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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:ETV6-RUNX1 (FusionGDB2 ID:HG2120TG861)

Fusion Gene Summary for ETV6-RUNX1

check button Fusion gene summary
Fusion gene informationFusion gene name: ETV6-RUNX1
Fusion gene ID: hg2120tg861
HgeneTgene
Gene symbol

ETV6

RUNX1

Gene ID

2120

861

Gene nameETS variant transcription factor 6RUNX family transcription factor 1
SynonymsTEL|TEL/ABL|THC5AML1|AML1-EVI-1|AMLCR1|CBF2alpha|CBFA2|EVI-1|PEBP2aB|PEBP2alpha
Cytomap('ETV6')('RUNX1')

12p13.2

21q22.12

Type of geneprotein-codingprotein-coding
Descriptiontranscription factor ETV6ETS translocation variant 6ETS variant 6ETS-related protein Tel1TEL1 oncogeneets variant gene 6 (TEL oncogene)runt-related transcription factor 1AML1-EVI-1 fusion proteinPEA2-alpha BPEBP2-alpha BSL3-3 enhancer factor 1 alpha B subunitSL3/AKV core-binding factor alpha B subunitacute myeloid leukemia 1 proteincore-binding factor, runt domain, alpha subunit 2
Modification date2020031320200322
UniProtAcc

P41212

Q01196

Ensembl transtripts involved in fusion geneENST00000396373, ENST00000544715, 
Fusion gene scores* DoF score59 X 37 X 25=5457536 X 59 X 13=27612
# samples 5863
** MAII scorelog2(58/54575*10)=-6.55604351475058
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(63/27612*10)=-5.45379975055797
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ETV6 [Title/Abstract] AND RUNX1 [Title/Abstract] AND fusion [Title/Abstract]

Identification of ETV6-RUNX1-like and DUX4-rearranged subtypes in paediatric B-cell precursor acute lymphoblastic leukaemia (pmid: 27265895)
Most frequent breakpointETV6(12022903)-RUNX1(36265263), # samples:2
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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneETV6

GO:0000122

negative regulation of transcription by RNA polymerase II

10514502

TgeneRUNX1

GO:0030097

hemopoiesis

21873977

TgeneRUNX1

GO:0045893

positive regulation of transcription, DNA-templated

10207087|14970218

TgeneRUNX1

GO:0045944

positive regulation of transcription by RNA polymerase II

9199349|10207087|14970218|21873977



check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4biphenotypic leukemia;acute lymphoblastic leukemia;lymphoblastic lymphomaAJ494735ETV6chr12

12035545

RUNX1chr21

36264754
ChimerKB3..ETV6chr12

12022903

+RUNX1chr21

36265260

-
ChimerKB4..ETV6chr12

12022357

+RUNX1chr21

12022357

-
ChimerKB4..ETV6chr12

12022903

+RUNX1chr21

36265260

-


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Fusion Gene ORF analysis for ETV6-RUNX1

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-5UTRENST00000396373ENST00000486278ETV6chr12

12022903

+RUNX1chr21

36265260

-
5CDS-intronENST00000396373ENST00000300305ETV6chr12

12022903

+RUNX1chr21

36265260

-
5CDS-intronENST00000396373ENST00000325074ETV6chr12

12022903

+RUNX1chr21

36265260

-
5CDS-intronENST00000396373ENST00000344691ETV6chr12

12022903

+RUNX1chr21

36265260

-
5CDS-intronENST00000396373ENST00000358356ETV6chr12

12022903

+RUNX1chr21

36265260

-
5CDS-intronENST00000396373ENST00000399240ETV6chr12

12022903

+RUNX1chr21

36265260

-
5CDS-intronENST00000396373ENST00000437180ETV6chr12

12022903

+RUNX1chr21

36265260

-
5CDS-intronENST00000396373ENST00000494829ETV6chr12

12022903

+RUNX1chr21

36265260

-
intron-5UTRENST00000544715ENST00000486278ETV6chr12

12022903

+RUNX1chr21

36265260

-
intron-intronENST00000396373ENST00000300305ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000396373ENST00000300305ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000396373ENST00000325074ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000396373ENST00000325074ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000396373ENST00000344691ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000396373ENST00000344691ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000396373ENST00000358356ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000396373ENST00000358356ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000396373ENST00000399240ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000396373ENST00000399240ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000396373ENST00000437180ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000396373ENST00000437180ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000396373ENST00000486278ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000396373ENST00000486278ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000396373ENST00000494829ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000396373ENST00000494829ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000544715ENST00000300305ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000544715ENST00000300305ETV6chr12

12022903

+RUNX1chr21

36265260

-
intron-intronENST00000544715ENST00000300305ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000544715ENST00000325074ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000544715ENST00000325074ETV6chr12

12022903

+RUNX1chr21

36265260

-
intron-intronENST00000544715ENST00000325074ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000544715ENST00000344691ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000544715ENST00000344691ETV6chr12

12022903

+RUNX1chr21

36265260

-
intron-intronENST00000544715ENST00000344691ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000544715ENST00000358356ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000544715ENST00000358356ETV6chr12

12022903

+RUNX1chr21

36265260

-
intron-intronENST00000544715ENST00000358356ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000544715ENST00000399240ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000544715ENST00000399240ETV6chr12

12022903

+RUNX1chr21

36265260

-
intron-intronENST00000544715ENST00000399240ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000544715ENST00000437180ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000544715ENST00000437180ETV6chr12

12022903

+RUNX1chr21

36265260

-
intron-intronENST00000544715ENST00000437180ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000544715ENST00000486278ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000544715ENST00000486278ETV6chr12

12022357

+RUNX1chr21

12022357

-
intron-intronENST00000544715ENST00000494829ETV6chr12

12035545

RUNX1chr21

36264754

intron-intronENST00000544715ENST00000494829ETV6chr12

12022903

+RUNX1chr21

36265260

-
intron-intronENST00000544715ENST00000494829ETV6chr12

12022357

+RUNX1chr21

12022357

-

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 ETV6-RUNX1


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)


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Fusion Protein Features for ETV6-RUNX1


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/:12022903/:36265263)
- 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
ETV6

P41212

RUNX1

Q01196

FUNCTION: Transcriptional repressor; binds to the DNA sequence 5'-CCGGAAGT-3'. Plays a role in hematopoiesis and malignant transformation. {ECO:0000269|PubMed:25581430}.FUNCTION: Forms the heterodimeric complex core-binding factor (CBF) with CBFB. RUNX members modulate the transcription of their target genes through recognizing the core consensus binding sequence 5'-TGTGGT-3', or very rarely, 5'-TGCGGT-3', within their regulatory regions via their runt domain, while CBFB is a non-DNA-binding regulatory subunit that allosterically enhances the sequence-specific DNA-binding capacity of RUNX. The heterodimers bind to the core site of a number of enhancers and promoters, including murine leukemia virus, polyomavirus enhancer, T-cell receptor enhancers, LCK, IL3 and GM-CSF promoters (Probable). Essential for the development of normal hematopoiesis (PubMed:17431401). Acts synergistically with ELF4 to transactivate the IL-3 promoter and with ELF2 to transactivate the BLK promoter (PubMed:10207087, PubMed:14970218). Inhibits KAT6B-dependent transcriptional activation (By similarity). Involved in lineage commitment of immature T cell precursors. CBF complexes repress ZBTB7B transcription factor during cytotoxic (CD8+) T cell development. They bind to RUNX-binding sequence within the ZBTB7B locus acting as transcriptional silencer and allowing for cytotoxic T cell differentiation. CBF complexes binding to the transcriptional silencer is essential for recruitment of nuclear protein complexes that catalyze epigenetic modifications to establish epigenetic ZBTB7B silencing (By similarity). Controls the anergy and suppressive function of regulatory T-cells (Treg) by associating with FOXP3. Activates the expression of IL2 and IFNG and down-regulates the expression of TNFRSF18, IL2RA and CTLA4, in conventional T-cells (PubMed:17377532). Positively regulates the expression of RORC in T-helper 17 cells (By similarity). {ECO:0000250|UniProtKB:Q03347, ECO:0000269|PubMed:10207087, ECO:0000269|PubMed:11965546, ECO:0000269|PubMed:14970218, ECO:0000269|PubMed:17377532, ECO:0000269|PubMed:17431401, ECO:0000305}.; FUNCTION: Isoform AML-1G shows higher binding activities for target genes and binds TCR-beta-E2 and RAG-1 target site with threefold higher affinity than other isoforms. It is less effective in the context of neutrophil terminal differentiation. {ECO:0000250|UniProtKB:Q03347}.; FUNCTION: Isoform AML-1L interferes with the transactivation activity of RUNX1. {ECO:0000269|PubMed:9199349}.

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 ETV6-RUNX1


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 ETV6-RUNX1


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 ETV6-RUNX1


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 ETV6-RUNX1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneETV6C4015537THROMBOCYTOPENIA 54CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneETV6C0023485Precursor B-Cell Lymphoblastic Leukemia-Lymphoma3CTD_human
HgeneETV6C0040034Thrombocytopenia3CTD_human;GENOMICS_ENGLAND
HgeneETV6C0023480Leukemia, Myelomonocytic, Chronic2ORPHANET
HgeneETV6C1332965Congenital Mesoblastic Nephroma2ORPHANET
HgeneETV6C0006413Burkitt Lymphoma1ORPHANET
HgeneETV6C0013146Drug abuse1CTD_human
HgeneETV6C0013170Drug habituation1CTD_human
HgeneETV6C0013222Drug Use Disorders1CTD_human
HgeneETV6C0023452Childhood Acute Lymphoblastic Leukemia1CTD_human
HgeneETV6C0023453L2 Acute Lymphoblastic Leukemia1CTD_human
HgeneETV6C0023467Leukemia, Myelocytic, Acute1CGI;CTD_human;GENOMICS_ENGLAND
HgeneETV6C0029231Organic Mental Disorders, Substance-Induced1CTD_human
HgeneETV6C0038580Substance Dependence1CTD_human
HgeneETV6C0038586Substance Use Disorders1CTD_human
HgeneETV6C0087031Juvenile-Onset Still Disease1CTD_human
HgeneETV6C0236969Substance-Related Disorders1CTD_human
HgeneETV6C0238463Papillary thyroid carcinoma1ORPHANET
HgeneETV6C0376544Hematopoietic Neoplasms1CTD_human
HgeneETV6C0376545Hematologic Neoplasms1CTD_human
HgeneETV6C0740858Substance abuse problem1CTD_human
HgeneETV6C1292769Precursor B-cell lymphoblastic leukemia1ORPHANET
HgeneETV6C1510472Drug Dependence1CTD_human
HgeneETV6C1832388Platelet Disorder, Familial, with Associated Myeloid Malignancy1ORPHANET
HgeneETV6C1838656Macrocytosis, Familial1CTD_human
HgeneETV6C1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1CTD_human
HgeneETV6C3495559Juvenile arthritis1CTD_human
HgeneETV6C3714758Juvenile psoriatic arthritis1CTD_human
HgeneETV6C4316881Prescription Drug Abuse1CTD_human
HgeneETV6C4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
HgeneETV6C4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human
TgeneC1832388Platelet Disorder, Familial, with Associated Myeloid Malignancy11CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0023467Leukemia, Myelocytic, Acute4CGI;CTD_human;GENOMICS_ENGLAND
TgeneC0026998Acute Myeloid Leukemia, M13CTD_human
TgeneC1879321Acute Myeloid Leukemia (AML-M2)3CTD_human
TgeneC0023485Precursor B-Cell Lymphoblastic Leukemia-Lymphoma2CTD_human
TgeneC0003873Rheumatoid Arthritis1CTD_human
TgeneC0006413Burkitt Lymphoma1ORPHANET
TgeneC0017636Glioblastoma1CTD_human
TgeneC0023452Childhood Acute Lymphoblastic Leukemia1CTD_human
TgeneC0023453L2 Acute Lymphoblastic Leukemia1CTD_human
TgeneC0023473Myeloid Leukemia, Chronic1ORPHANET
TgeneC0033578Prostatic Neoplasms1CTD_human
TgeneC0040034Thrombocytopenia1GENOMICS_ENGLAND
TgeneC0334588Giant Cell Glioblastoma1CTD_human
TgeneC0349639Juvenile Myelomonocytic Leukemia1CTD_human
TgeneC0376358Malignant neoplasm of prostate1CTD_human
TgeneC1292769Precursor B-cell lymphoblastic leukemia1ORPHANET
TgeneC1621958Glioblastoma Multiforme1CTD_human
TgeneC1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1CTD_human
TgeneC2713368Hematopoetic Myelodysplasia1CTD_human
TgeneC3463824MYELODYSPLASTIC SYNDROME1CTD_human