819
CDK12-FAM20Achr1737628016chr17665518842242HLA-B27:05SPVRLPLNSSL0.99270.7508819
CDK12-FAM20Achr1737628016chr17665518842242HLA-B35:03SPVRLPLNSSL0.95820.775819
CDK12-FAM20Achr1737628016chr17665518842242HLA-B35:04SPVRLPLNSSL0.89460.7651819
CDK12-FAM20Achr1737628016chr17665518842242HLA-B35:02SPVRLPLNSSL0.89460.7651819
CDK12-FAM20Achr1737628016chr17665518842242HLA-C01:17ISPVRLPL0.99730.8666715
CDK12-FAM20Achr1737628016chr17665518842242HLA-C01:30ISPVRLPL0.99290.9307715
CDK12-FAM20Achr1737628016chr17665518842242HLA-C03:07SISPVRLPL0.99930.9315615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C03:08SISPVRLPL0.99920.8292615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C15:06SISPVRLPL0.99920.8214615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C03:19SISPVRLPL0.9990.9579615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C02:06SISPVRLPL0.99380.8751615
CDK12-FAM20Achr1737628016chr17665518842242HLA-B07:12SISPVRLPL0.98640.5011615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C03:14SISPVRLPL0.96430.9298615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C01:30SISPVRLPL0.70150.9112615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C01:17SISPVRLPL0.67490.8671615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C15:06SSISPVRLPL0.99960.8231515
CDK12-FAM20Achr1737628016chr17665518842242HLA-B07:12SPVRLPLNSSL0.99970.6748819
CDK12-FAM20Achr1737628016chr17665518842242HLA-B39:10SPVRLPLNSSL0.92880.8194819
CDK12-FAM20Achr1737628016chr17665518842242HLA-B35:12SPVRLPLNSSL0.89460.7651819
CDK12-FAM20Achr1737628016chr17665518842242HLA-B27:03SPVRLPLNSSL0.83390.7923819
CDK12-FAM20Achr1737628016chr17665518842242HLA-C01:03ISPVRLPL0.9970.819715
CDK12-FAM20Achr1737628016chr17665518842242HLA-C01:02ISPVRLPL0.9970.8676715
CDK12-FAM20Achr1737628016chr17665518842242HLA-C03:04SISPVRLPL0.99920.9729615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C03:03SISPVRLPL0.99920.9729615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C15:05SISPVRLPL0.99890.8559615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C03:05SISPVRLPL0.99870.8902615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C15:02SISPVRLPL0.99840.8013615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C03:17SISPVRLPL0.99840.9152615
CDK12-FAM20Achr1737628016chr17665518842242HLA-B07:13SISPVRLPL0.9960.6991615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C03:06SISPVRLPL0.9950.9565615
CDK12-FAM20Achr1737628016chr17665518842242HLA-B15:73SISPVRLPL0.98830.8193615
CDK12-FAM20Achr1737628016chr17665518842242HLA-B15:30SISPVRLPL0.96910.6628615
CDK12-FAM20Achr1737628016chr17665518842242HLA-A32:01SISPVRLPL0.96370.8501615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C01:02SISPVRLPL0.69720.8682615
CDK12-FAM20Achr1737628016chr17665518842242HLA-C17:01SISPVRLPL0.69040.716615
CDK12-FAM20Achr1737628016chr17665518842242HLA-B27:06SPVRLPLNSSL0.99520.6804819
CDK12-FAM20Achr1737628016chr17665518842242HLA-B27:10SPVRLPLNSSL0.99470.8341819
CDK12-FAM20Achr1737628016chr17665518842242HLA-B27:08SPVRLPLNSSL0.99240.6316819
CDK12-FAM20Achr1737628016chr17665518842242HLA-B27:09SPVRLPLNSSL0.99140.7094819
CDK12-FAM20Achr1737628016chr17665518842242HLA-B35:13SPVRLPLNSSL0.95250.7797819
CDK12-FAM20Achr1737628016chr17665518842242HLA-B67:01SPVRLPLNSSL0.91970.5769819
CDK12-FAM20Achr1737628016chr17665518842242HLA-B35:09SPVRLPLNSSL0.89460.7651819

Top

Potential FusionNeoAntigen Information of CDK12-FAM20A in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)

Top

Fusion breakpoint peptide structures of CDK12-FAM20A

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* 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 nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
8672SISPVRLPLNSSLGCDK12FAM20Achr1737628016chr17665518842242

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CDK12-FAM20A

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score
HLA-B14:023BVN8672SISPVRLPLNSSLG-7.9962-8.1096
HLA-B14:023BVN8672SISPVRLPLNSSLG-5.70842-6.74372
HLA-B52:013W398672SISPVRLPLNSSLG-6.83737-6.95077
HLA-B52:013W398672SISPVRLPLNSSLG-4.4836-5.5189
HLA-A11:014UQ28672SISPVRLPLNSSLG-10.0067-10.1201
HLA-A11:014UQ28672SISPVRLPLNSSLG-9.03915-10.0745
HLA-A24:025HGA8672SISPVRLPLNSSLG-6.56204-6.67544
HLA-A24:025HGA8672SISPVRLPLNSSLG-5.42271-6.45801
HLA-B44:053DX88672SISPVRLPLNSSLG-7.85648-8.89178
HLA-B44:053DX88672SISPVRLPLNSSLG-5.3978-5.5112
HLA-A02:016TDR8672SISPVRLPLNSSLG-3.37154-4.40684

Top

Vaccine Design for the FusionNeoAntigens of CDK12-FAM20A

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence
CDK12-FAM20Achr1737628016chr1766551884515SSISPVRLPLACCTGGAGATGATGACATGGATAGGCGACA
CDK12-FAM20Achr1737628016chr1766551884615SISPVRLPLTGGAGATGATGACATGGATAGGCGACA
CDK12-FAM20Achr1737628016chr1766551884715ISPVRLPLAGATGATGACATGGATAGGCGACA
CDK12-FAM20Achr1737628016chr1766551884819SPVRLPLNSSLTGATGACATGGATAGGCGACACAAGATGTACAG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence

Top

Information of the samples that have these potential fusion neoantigens of CDK12-FAM20A

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample
BRCACDK12-FAM20Achr1737628016ENST00000430627chr1766551884ENST00000592554TCGA-3C-AALI-01A

Top

Potential target of CAR-T therapy development for CDK12-FAM20A

check button Predicted 3D structure. We used RoseTTAFold.

check buttonRetention 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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* 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.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

Top

Related Drugs to CDK12-FAM20A

check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

Top

Related Diseases to CDK12-FAM20A

check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource