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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:SMARCA4-BRD4 (FusionGDB2 ID:HG6597TG23476)

Fusion Gene Summary for SMARCA4-BRD4

check button Fusion gene summary
Fusion gene informationFusion gene name: SMARCA4-BRD4
Fusion gene ID: hg6597tg23476
HgeneTgene
Gene symbol

SMARCA4

BRD4

Gene ID

6597

23476

Gene nameSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4bromodomain containing 4
SynonymsBAF190|BAF190A|BRG1|CSS4|MRD16|RTPS2|SNF2|SNF2-beta|SNF2L4|SNF2LB|SWI2|hSNF2bCAP|HUNK1|HUNKI|MCAP
Cytomap('SMARCA4')('BRD4')

19p13.2

19p13.12

Type of geneprotein-codingprotein-coding
Descriptiontranscription activator BRG1ATP-dependent helicase SMARCA4BRG1-associated factor 190ABRM/SWI2-related gene 1SNF2-like 4brahma protein-like 1global transcription activator homologous sequencehomeotic gene regulatormitotic growth and transcription abromodomain-containing protein 4chromosome-associated proteinmitotic chromosome-associated protein
Modification date2020031520200329
UniProtAcc.

O60885

Ensembl transtripts involved in fusion geneENST00000344626, ENST00000358026, 
ENST00000429416, ENST00000444061, 
ENST00000541122, ENST00000589677, 
ENST00000413806, ENST00000450717, 
ENST00000538456, ENST00000590574, 
Fusion gene scores* DoF score29 X 29 X 17=1429715 X 19 X 13=3705
# samples 5528
** MAII scorelog2(55/14297*10)=-4.70013702309346
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(28/3705*10)=-3.72597481024823
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMARCA4 [Title/Abstract] AND BRD4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSMARCA4(11071850)-BRD4(15367984), # samples:1
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
HgeneSMARCA4

GO:0006337

nucleosome disassembly

8895581

HgeneSMARCA4

GO:0006338

chromatin remodeling

10943845|11726552

HgeneSMARCA4

GO:0045892

negative regulation of transcription, DNA-templated

12065415

HgeneSMARCA4

GO:0045944

positive regulation of transcription by RNA polymerase II

15774904|17938176

HgeneSMARCA4

GO:0051091

positive regulation of DNA-binding transcription factor activity

11950834|17938176

HgeneSMARCA4

GO:1902661

positive regulation of glucose mediated signaling pathway

22368283

TgeneBRD4

GO:0032968

positive regulation of transcription elongation from RNA polymerase II promoter

19103749|23086925

TgeneBRD4

GO:0043123

positive regulation of I-kappaB kinase/NF-kappaB signaling

19103749

TgeneBRD4

GO:0045944

positive regulation of transcription by RNA polymerase II

23086925|23317504|24360279

TgeneBRD4

GO:0050727

regulation of inflammatory response

19103749

TgeneBRD4

GO:1901407

regulation of phosphorylation of RNA polymerase II C-terminal domain

23086925



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
ChimerDB4SARCTCGA-DX-A48N-01ASMARCA4chr19

11071850

+BRD4chr19

15367984

-


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Fusion Gene ORF analysis for SMARCA4-BRD4

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
5UTR-3CDSENST00000344626ENST00000263377SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000344626ENST00000360016SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000344626ENST00000371835SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000358026ENST00000263377SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000358026ENST00000360016SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000358026ENST00000371835SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000429416ENST00000263377SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000429416ENST00000360016SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000429416ENST00000371835SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000444061ENST00000263377SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000444061ENST00000360016SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000444061ENST00000371835SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000541122ENST00000263377SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000541122ENST00000360016SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000541122ENST00000371835SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000589677ENST00000263377SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000589677ENST00000360016SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-3CDSENST00000589677ENST00000371835SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-5UTRENST00000344626ENST00000602230SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-5UTRENST00000358026ENST00000602230SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-5UTRENST00000429416ENST00000602230SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-5UTRENST00000444061ENST00000602230SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-5UTRENST00000541122ENST00000602230SMARCA4chr19

11071850

+BRD4chr19

15367984

-
5UTR-5UTRENST00000589677ENST00000602230SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-3CDSENST00000413806ENST00000263377SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-3CDSENST00000413806ENST00000360016SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-3CDSENST00000413806ENST00000371835SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-3CDSENST00000450717ENST00000263377SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-3CDSENST00000450717ENST00000360016SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-3CDSENST00000450717ENST00000371835SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-3CDSENST00000538456ENST00000263377SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-3CDSENST00000538456ENST00000360016SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-3CDSENST00000538456ENST00000371835SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-3CDSENST00000590574ENST00000263377SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-3CDSENST00000590574ENST00000360016SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-3CDSENST00000590574ENST00000371835SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-5UTRENST00000413806ENST00000602230SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-5UTRENST00000450717ENST00000602230SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-5UTRENST00000538456ENST00000602230SMARCA4chr19

11071850

+BRD4chr19

15367984

-
intron-5UTRENST00000590574ENST00000602230SMARCA4chr19

11071850

+BRD4chr19

15367984

-

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 SMARCA4-BRD4


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 SMARCA4-BRD4


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/:11071850/:15367984)
- 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
.BRD4

O60885

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: Chromatin reader protein that recognizes and binds acetylated histones and plays a key role in transmission of epigenetic memory across cell divisions and transcription regulation. Remains associated with acetylated chromatin throughout the entire cell cycle and provides epigenetic memory for postmitotic G1 gene transcription by preserving acetylated chromatin status and maintaining high-order chromatin structure (PubMed:23589332, PubMed:23317504, PubMed:22334664). During interphase, plays a key role in regulating the transcription of signal-inducible genes by associating with the P-TEFb complex and recruiting it to promoters. Also recruits P-TEFb complex to distal enhancers, so called anti-pause enhancers in collaboration with JMJD6. BRD4 and JMJD6 are required to form the transcriptionally active P-TEFb complex by displacing negative regulators such as HEXIM1 and 7SKsnRNA complex from P-TEFb, thereby transforming it into an active form that can then phosphorylate the C-terminal domain (CTD) of RNA polymerase II (PubMed:23589332, PubMed:19596240, PubMed:16109377, PubMed:16109376, PubMed:24360279). Promotes phosphorylation of 'Ser-2' of the C-terminal domain (CTD) of RNA polymerase II (PubMed:23086925). According to a report, directly acts as an atypical protein kinase and mediates phosphorylation of 'Ser-2' of the C-terminal domain (CTD) of RNA polymerase II; these data however need additional evidences in vivo (PubMed:22509028). In addition to acetylated histones, also recognizes and binds acetylated RELA, leading to further recruitment of the P-TEFb complex and subsequent activation of NF-kappa-B (PubMed:19103749). Also acts as a regulator of p53/TP53-mediated transcription: following phosphorylation by CK2, recruited to p53/TP53 specific target promoters (PubMed:23317504). {ECO:0000269|PubMed:16109376, ECO:0000269|PubMed:16109377, ECO:0000269|PubMed:19103749, ECO:0000269|PubMed:19596240, ECO:0000269|PubMed:22334664, ECO:0000269|PubMed:22509028, ECO:0000269|PubMed:23086925, ECO:0000269|PubMed:23317504, ECO:0000269|PubMed:23589332, ECO:0000269|PubMed:24360279}.; FUNCTION: [Isoform B]: Acts as a chromatin insulator in the DNA damage response pathway. Inhibits DNA damage response signaling by recruiting the condensin-2 complex to acetylated histones, leading to chromatin structure remodeling, insulating the region from DNA damage response by limiting spreading of histone H2AX/H2A.x phosphorylation. {ECO:0000269|PubMed:23728299}.

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 SMARCA4-BRD4


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 SMARCA4-BRD4


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 SMARCA4-BRD4


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 SMARCA4-BRD4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSMARCA4C2750074Rhabdoid Tumor Predisposition Syndrome 27CLINGEN;CTD_human;GENOMICS_ENGLAND
HgeneSMARCA4C0262584Carcinoma, Small Cell4CTD_human
HgeneSMARCA4C0919267ovarian neoplasm4CGI;CTD_human
HgeneSMARCA4C1140680Malignant neoplasm of ovary4CGI;CTD_human
HgeneSMARCA4C0009405Hereditary Nonpolyposis Colorectal Neoplasms2CLINGEN
HgeneSMARCA4C1112155Hereditary non-polyposis colorectal cancer syndrome2CLINGEN
HgeneSMARCA4C1333990Hereditary Nonpolyposis Colorectal Cancer2CLINGEN
HgeneSMARCA4C1333991Hereditary Non-Polyposis Colon Cancer Type 22CLINGEN
HgeneSMARCA4C2936783Colorectal cancer, hereditary nonpolyposis, type 12CLINGEN
HgeneSMARCA4C2985524Rhabdoid tumor predisposition syndrome2ORPHANET
HgeneSMARCA4C0006413Burkitt Lymphoma1CTD_human
HgeneSMARCA4C0009171Cocaine Abuse1CTD_human
HgeneSMARCA4C0036920Sezary Syndrome1CTD_human
HgeneSMARCA4C0039981Thoracic Neoplasms1CTD_human
HgeneSMARCA4C0149925Small cell carcinoma of lung1CTD_human
HgeneSMARCA4C0205944Sarcoma, Epithelioid1CTD_human
HgeneSMARCA4C0205945Sarcoma, Spindle Cell1CTD_human
HgeneSMARCA4C0236736Cocaine-Related Disorders1CTD_human
HgeneSMARCA4C0265338Coffin-Siris syndrome1CTD_human;GENOMICS_ENGLAND
HgeneSMARCA4C0343640African Burkitt's lymphoma1CTD_human
HgeneSMARCA4C0600427Cocaine Dependence1CTD_human
HgeneSMARCA4C1261473Sarcoma1CTD_human
HgeneSMARCA4C1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1CTD_human
HgeneSMARCA4C2239246Endometrial stromal sarcoma, high grade1GENOMICS_ENGLAND
HgeneSMARCA4C3281201MENTAL RETARDATION, AUTOSOMAL DOMINANT 121GENOMICS_ENGLAND
HgeneSMARCA4C3553249COFFIN-SIRIS SYNDROME 41GENOMICS_ENGLAND;UNIPROT
HgeneSMARCA4C4721444Burkitt Leukemia1CTD_human
TgeneC0017636Glioblastoma2CTD_human
TgeneC0334588Giant Cell Glioblastoma2CTD_human
TgeneC1621958Glioblastoma Multiforme2CTD_human
TgeneC0002170Alopecia1CTD_human
TgeneC0007102Malignant tumor of colon1CTD_human
TgeneC0009375Colonic Neoplasms1CTD_human
TgeneC0018798Congenital Heart Defects1GENOMICS_ENGLAND
TgeneC0019193Hepatitis, Toxic1CTD_human
TgeneC0020507Hyperplasia1CTD_human
TgeneC0020542Pulmonary Hypertension1CTD_human
TgeneC0025149Medulloblastoma1CTD_human
TgeneC0025958Microcephaly1GENOMICS_ENGLAND
TgeneC0029463Osteosarcoma1CTD_human
TgeneC0033578Prostatic Neoplasms1CTD_human
TgeneC0040136Thyroid Neoplasm1CTD_human
TgeneC0085413Polycystic Kidney, Autosomal Dominant1CTD_human
TgeneC0086873Pseudopelade1CTD_human
TgeneC0151468Thyroid Gland Follicular Adenoma1CTD_human
TgeneC0162311Androgenetic Alopecia1CTD_human
TgeneC0205833Medullomyoblastoma1CTD_human
TgeneC0263477Female pattern alopecia (disorder)1CTD_human
TgeneC0270972Cornelia De Lange Syndrome1CTD_human
TgeneC0278510Childhood Medulloblastoma1CTD_human
TgeneC0278876Adult Medulloblastoma1CTD_human
TgeneC0376358Malignant neoplasm of prostate1CTD_human
TgeneC0549473Thyroid carcinoma1CTD_human
TgeneC0751291Desmoplastic Medulloblastoma1CTD_human
TgeneC0860207Drug-Induced Liver Disease1CTD_human
TgeneC0887850Polycystic Kidney, Type 1 Autosomal Dominant Disease1CTD_human
TgeneC1262760Hepatitis, Drug-Induced1CTD_human
TgeneC1275668Melanotic medulloblastoma1CTD_human
TgeneC1707291NUT midline carcinoma1ORPHANET
TgeneC1802395Congenital muscular hypertrophy-cerebral syndrome1CTD_human
TgeneC1853099Cornelia de Lange Syndrome 31CTD_human
TgeneC2751306Polycystic kidney disease, type 21CTD_human
TgeneC3658290Drug-Induced Acute Liver Injury1CTD_human
TgeneC3714756Intellectual Disability1GENOMICS_ENGLAND
TgeneC4025871Abnormality of the face1GENOMICS_ENGLAND
TgeneC4083212Alopecia, Male Pattern1CTD_human
TgeneC4277682Chemical and Drug Induced Liver Injury1CTD_human
TgeneC4279912Chemically-Induced Liver Toxicity1CTD_human
TgeneC4551851Cornelia de Lange Syndrome 11CTD_human