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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:SMAD3-DLGAP4 (FusionGDB2 ID:HG4088TG22839)

Fusion Gene Summary for SMAD3-DLGAP4

check button Fusion gene summary
Fusion gene informationFusion gene name: SMAD3-DLGAP4
Fusion gene ID: hg4088tg22839
HgeneTgene
Gene symbol

SMAD3

DLGAP4

Gene ID

4088

22839

Gene nameSMAD family member 3DLG associated protein 4
SynonymsHSPC193|HsT17436|JV15-2|LDS1C|LDS3|MADH3DAP-4|DAP4|DLP4|SAPAP-4|SAPAP4
Cytomap('SMAD3')('DLGAP4')

15q22.33

20q11.23

Type of geneprotein-codingprotein-coding
Descriptionmothers against decapentaplegic homolog 3MAD homolog 3MAD, mothers against decapentaplegic homolog 3SMA- and MAD-related protein 3SMAD, mothers against DPP homolog 3hMAD-3hSMAD3mad homolog JV15-2mad protein homologmad3mothers against DPP homologdisks large-associated protein 4PSD-95/SAP90-binding protein 4SAP90/PSD-95-associated protein 4discs large homolog associated protein 4
Modification date2020032920200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000327367, ENST00000439724, 
ENST00000537194, ENST00000540846, 
ENST00000559092, 
Fusion gene scores* DoF score17 X 13 X 12=265224 X 23 X 8=4416
# samples 3029
** MAII scorelog2(30/2652*10)=-3.14404636961671
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(29/4416*10)=-3.92861536676323
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMAD3 [Title/Abstract] AND DLGAP4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSMAD3(67358698)-DLGAP4(35125108), # samples:3
Anticipated loss of major functional domain due to fusion event.SMAD3-DLGAP4 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
SMAD3-DLGAP4 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
SMAD3-DLGAP4 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
HgeneSMAD3

GO:0000122

negative regulation of transcription by RNA polymerase II

8774881

HgeneSMAD3

GO:0006357

regulation of transcription by RNA polymerase II

21947082

HgeneSMAD3

GO:0007179

transforming growth factor beta receptor signaling pathway

9732876|18548003|21947082

HgeneSMAD3

GO:0007183

SMAD protein complex assembly

9111321|10823886

HgeneSMAD3

GO:0010628

positive regulation of gene expression

21307346

HgeneSMAD3

GO:0010718

positive regulation of epithelial to mesenchymal transition

21307346

HgeneSMAD3

GO:0030308

negative regulation of cell growth

8774881

HgeneSMAD3

GO:0045429

positive regulation of nitric oxide biosynthetic process

27038547

HgeneSMAD3

GO:0045599

negative regulation of fat cell differentiation

19816956

HgeneSMAD3

GO:0045893

positive regulation of transcription, DNA-templated

9111321|9311995|9732876

HgeneSMAD3

GO:0045944

positive regulation of transcription by RNA polymerase II

8774881|18832382

HgeneSMAD3

GO:0051481

negative regulation of cytosolic calcium ion concentration

27038547

HgeneSMAD3

GO:0071560

cellular response to transforming growth factor beta stimulus

12902338

HgeneSMAD3

GO:1901203

positive regulation of extracellular matrix assembly

21307346



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
ChimerDB4KIRCTCGA-CW-6087-01ASMAD3chr15

67358698

-DLGAP4chr20

35125108

+
ChimerDB4KIRCTCGA-CW-6087-01ASMAD3chr15

67358698

+DLGAP4chr20

35125108

+


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Fusion Gene ORF analysis for SMAD3-DLGAP4

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-3UTRENST00000327367ENST00000340491SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
5CDS-3UTRENST00000327367ENST00000475894SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
Frame-shiftENST00000327367ENST00000339266SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
Frame-shiftENST00000327367ENST00000373907SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
Frame-shiftENST00000327367ENST00000373913SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
Frame-shiftENST00000327367ENST00000401952SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000439724ENST00000339266SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000439724ENST00000373907SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000439724ENST00000373913SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000439724ENST00000401952SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000537194ENST00000339266SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000537194ENST00000373907SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000537194ENST00000373913SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000537194ENST00000401952SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000540846ENST00000339266SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000540846ENST00000373907SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000540846ENST00000373913SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000540846ENST00000401952SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000559092ENST00000339266SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000559092ENST00000373907SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000559092ENST00000373913SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3CDSENST00000559092ENST00000401952SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3UTRENST00000439724ENST00000340491SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3UTRENST00000439724ENST00000475894SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3UTRENST00000537194ENST00000340491SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3UTRENST00000537194ENST00000475894SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3UTRENST00000540846ENST00000340491SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3UTRENST00000540846ENST00000475894SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3UTRENST00000559092ENST00000340491SMAD3chr15

67358698

+DLGAP4chr20

35125108

+
intron-3UTRENST00000559092ENST00000475894SMAD3chr15

67358698

+DLGAP4chr20

35125108

+

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 SMAD3-DLGAP4


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)
SMAD3chr1567358698+DLGAP4chr2035125107+5.73E-091
SMAD3chr1567358698+DLGAP4chr2035125107+5.73E-091


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 SMAD3-DLGAP4


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/:67358698/:35125108)
- 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
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 SMAD3-DLGAP4


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 SMAD3-DLGAP4


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 SMAD3-DLGAP4


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 SMAD3-DLGAP4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSMAD3C3151087LOEYS-DIETZ SYNDROME 38CLINGEN;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneSMAD3C4707243Familial thoracic aortic aneurysm and aortic dissection5CLINGEN;GENOMICS_ENGLAND
HgeneSMAD3C0029408Degenerative polyarthritis2CTD_human
HgeneSMAD3C0086743Osteoarthrosis Deformans2CTD_human
HgeneSMAD3C0376634Craniofacial Abnormalities2CTD_human
HgeneSMAD3C2697932Loeys-Dietz Syndrome2CTD_human;GENOMICS_ENGLAND
HgeneSMAD3C0002949Aneurysm, Dissecting1CTD_human
HgeneSMAD3C0003486Aortic Aneurysm1CTD_human
HgeneSMAD3C0009171Cocaine Abuse1CTD_human
HgeneSMAD3C0009402Colorectal Carcinoma1CTD_human;UNIPROT
HgeneSMAD3C0009404Colorectal Neoplasms1CTD_human
HgeneSMAD3C0010346Crohn Disease1CTD_human
HgeneSMAD3C0023267Fibroid Tumor1CTD_human
HgeneSMAD3C0023890Liver Cirrhosis1CTD_human
HgeneSMAD3C0023891Liver Cirrhosis, Alcoholic1CTD_human
HgeneSMAD3C0029410Osteoarthritis of hip1CTD_human
HgeneSMAD3C0034067Pulmonary Emphysema1GENOMICS_ENGLAND
HgeneSMAD3C0041956Ureteral obstruction1CTD_human
HgeneSMAD3C0042133Uterine Fibroids1CTD_human
HgeneSMAD3C0042138Uterine Neoplasms1CTD_human
HgeneSMAD3C0087031Juvenile-Onset Still Disease1CTD_human
HgeneSMAD3C0153567Uterine Cancer1CTD_human
HgeneSMAD3C0156147Crohn's disease of large bowel1CTD_human
HgeneSMAD3C0236736Cocaine-Related Disorders1CTD_human
HgeneSMAD3C0239946Fibrosis, Liver1CTD_human
HgeneSMAD3C0267380Crohn's disease of the ileum1CTD_human
HgeneSMAD3C0340643Dissection of aorta1CTD_human
HgeneSMAD3C0600427Cocaine Dependence1CTD_human
HgeneSMAD3C0600519Ventricular Remodeling1CTD_human
HgeneSMAD3C0600520Left Ventricle Remodeling1CTD_human
HgeneSMAD3C0678202Regional enteritis1CTD_human
HgeneSMAD3C0949272IIeocolitis1CTD_human
HgeneSMAD3C1836635Loeys-Dietz Aortic Aneurysm Syndrome1CTD_human
HgeneSMAD3C3495559Juvenile arthritis1CTD_human
HgeneSMAD3C3714758Juvenile psoriatic arthritis1CTD_human
HgeneSMAD3C4277533Dissection, Blood Vessel1CTD_human
HgeneSMAD3C4551955Loeys-Dietz Syndrome, Type 1a1CTD_human
HgeneSMAD3C4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
HgeneSMAD3C4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human