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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:RUNX1-YTHDF2

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RUNX1-YTHDF2
FusionPDB ID: 78699
FusionGDB2.0 ID: 78699
HgeneTgene
Gene symbol

RUNX1

YTHDF2

Gene ID

861

51441

Gene nameRUNX family transcription factor 1YTH N6-methyladenosine RNA binding protein 2
SynonymsAML1|AML1-EVI-1|AMLCR1|CBF2alpha|CBFA2|EVI-1|PEBP2aB|PEBP2alphaCAHL|HGRG8|NY-REN-2
Cytomap

21q22.12

1p35.3

Type of geneprotein-codingprotein-coding
Descriptionrunt-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 2YTH domain-containing family protein 29430020E02RikCLL-associated antigen KW-14YTH N(6)-methyladenosine RNA binding protein 2YTH domain family, member 2high-glucose-regulated protein 8renal carcinoma antigen NY-REN-2
Modification date2020032220200313
UniProtAcc

Q06455

.
Ensembl transtripts involved in fusion geneENST idsENST00000300305, ENST00000325074, 
ENST00000344691, ENST00000358356, 
ENST00000399240, ENST00000437180, 
ENST00000486278, ENST00000494829, 
ENST00000478283, ENST00000373812, 
ENST00000541996, ENST00000542507, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score46 X 68 X 13=4066410 X 8 X 8=640
# samples 8914
** MAII scorelog2(89/40664*10)=-5.51380298959468
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/640*10)=-2.1926450779424
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: RUNX1 [Title/Abstract] AND YTHDF2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RUNX1(36231803)-YTHDF2(29095441), # samples:1
RUNX1(36231770)-YTHDF2(29095441), # samples:1
Anticipated loss of major functional domain due to fusion event.RUNX1-YTHDF2 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.
RUNX1-YTHDF2 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.
RUNX1-YTHDF2 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.
RUNX1-YTHDF2 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.
RUNX1-YTHDF2 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
RUNX1-YTHDF2 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
RUNX1-YTHDF2 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
RUNX1-YTHDF2 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
HgeneRUNX1

GO:0030097

hemopoiesis

21873977

HgeneRUNX1

GO:0045893

positive regulation of transcription, DNA-templated

10207087|14970218

HgeneRUNX1

GO:0045944

positive regulation of transcription by RNA polymerase II

9199349|10207087|14970218|21873977

TgeneYTHDF2

GO:0006402

mRNA catabolic process

27558897|30559377|30930054

TgeneYTHDF2

GO:0061157

mRNA destabilization

27558897|30559377|30930054

TgeneYTHDF2

GO:1903679

positive regulation of cap-independent translational initiation

26458103


check buttonFusion gene breakpoints across RUNX1 (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 YTHDF2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4acute myeloid leukemiaEU093085RUNX1chr21

36231803

YTHDF2chr1

29095441
ChiTaRS5.0N/AEU093085RUNX1chr21

36231770

-YTHDF2chr1

29095441

+


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Fusion ORF Analysis


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)
ENST00000437180RUNX1chr2136231770-ENST00000373812YTHDF2chr129095441+1650803190888232

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
ENST00000437180ENST00000373812RUNX1chr2136231770-YTHDF2chr129095441+0.0140379380.9859621

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Fusion Amino Acid Sequences


check button 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

>78699_78699_1_RUNX1-YTHDF2_RUNX1_chr21_36231770_ENST00000437180_YTHDF2_chr1_29095441_ENST00000373812_length(amino acids)=232AA_BP=200
MASDSIFESFPSYPQCFMRECILGMNPSRDVHDASTSRRFTPPSTALSPGKMSEALPLGAPDAGAALAGKLRSGDRSMVEVLADHPGELV
RTDSPNFLCSVLPTHWRCNKTLPIAFKVVALGDVPDGTLVTVMAGNDENYSAELRNATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVF

--------------------------------------------------------------

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Fusion Protein Functional Features


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/chr21:36231803/chr1:29095441)
- 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
RUNX1

Q06455

.
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, PubMed:10688654). Can repress the expression of MMP7 in a ZBTB33-dependent manner (PubMed:23251453). Can repress transactivation mediated by TCF12 (PubMed:16803958). Acts as a negative regulator of adipogenesis (By similarity). The AML1-MTG8/ETO fusion protein frequently found in leukemic cells is involved in leukemogenesis and contributes to hematopoietic stem/progenitor cell self-renewal (PubMed:23812588). {ECO:0000250|UniProtKB:Q61909, ECO:0000269|PubMed:10688654, ECO:0000269|PubMed:10973986, ECO:0000269|PubMed:16803958, ECO:0000269|PubMed:23251453, ECO:0000269|PubMed:23812588, ECO:0000303|PubMed:12559562, ECO:0000303|PubMed:15203199}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRUNX1chr21:36231770chr1:29095441ENST00000300305-5850_178204.33333333333334481.0DomainRunt
HgeneRUNX1chr21:36231770chr1:29095441ENST00000325074-4750_178192.33333333333334469.0DomainRunt
HgeneRUNX1chr21:36231770chr1:29095441ENST00000344691-3650_178177.33333333333334454.0DomainRunt
HgeneRUNX1chr21:36231770chr1:29095441ENST00000358356-3550_178177.33333333333334251.0DomainRunt
HgeneRUNX1chr21:36231770chr1:29095441ENST00000437180-6950_178204.33333333333334481.0DomainRunt

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRUNX1chr21:36231770chr1:29095441ENST00000300305-58187_453204.33333333333334481.0Compositional biasNote=Pro/Ser/Thr-rich
HgeneRUNX1chr21:36231770chr1:29095441ENST00000325074-47187_453192.33333333333334469.0Compositional biasNote=Pro/Ser/Thr-rich
HgeneRUNX1chr21:36231770chr1:29095441ENST00000344691-36187_453177.33333333333334454.0Compositional biasNote=Pro/Ser/Thr-rich
HgeneRUNX1chr21:36231770chr1:29095441ENST00000358356-35187_453177.33333333333334251.0Compositional biasNote=Pro/Ser/Thr-rich
HgeneRUNX1chr21:36231770chr1:29095441ENST00000437180-69187_453204.33333333333334481.0Compositional biasNote=Pro/Ser/Thr-rich
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000037381235410_544572.0580.0DomainYTH
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000054199624410_544522.0530.0DomainYTH
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000054250746410_544572.0580.0DomainYTH
TgeneYTHDF2chr21:36231770chr1:29095441ENST00000373812351_46572.0580.0RegionDisordered
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000037381235230_387572.0580.0RegionDisordered
TgeneYTHDF2chr21:36231770chr1:29095441ENST00000373812352_384572.0580.0RegionLocalization to mRNA processing bodies (P-bodies)
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000037381235416_418572.0580.0RegionN6-methyladenosine binding
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000037381235432_433572.0580.0RegionN6-methyladenosine binding
TgeneYTHDF2chr21:36231770chr1:29095441ENST00000541996241_46522.0530.0RegionDisordered
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000054199624230_387522.0530.0RegionDisordered
TgeneYTHDF2chr21:36231770chr1:29095441ENST00000541996242_384522.0530.0RegionLocalization to mRNA processing bodies (P-bodies)
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000054199624416_418522.0530.0RegionN6-methyladenosine binding
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000054199624432_433522.0530.0RegionN6-methyladenosine binding
TgeneYTHDF2chr21:36231770chr1:29095441ENST00000542507461_46572.0580.0RegionDisordered
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000054250746230_387572.0580.0RegionDisordered
TgeneYTHDF2chr21:36231770chr1:29095441ENST00000542507462_384572.0580.0RegionLocalization to mRNA processing bodies (P-bodies)
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000054250746416_418572.0580.0RegionN6-methyladenosine binding
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000054250746432_433572.0580.0RegionN6-methyladenosine binding


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors
RUNX1SUV39H1, KAT6B, CBFB, AES, PAX5, YAP1, JUN, FOS, SMAD3, SMAD1, SMAD2, SMAD5, VDR, ELF4, ELF2, CEBPB, TLE1, CBFA2T2, TRAF6, FHL2, MYOD1, HIPK2, EP300, HDAC1, HDAC3, KAT6A, tat, TCF12, TCF3, RUNX1T1, NCOR1, SIAH1, UBE2L6, RUNX1, PML, RARA, HDAC2, SIN3A, NR4A2, TRIM33, STUB1, Vdr, SMARCA4, SMARCB1, SMARCC1, CDK1, TAL1, COPRS, KMT2A, RBM14, SPEN, DNMT1, ELAVL1, CBFA2T3, PRMT1, HLA-DMA, CREBBP, UXT, CTBP2, NOTCH1, MYC, NCOR2, FOXP3, SOX2, CTBP1, HDAC11, RAG1, SPI1, ELF1, Cep72, CDK6, vif, KLF6, NFATC1, NFATC2, ZNF131, BRCA1, CDK9, FANCD2, Cbfb, CTNNB1, WWP1, RNF38, RNF44, DTX2, TRIM5, UHRF2, DZIP3, NEDD4, NKX2-1, HIF1A, ACTB, ARID1A, ARID3A, ASH2L, ACTL6A, BRD9, C2orf44, CCNK, CDC16, CDKN2AIP, CLTC, NELFB, CPSF3, CPSF6, CSTF2, CSTF2T, CTPS1, DDX1, DDX17, DDX21, DDX3X, DDX41, DDX5, DHX15, DHX36, DHX9, DPF2, EEF1A1, EEF1A2, EWSR1, EZR, FAF1, FERMT3, FIP1L1, FUBP1, FUS, GATAD2A, GATAD2B, GMPS, HIC2, HNRNPH1, HNRNPM, HNRNPR, HNRNPU, HSPA1A, HSPA2, HSPA5, HSPA8, HSPA9, IGF2BP1, INTS10, INTS9, KHSRP, KIF2B, LARP7, LCP1, LMNA, LMNB1, LRRC40, LRWD1, MED1, MED12, MED16, MED17, MED26, MEN1, MLLT1, MTA2, NDC80, NOP56, NONO, NUP85, ORC2, PABPC1, PABPC4, PAXIP1, PRMT5, PSIP1, PSPC1, RAD18, RANGAP1, RARS, RBBP5, RBM39, RPA1, RPAP2, SF1, SF3B2, SF3B3, SFPQ, SMARCC2, SMARCD1, SNRNP70, SNRPD1, SNX9, U2SURP, SRP68, SYNCRIP, TAF15, TFRC, TKT, TRAP1, TRIM25, TUBA1B, TUBB2A, UBP1, USP39, WDR76, XRCC6, XRN2, ZNF326, DMBT1, DNAJA3, DNAJB11, DPYSL2, DYNLL1, EIF3A, EIF3G, EIF4A2, EMG1, DCPS, IKZF3, IKZF1, MAD2L2, KIAA1429, Hipk2, HIST1H4A, ORF3b, MAPK1, TEAD2, SNRPC, BAG3, TEKT5, BAG4, NFKBID, VPS37C, FAM222B, OLIG3, GCC1, HGS, TEAD4, FBXO17, CIC, GSK3A, ATG7, FBXW12, RUNX2, FOXF2, NAAA, GPR55, BTF3,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
RUNX1all structure
YTHDF2


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
HgeneRUNX1chr21:36231770chr1:29095441ENST00000300305-58362_402204.33333333333334481.0FOXP3
HgeneRUNX1chr21:36231770chr1:29095441ENST00000325074-47362_402192.33333333333334469.0FOXP3
HgeneRUNX1chr21:36231770chr1:29095441ENST00000344691-36362_402177.33333333333334454.0FOXP3
HgeneRUNX1chr21:36231770chr1:29095441ENST00000358356-35362_402177.33333333333334251.0FOXP3
HgeneRUNX1chr21:36231770chr1:29095441ENST00000437180-69362_402204.33333333333334481.0FOXP3
HgeneRUNX1chr21:36231770chr1:29095441ENST00000300305-58291_371204.33333333333334481.0KAT6A
HgeneRUNX1chr21:36231770chr1:29095441ENST00000325074-47291_371192.33333333333334469.0KAT6A
HgeneRUNX1chr21:36231770chr1:29095441ENST00000344691-36291_371177.33333333333334454.0KAT6A
HgeneRUNX1chr21:36231770chr1:29095441ENST00000358356-35291_371177.33333333333334251.0KAT6A
HgeneRUNX1chr21:36231770chr1:29095441ENST00000437180-69291_371204.33333333333334481.0KAT6A
HgeneRUNX1chr21:36231770chr1:29095441ENST00000300305-58307_400204.33333333333334481.0KAT6B
HgeneRUNX1chr21:36231770chr1:29095441ENST00000325074-47307_400192.33333333333334469.0KAT6B
HgeneRUNX1chr21:36231770chr1:29095441ENST00000344691-36307_400177.33333333333334454.0KAT6B
HgeneRUNX1chr21:36231770chr1:29095441ENST00000358356-35307_400177.33333333333334251.0KAT6B
HgeneRUNX1chr21:36231770chr1:29095441ENST00000437180-69307_400204.33333333333334481.0KAT6B
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000037381235385_579572.0580.0m6A-containing mRNAs
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000054199624385_579522.0530.0m6A-containing mRNAs
TgeneYTHDF2chr21:36231770chr1:29095441ENST0000054250746385_579572.0580.0m6A-containing mRNAs


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Related Drugs to RUNX1-YTHDF2


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

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Related Diseases to RUNX1-YTHDF2


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
HgeneRUNX1C1832388Platelet Disorder, Familial, with Associated Myeloid Malignancy11CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneRUNX1C0023467Leukemia, Myelocytic, Acute4CGI;CTD_human;GENOMICS_ENGLAND
HgeneRUNX1C0026998Acute Myeloid Leukemia, M13CTD_human
HgeneRUNX1C1879321Acute Myeloid Leukemia (AML-M2)3CTD_human
HgeneRUNX1C0023485Precursor B-Cell Lymphoblastic Leukemia-Lymphoma2CTD_human
HgeneRUNX1C0003873Rheumatoid Arthritis1CTD_human
HgeneRUNX1C0006413Burkitt Lymphoma1ORPHANET
HgeneRUNX1C0017636Glioblastoma1CTD_human
HgeneRUNX1C0023452Childhood Acute Lymphoblastic Leukemia1CTD_human
HgeneRUNX1C0023453L2 Acute Lymphoblastic Leukemia1CTD_human
HgeneRUNX1C0023473Myeloid Leukemia, Chronic1ORPHANET
HgeneRUNX1C0033578Prostatic Neoplasms1CTD_human
HgeneRUNX1C0040034Thrombocytopenia1GENOMICS_ENGLAND
HgeneRUNX1C0334588Giant Cell Glioblastoma1CTD_human
HgeneRUNX1C0349639Juvenile Myelomonocytic Leukemia1CTD_human
HgeneRUNX1C0376358Malignant neoplasm of prostate1CTD_human
HgeneRUNX1C1292769Precursor B-cell lymphoblastic leukemia1ORPHANET
HgeneRUNX1C1621958Glioblastoma Multiforme1CTD_human
HgeneRUNX1C1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1CTD_human
HgeneRUNX1C2713368Hematopoetic Myelodysplasia1CTD_human
HgeneRUNX1C3463824MYELODYSPLASTIC SYNDROME1CTD_human