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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:DLC1-RUNX1 (FusionGDB2 ID:22979)

Fusion Gene Summary for DLC1-RUNX1

check button Fusion gene summary
Fusion gene informationFusion gene name: DLC1-RUNX1
Fusion gene ID: 22979
HgeneTgene
Gene symbol

DLC1

RUNX1

Gene ID

10395

861

Gene nameDLC1 Rho GTPase activating proteinRUNX family transcription factor 1
SynonymsARHGAP7|HP|STARD12|p122-RhoGAPAML1|AML1-EVI-1|AMLCR1|CBF2alpha|CBFA2|EVI-1|PEBP2aB|PEBP2alpha
Cytomap

8p22

21q22.12

Type of geneprotein-codingprotein-coding
Descriptionrho GTPase-activating protein 7Rho-GTPase-activating protein 7START domain-containing protein 12StAR-related lipid transfer (START) domain containing 12deleted in liver cancer 1 proteindeleted in liver cancer 1 variant 2deleted in liver cancer variarunt-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

Q96QB1

Q06455

Ensembl transtripts involved in fusion geneENST00000512044, ENST00000276297, 
ENST00000316609, ENST00000358919, 
ENST00000510318, ENST00000511869, 
ENST00000520226, 		ENST00000358356, 
ENST00000399240, ENST00000486278, 
ENST00000494829, ENST00000300305, 
ENST00000325074, ENST00000344691, 
ENST00000437180, 
Fusion gene scores* DoF score5 X 4 X 4=8036 X 59 X 13=27612
# samples 563
** MAII scorelog2(5/80*10)=-0.678071905112638
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: DLC1 [Title/Abstract] AND RUNX1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointDLC1(13133771)-RUNX1(36206898), # samples:1
Anticipated loss of major functional domain due to fusion event.DLC1-RUNX1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
DLC1-RUNX1 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
DLC1-RUNX1 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
DLC1-RUNX1 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
HgeneDLC1

GO:0006915

apoptotic process

17292327

HgeneDLC1

GO:0006919

activation of cysteine-type endopeptidase activity involved in apoptotic process

17888903

HgeneDLC1

GO:0008285

negative regulation of cell proliferation

12545165|17932950

HgeneDLC1

GO:0030336

negative regulation of cell migration

17932950|19158340

HgeneDLC1

GO:0035307

positive regulation of protein dephosphorylation

17292327

HgeneDLC1

GO:0051497

negative regulation of stress fiber assembly

17932950

HgeneDLC1

GO:0051895

negative regulation of focal adhesion assembly

19158340

HgeneDLC1

GO:1900119

positive regulation of execution phase of apoptosis

17888903

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 buttonFusion gene breakpoints across DLC1 (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 RUNX1 (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
ChimerDB4STADTCGA-CD-A4MH-01ADLC1chr8

13133771

-RUNX1chr21

36206898

-


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Fusion Gene ORF analysis for DLC1-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-intronENST00000512044ENST00000358356DLC1chr8

13133771

-RUNX1chr21

36206898

-
5CDS-intronENST00000512044ENST00000399240DLC1chr8

13133771

-RUNX1chr21

36206898

-
5CDS-intronENST00000512044ENST00000486278DLC1chr8

13133771

-RUNX1chr21

36206898

-
5CDS-intronENST00000512044ENST00000494829DLC1chr8

13133771

-RUNX1chr21

36206898

-
Frame-shiftENST00000512044ENST00000300305DLC1chr8

13133771

-RUNX1chr21

36206898

-
Frame-shiftENST00000512044ENST00000325074DLC1chr8

13133771

-RUNX1chr21

36206898

-
Frame-shiftENST00000512044ENST00000344691DLC1chr8

13133771

-RUNX1chr21

36206898

-
Frame-shiftENST00000512044ENST00000437180DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000276297ENST00000300305DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000276297ENST00000325074DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000276297ENST00000344691DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000276297ENST00000437180DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000316609ENST00000300305DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000316609ENST00000325074DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000316609ENST00000344691DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000316609ENST00000437180DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000358919ENST00000300305DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000358919ENST00000325074DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000358919ENST00000344691DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000358919ENST00000437180DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000510318ENST00000300305DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000510318ENST00000325074DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000510318ENST00000344691DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000510318ENST00000437180DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000511869ENST00000300305DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000511869ENST00000325074DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000511869ENST00000344691DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000511869ENST00000437180DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000520226ENST00000300305DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000520226ENST00000325074DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000520226ENST00000344691DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-3CDSENST00000520226ENST00000437180DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000276297ENST00000358356DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000276297ENST00000399240DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000276297ENST00000486278DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000276297ENST00000494829DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000316609ENST00000358356DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000316609ENST00000399240DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000316609ENST00000486278DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000316609ENST00000494829DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000358919ENST00000358356DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000358919ENST00000399240DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000358919ENST00000486278DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000358919ENST00000494829DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000510318ENST00000358356DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000510318ENST00000399240DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000510318ENST00000486278DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000510318ENST00000494829DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000511869ENST00000358356DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000511869ENST00000399240DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000511869ENST00000486278DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000511869ENST00000494829DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000520226ENST00000358356DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000520226ENST00000399240DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000520226ENST00000486278DLC1chr8

13133771

-RUNX1chr21

36206898

-
intron-intronENST00000520226ENST00000494829DLC1chr8

13133771

-RUNX1chr21

36206898

-

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 DLC1-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)

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.

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Fusion Protein Features for DLC1-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/:13133771/:36206898)
- 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
DLC1

Q96QB1

RUNX1

Q06455

FUNCTION: Functions as a GTPase-activating protein for the small GTPases RHOA, RHOB, RHOC and CDC42, terminating their downstream signaling. This induces morphological changes and detachment through cytoskeletal reorganization, playing a critical role in biological processes such as cell migration and proliferation. Also functions in vivo as an activator of the phospholipase PLCD1. Active DLC1 increases cell migration velocity but reduces directionality. {ECO:0000269|PubMed:18786931, ECO:0000269|PubMed:19170769, ECO:0000269|PubMed:19710422}.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}.

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 DLC1-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 DLC1-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 DLC1-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 DLC1-RUNX1


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