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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:SMARCA4-LDLR (FusionGDB2 ID:83312)

Fusion Gene Summary for SMARCA4-LDLR

Fusion gene summary

Fusion gene information	Fusion gene name: SMARCA4-LDLR
	Fusion gene ID: 83312
		Hgene	Tgene
	Gene symbol	SMARCA4	LDLR
	Gene ID	6597	3949
	Gene name	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	low density lipoprotein receptor
	Synonyms	BAF190\|BAF190A\|BRG1\|CSS4\|MRD16\|RTPS2\|SNF2\|SNF2-beta\|SNF2L4\|SNF2LB\|SWI2\|hSNF2b	FH\|FHC\|FHCL1\|LDLCQ2
	Cytomap	19p13.2	19p13.2
	Type of gene	protein-coding	protein-coding
	Description	transcription 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 a	low-density lipoprotein receptorLDL receptorlow-density lipoprotein receptor class A domain-containing protein 3
	Modification date	20200315	20200322
	UniProtAcc	.	Q5SW96
	Ensembl transtripts involved in fusion gene	ENST00000358026, ENST00000344626, ENST00000429416, ENST00000541122, ENST00000589677, ENST00000444061, ENST00000590574, ENST00000413806, ENST00000450717, ENST00000538456,	ENST00000558518, ENST00000557933, ENST00000455727, ENST00000535915, ENST00000545707, ENST00000558013, ENST00000560628,
Fusion gene scores	* DoF score	29 X 29 X 17=14297	4 X 6 X 4=96
	# samples	55	5
	** MAII score	log2(55/14297*10)=-4.70013702309346 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/96*10)=-0.941106310946431 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: SMARCA4 [Title/Abstract] AND LDLR [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	LDLR(11234020)-SMARCA4(11172460), # samples:2 SMARCA4(11123788)-LDLR(11215895), # samples:1 SMARCA4(11071850)-LDLR(11238683), # samples:1
Anticipated loss of major functional domain due to fusion event.	LDLR-SMARCA4 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. LDLR-SMARCA4 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. LDLR-SMARCA4 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF. LDLR-SMARCA4 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF. LDLR-SMARCA4 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. LDLR-SMARCA4 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF. SMARCA4-LDLR seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. SMARCA4-LDLR seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF. SMARCA4-LDLR seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. SMARCA4-LDLR seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF. SMARCA4-LDLR seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF. SMARCA4-LDLR 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	SMARCA4	GO:0006337	nucleosome disassembly	8895581
Hgene	SMARCA4	GO:0006338	chromatin remodeling	10943845\|11726552
Hgene	SMARCA4	GO:0045892	negative regulation of transcription, DNA-templated	12065415
Hgene	SMARCA4	GO:0045944	positive regulation of transcription by RNA polymerase II	15774904\|17938176
Hgene	SMARCA4	GO:0051091	positive regulation of DNA-binding transcription factor activity	11950834\|17938176
Hgene	SMARCA4	GO:1902661	positive regulation of glucose mediated signaling pathway	22368283

Fusion gene breakpoints across SMARCA4 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across LDLR (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	BRCA	TCGA-AR-A2LR	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
ChimerDB4	OV	TCGA-23-1123	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+

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Fusion Gene ORF analysis for SMARCA4-LDLR

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
Frame-shift	ENST00000358026	ENST00000558518	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000358026	ENST00000557933	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000358026	ENST00000455727	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000358026	ENST00000535915	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000358026	ENST00000545707	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000358026	ENST00000558013	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000358026	ENST00000560628	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000344626	ENST00000558518	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000344626	ENST00000557933	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000344626	ENST00000455727	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000344626	ENST00000535915	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000344626	ENST00000545707	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000344626	ENST00000558013	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000344626	ENST00000560628	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000429416	ENST00000558518	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000429416	ENST00000557933	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000429416	ENST00000455727	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000429416	ENST00000535915	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000429416	ENST00000545707	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000429416	ENST00000558013	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000429416	ENST00000560628	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000541122	ENST00000558518	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000541122	ENST00000557933	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000541122	ENST00000455727	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000541122	ENST00000535915	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000541122	ENST00000545707	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000541122	ENST00000558013	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000541122	ENST00000560628	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000589677	ENST00000558518	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000589677	ENST00000557933	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000589677	ENST00000455727	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000589677	ENST00000535915	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000589677	ENST00000545707	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000589677	ENST00000558013	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000589677	ENST00000560628	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000444061	ENST00000558518	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000444061	ENST00000557933	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000444061	ENST00000455727	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000444061	ENST00000535915	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000444061	ENST00000545707	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000444061	ENST00000558013	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000444061	ENST00000560628	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000590574	ENST00000558518	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000590574	ENST00000557933	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000590574	ENST00000455727	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000590574	ENST00000535915	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000590574	ENST00000545707	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000590574	ENST00000558013	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000590574	ENST00000560628	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000413806	ENST00000558518	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000413806	ENST00000557933	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000413806	ENST00000455727	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000413806	ENST00000535915	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000413806	ENST00000545707	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000413806	ENST00000558013	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000413806	ENST00000560628	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000450717	ENST00000558518	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
Frame-shift	ENST00000450717	ENST00000557933	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000450717	ENST00000455727	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000450717	ENST00000535915	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000450717	ENST00000545707	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000450717	ENST00000558013	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5CDS-intron	ENST00000450717	ENST00000560628	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
intron-3CDS	ENST00000538456	ENST00000558518	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
intron-3CDS	ENST00000538456	ENST00000557933	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
intron-intron	ENST00000538456	ENST00000455727	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
intron-intron	ENST00000538456	ENST00000535915	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
intron-intron	ENST00000538456	ENST00000545707	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
intron-intron	ENST00000538456	ENST00000558013	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
intron-intron	ENST00000538456	ENST00000560628	SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+
5UTR-3CDS	ENST00000358026	ENST00000558518	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000358026	ENST00000557933	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000358026	ENST00000455727	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000358026	ENST00000535915	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000358026	ENST00000545707	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000358026	ENST00000558013	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-intron	ENST00000358026	ENST00000560628	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000344626	ENST00000558518	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000344626	ENST00000557933	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000344626	ENST00000455727	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000344626	ENST00000535915	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000344626	ENST00000545707	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000344626	ENST00000558013	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-intron	ENST00000344626	ENST00000560628	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000429416	ENST00000558518	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000429416	ENST00000557933	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000429416	ENST00000455727	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000429416	ENST00000535915	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000429416	ENST00000545707	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000429416	ENST00000558013	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-intron	ENST00000429416	ENST00000560628	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000541122	ENST00000558518	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000541122	ENST00000557933	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000541122	ENST00000455727	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000541122	ENST00000535915	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000541122	ENST00000545707	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000541122	ENST00000558013	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-intron	ENST00000541122	ENST00000560628	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000589677	ENST00000558518	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000589677	ENST00000557933	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000589677	ENST00000455727	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000589677	ENST00000535915	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000589677	ENST00000545707	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000589677	ENST00000558013	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-intron	ENST00000589677	ENST00000560628	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000444061	ENST00000558518	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000444061	ENST00000557933	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000444061	ENST00000455727	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000444061	ENST00000535915	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000444061	ENST00000545707	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-3CDS	ENST00000444061	ENST00000558013	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
5UTR-intron	ENST00000444061	ENST00000560628	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000590574	ENST00000558518	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000590574	ENST00000557933	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000590574	ENST00000455727	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000590574	ENST00000535915	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000590574	ENST00000545707	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000590574	ENST00000558013	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-intron	ENST00000590574	ENST00000560628	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000413806	ENST00000558518	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000413806	ENST00000557933	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000413806	ENST00000455727	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000413806	ENST00000535915	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000413806	ENST00000545707	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000413806	ENST00000558013	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-intron	ENST00000413806	ENST00000560628	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000450717	ENST00000558518	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000450717	ENST00000557933	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000450717	ENST00000455727	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000450717	ENST00000535915	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000450717	ENST00000545707	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000450717	ENST00000558013	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-intron	ENST00000450717	ENST00000560628	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000538456	ENST00000558518	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000538456	ENST00000557933	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000538456	ENST00000455727	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000538456	ENST00000535915	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000538456	ENST00000545707	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-3CDS	ENST00000538456	ENST00000558013	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+
intron-intron	ENST00000538456	ENST00000560628	SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

DeepORF 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.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

No-coding score

Coding score

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Fusion Genomic Features for SMARCA4-LDLR

FusionAI 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.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+	2.06E-10	1
SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+	1.96E-16	1
SMARCA4	chr19	11123788	+	LDLR	chr19	11215895	+	2.06E-10	1
SMARCA4	chr19	11071850	+	LDLR	chr19	11238683	+	1.96E-16	1

Distribution 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.

Distribution 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 SMARCA4-LDLR

Go to
FGviewer for the breakpoints of :-:
.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	LDLR Q5SW96
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.	FUNCTION: Adapter protein (clathrin-associated sorting protein (CLASP)) required for efficient endocytosis of the LDL receptor (LDLR) in polarized cells such as hepatocytes and lymphocytes, but not in non-polarized cells (fibroblasts). May be required for LDL binding and internalization but not for receptor clustering in coated pits. May facilitate the endocytocis of LDLR and LDLR-LDL complexes from coated pits by stabilizing the interaction between the receptor and the structural components of the pits. May also be involved in the internalization of other LDLR family members. Binds to phosphoinositides, which regulate clathrin bud assembly at the cell surface. Required for trafficking of LRP2 to the endocytic recycling compartment which is necessary for LRP2 proteolysis, releasing a tail fragment which translocates to the nucleus and mediates transcriptional repression (By similarity). {ECO:0000250\|UniProtKB:D3ZAR1, ECO:0000269\|PubMed:15728179}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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Fusion Gene Sequence for SMARCA4-LDLR

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-LDLR

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for SMARCA4-LDLR

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for SMARCA4-LDLR

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	SMARCA4	C2750074	Rhabdoid Tumor Predisposition Syndrome 2	7	CLINGEN;CTD_human;GENOMICS_ENGLAND
Hgene	SMARCA4	C0262584	Carcinoma, Small Cell	4	CTD_human
Hgene	SMARCA4	C0919267	ovarian neoplasm	4	CGI;CTD_human
Hgene	SMARCA4	C1140680	Malignant neoplasm of ovary	4	CGI;CTD_human
Hgene	SMARCA4	C0009405	Hereditary Nonpolyposis Colorectal Neoplasms	2	CLINGEN
Hgene	SMARCA4	C1112155	Hereditary non-polyposis colorectal cancer syndrome	2	CLINGEN
Hgene	SMARCA4	C1333990	Hereditary Nonpolyposis Colorectal Cancer	2	CLINGEN
Hgene	SMARCA4	C1333991	Hereditary Non-Polyposis Colon Cancer Type 2	2	CLINGEN
Hgene	SMARCA4	C2936783	Colorectal cancer, hereditary nonpolyposis, type 1	2	CLINGEN
Hgene	SMARCA4	C2985524	Rhabdoid tumor predisposition syndrome	2	ORPHANET
Hgene	SMARCA4	C0006413	Burkitt Lymphoma	1	CTD_human
Hgene	SMARCA4	C0009171	Cocaine Abuse	1	CTD_human
Hgene	SMARCA4	C0036920	Sezary Syndrome	1	CTD_human
Hgene	SMARCA4	C0039981	Thoracic Neoplasms	1	CTD_human
Hgene	SMARCA4	C0149925	Small cell carcinoma of lung	1	CTD_human
Hgene	SMARCA4	C0205944	Sarcoma, Epithelioid	1	CTD_human
Hgene	SMARCA4	C0205945	Sarcoma, Spindle Cell	1	CTD_human
Hgene	SMARCA4	C0236736	Cocaine-Related Disorders	1	CTD_human
Hgene	SMARCA4	C0265338	Coffin-Siris syndrome	1	CTD_human;GENOMICS_ENGLAND
Hgene	SMARCA4	C0343640	African Burkitt's lymphoma	1	CTD_human
Hgene	SMARCA4	C0600427	Cocaine Dependence	1	CTD_human
Hgene	SMARCA4	C1261473	Sarcoma	1	CTD_human
Hgene	SMARCA4	C1961099	Precursor T-Cell Lymphoblastic Leukemia-Lymphoma	1	CTD_human
Hgene	SMARCA4	C2239246	Endometrial stromal sarcoma, high grade	1	GENOMICS_ENGLAND
Hgene	SMARCA4	C3281201	MENTAL RETARDATION, AUTOSOMAL DOMINANT 12	1	GENOMICS_ENGLAND
Hgene	SMARCA4	C3553249	COFFIN-SIRIS SYNDROME 4	1	GENOMICS_ENGLAND;UNIPROT
Hgene	SMARCA4	C4721444	Burkitt Leukemia	1	CTD_human
Tgene	LDLR	C0745103	Hyperlipoproteinemia Type IIa	61	CTD_human;GENOMICS_ENGLAND;UNIPROT
Tgene	LDLR	C0020445	Hypercholesterolemia, Familial	9	CTD_human;GENOMICS_ENGLAND
Tgene	LDLR	C1704417	Hyperlipoproteinemia Type IIb	7	CTD_human
Tgene	LDLR	C0020443	Hypercholesterolemia	6	CTD_human;GENOMICS_ENGLAND
Tgene	LDLR	C0004153	Atherosclerosis	5	CTD_human
Tgene	LDLR	C1563937	Atherogenesis	5	CTD_human
Tgene	LDLR	C0400966	Non-alcoholic Fatty Liver Disease	3	CTD_human
Tgene	LDLR	C3241937	Nonalcoholic Steatohepatitis	3	CTD_human
Tgene	LDLR	C0010054	Coronary Arteriosclerosis	2	CTD_human
Tgene	LDLR	C0020473	Hyperlipidemia	2	CTD_human
Tgene	LDLR	C1706412	Lipidemias	2	CTD_human
Tgene	LDLR	C1956346	Coronary Artery Disease	2	CTD_human
Tgene	LDLR	C0010068	Coronary heart disease	1	CTD_human
Tgene	LDLR	C0015695	Fatty Liver	1	CTD_human
Tgene	LDLR	C0020507	Hyperplasia	1	CTD_human
Tgene	LDLR	C0028754	Obesity	1	CTD_human
Tgene	LDLR	C0034362	Q Fever	1	CTD_human
Tgene	LDLR	C0085762	Alcohol abuse	1	PSYGENET
Tgene	LDLR	C0242339	Dyslipidemias	1	CTD_human
Tgene	LDLR	C0519066	Acute Q fever	1	CTD_human
Tgene	LDLR	C0598784	Dyslipoproteinemias	1	CTD_human
Tgene	LDLR	C1443892	Chronic Q Fever	1	CTD_human
Tgene	LDLR	C1862939	AMYOTROPHIC LATERAL SCLEROSIS 1	1	CTD_human
Tgene	LDLR	C1862941	Amyotrophic Lateral Sclerosis, Sporadic	1	CTD_human
Tgene	LDLR	C2711227	Steatohepatitis	1	CTD_human
Tgene	LDLR	C2973787	Coxiella burnetii Infection	1	CTD_human
Tgene	LDLR	C4551993	Amyotrophic Lateral Sclerosis, Familial	1	CTD_human