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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:CBFA2T2-HM13 (FusionGDB2 ID:13343)

Fusion Gene Summary for CBFA2T2-HM13

check button Fusion gene summary
Fusion gene informationFusion gene name: CBFA2T2-HM13
Fusion gene ID: 13343
HgeneTgene
Gene symbol

CBFA2T2

HM13

Gene ID

9139

81502

Gene nameCBFA2/RUNX1 partner transcriptional co-repressor 2histocompatibility minor 13
SynonymsEHT|MTGR1|ZMYND3|p85H13|IMP1|IMPAS|IMPAS-1|MSTP086|PSENL3|PSL3|SPP|SPPL1
Cytomap

20q11.21-q11.22

20q11.21

Type of geneprotein-codingprotein-coding
Descriptionprotein CBFA2T2CBFA2/RUNX1 translocation partner 2ETO homolog on chromosome 20ETO homologous on chromosome 20MTG8-like proteinMTG8-related protein 1core-binding factor, runt domain, alpha subunit 2; translocated to, 2myeloid translocation gene-relaminor histocompatibility antigen H13intramembrane protease 1minor histocompatibility antigen 13presenilin-like protein 3signal peptide peptidase betasignal peptide peptidase like 1
Modification date2020031320200313
UniProtAcc

O43439

Q8TCT9

Ensembl transtripts involved in fusion geneENST00000342704, ENST00000375279, 
ENST00000344201, ENST00000346541, 
ENST00000359606, ENST00000397798, 
ENST00000397800, ENST00000491618, 
ENST00000492345, ENST00000543126, 
ENST00000492709, ENST00000335574, 
ENST00000340852, ENST00000376127, 
ENST00000398174, 
Fusion gene scores* DoF score26 X 9 X 12=280816 X 19 X 12=3648
# samples 2725
** MAII scorelog2(27/2808*10)=-3.37851162325373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(25/3648*10)=-3.86710572950266
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CBFA2T2 [Title/Abstract] AND HM13 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCBFA2T2(32078107)-HM13(30132750), # samples:3
Anticipated loss of major functional domain due to fusion event.CBFA2T2-HM13 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CBFA2T2-HM13 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted 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
HgeneCBFA2T2

GO:0010976

positive regulation of neuron projection development

19026687

HgeneCBFA2T2

GO:0045892

negative regulation of transcription, DNA-templated

23251453

TgeneHM13

GO:0033619

membrane protein proteolysis

14741365


check buttonFusion gene breakpoints across CBFA2T2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across HM13 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4HNSCTCGA-CN-6024-01ACBFA2T2chr20

32078107

-HM13chr20

30132750

+
ChimerDB4HNSCTCGA-CN-6024-01ACBFA2T2chr20

32078107

+HM13chr20

30132750

+
ChimerDB4HNSCTCGA-CN-6024CBFA2T2chr20

32078107

+HM13chr20

30132750

+


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Fusion Gene ORF analysis for CBFA2T2-HM13

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-3UTRENST00000342704ENST00000492709CBFA2T2chr20

32078107

+HM13chr20

30132750

+
5UTR-3CDSENST00000375279ENST00000335574CBFA2T2chr20

32078107

+HM13chr20

30132750

+
5UTR-3CDSENST00000375279ENST00000340852CBFA2T2chr20

32078107

+HM13chr20

30132750

+
5UTR-3CDSENST00000375279ENST00000376127CBFA2T2chr20

32078107

+HM13chr20

30132750

+
5UTR-3CDSENST00000375279ENST00000398174CBFA2T2chr20

32078107

+HM13chr20

30132750

+
5UTR-3UTRENST00000375279ENST00000492709CBFA2T2chr20

32078107

+HM13chr20

30132750

+
Frame-shiftENST00000342704ENST00000335574CBFA2T2chr20

32078107

+HM13chr20

30132750

+
Frame-shiftENST00000342704ENST00000340852CBFA2T2chr20

32078107

+HM13chr20

30132750

+
Frame-shiftENST00000342704ENST00000376127CBFA2T2chr20

32078107

+HM13chr20

30132750

+
Frame-shiftENST00000342704ENST00000398174CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000344201ENST00000335574CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000344201ENST00000340852CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000344201ENST00000376127CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000344201ENST00000398174CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000346541ENST00000335574CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000346541ENST00000340852CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000346541ENST00000376127CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000346541ENST00000398174CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000359606ENST00000335574CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000359606ENST00000340852CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000359606ENST00000376127CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000359606ENST00000398174CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000397798ENST00000335574CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000397798ENST00000340852CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000397798ENST00000376127CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000397798ENST00000398174CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000397800ENST00000335574CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000397800ENST00000340852CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000397800ENST00000376127CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000397800ENST00000398174CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000491618ENST00000335574CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000491618ENST00000340852CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000491618ENST00000376127CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000491618ENST00000398174CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000492345ENST00000335574CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000492345ENST00000340852CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000492345ENST00000376127CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000492345ENST00000398174CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000543126ENST00000335574CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000543126ENST00000340852CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000543126ENST00000376127CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3CDSENST00000543126ENST00000398174CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3UTRENST00000344201ENST00000492709CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3UTRENST00000346541ENST00000492709CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3UTRENST00000359606ENST00000492709CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3UTRENST00000397798ENST00000492709CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3UTRENST00000397800ENST00000492709CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3UTRENST00000491618ENST00000492709CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3UTRENST00000492345ENST00000492709CBFA2T2chr20

32078107

+HM13chr20

30132750

+
intron-3UTRENST00000543126ENST00000492709CBFA2T2chr20

32078107

+HM13chr20

30132750

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

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

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Fusion Genomic Features for CBFA2T2-HM13


check buttonFusionAI 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.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
CBFA2T2chr2032078107+HM13chr2030132749+3.36E-171
CBFA2T2chr2032078107+HM13chr2030132749+3.36E-171
CBFA2T2chr2032078107+HM13chr2030132749+3.36E-171
CBFA2T2chr2032078107+HM13chr2030132749+3.36E-171

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for CBFA2T2-HM13


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/:32078107/:30132750)
- 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 buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CBFA2T2

O43439

HM13

Q8TCT9

FUNCTION: Transcriptional corepressor which facilitates transcriptional repression via its association with DNA-binding transcription factors and recruitment of other corepressors and histone-modifying enzymes (PubMed:12559562, PubMed:15203199). Via association with PRDM14 is involved in regulation of embryonic stem cell (ESC) pluripotency (PubMed:27281218). Involved in primordial germ cell (PCG) formation. Stabilizes PRDM14 and OCT4 on chromatin in a homooligomerization-dependent manner (By similarity). Can repress the expression of MMP7 in a ZBTB33-dependent manner (PubMed:23251453). May function as a complex with the chimeric protein RUNX1/AML1-CBFA2T1/MTG8 (AML1-MTG8/ETO fusion protein) which is produced in acute myeloid leukemia with the chromosomal translocation t(8;21). May thus be involved in the repression of AML1-dependent transcription and the induction of G-CSF/CSF3-dependent cell growth. May be a tumor suppressor gene candidate involved in myeloid tumors with the deletion of the 20q11 region. Through heteromerization with CBFA2T3/MTG16 may be involved in regulation of the proliferation and the differentiation of erythroid progenitors by repressing the expression of TAL1 target genes (By similarity). Required for the maintenance of the secretory cell lineage in the small intestine. Can inhibit Notch signaling probably by association with RBPJ and may be involved in GFI1-mediated Paneth cell differentiation (By similarity). {ECO:0000250|UniProtKB:O70374, ECO:0000269|PubMed:23251453, ECO:0000303|PubMed:12559562, ECO:0000303|PubMed:15203199}.FUNCTION: Catalyzes intramembrane proteolysis of some signal peptides after they have been cleaved from a preprotein, resulting in the release of the fragment from the ER membrane into the cytoplasm. Required to generate lymphocyte cell surface (HLA-E) epitopes derived from MHC class I signal peptides (PubMed:11714810). May be necessary for the removal of the signal peptide that remains attached to the hepatitis C virus core protein after the initial proteolytic processing of the polyprotein (PubMed:12145199). Involved in the intramembrane cleavage of the integral membrane protein PSEN1 (PubMed:12077416, PubMed:11714810, PubMed:14741365). Cleaves the integral membrane protein XBP1 isoform 1 in a DERL1/RNF139-dependent manner (PubMed:25239945). May play a role in graft rejection (By similarity). {ECO:0000250|UniProtKB:Q9D8V0, ECO:0000269|PubMed:11714810, ECO:0000269|PubMed:12077416, ECO:0000269|PubMed:12145199, ECO:0000269|PubMed:14741365, ECO:0000269|PubMed:25239945}.

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, 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

download page


* 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for CBFA2T2-HM13


check button 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 CBFA2T2-HM13


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for CBFA2T2-HM13


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for CBFA2T2-HM13


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