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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:VPS53-SMG6

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: VPS53-SMG6
	FusionPDB ID: 98490
	FusionGDB2.0 ID: 98490
		Hgene	Tgene
	Gene symbol	VPS53	SMG6
	Gene ID	55275	23293
	Gene name	VPS53 subunit of GARP complex	SMG6 nonsense mediated mRNA decay factor
	Synonyms	HCCS1\|PCH2E\|hVps53L\|pp13624	C17orf31\|EST1A\|SMG-6\|hSMG5/7a
	Cytomap	17p13.3	17p13.3
	Type of gene	protein-coding	protein-coding
	Description	vacuolar protein sorting-associated protein 53 homologVPS53, GARP complex subunit	telomerase-binding protein EST1AEST1 telomerase component homolog Aever shorter telomeres 1Asmg-6 homolog, nonsense mediated mRNA decay factortelomerase subunit EST1A
	Modification date	20200313	20200320
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000291074, ENST00000401468, ENST00000437048, ENST00000571805, ENST00000446250, ENST00000574029, ENST00000576149,	ENST00000573166, ENST00000263073, ENST00000354901, ENST00000536871, ENST00000544865,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	18 X 15 X 14=3780	21 X 16 X 8=2688
	# samples	24	22
	** MAII score	log2(24/3780*10)=-3.97727992349992 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(22/2688*10)=-3.6109577092541 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: VPS53 [Title/Abstract] AND SMG6 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SMG6(2075952)-VPS53(565135), # samples:1 VPS53(600658)-SMG6(1989195), # samples:3
Anticipated loss of major functional domain due to fusion event.	VPS53-SMG6 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. VPS53-SMG6 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. VPS53-SMG6 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. VPS53-SMG6 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. SMG6-VPS53 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. SMG6-VPS53 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.

* 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
Tgene	SMG6	GO:1904354	negative regulation of telomere capping	12676087

Fusion gene breakpoints across VPS53 (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 SMG6 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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	LIHC	TCGA-EP-A2KA-01A	VPS53	chr17	600658	-	SMG6	chr17	1989195	-

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

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)
ENST00000437048	VPS53	chr17	600658	-	ENST00000544865	SMG6	chr17	1989195	-	2988	432	147	1334	395
ENST00000437048	VPS53	chr17	600658	-	ENST00000263073	SMG6	chr17	1989195	-	2984	432	147	1334	395
ENST00000437048	VPS53	chr17	600658	-	ENST00000354901	SMG6	chr17	1989195	-	2977	432	147	1334	395
ENST00000437048	VPS53	chr17	600658	-	ENST00000536871	SMG6	chr17	1989195	-	1422	432	147	1334	395
ENST00000291074	VPS53	chr17	600658	-	ENST00000544865	SMG6	chr17	1989195	-	2975	419	134	1321	395
ENST00000291074	VPS53	chr17	600658	-	ENST00000263073	SMG6	chr17	1989195	-	2971	419	134	1321	395
ENST00000291074	VPS53	chr17	600658	-	ENST00000354901	SMG6	chr17	1989195	-	2964	419	134	1321	395
ENST00000291074	VPS53	chr17	600658	-	ENST00000536871	SMG6	chr17	1989195	-	1409	419	134	1321	395
ENST00000571805	VPS53	chr17	600658	-	ENST00000544865	SMG6	chr17	1989195	-	2978	422	137	1324	395
ENST00000571805	VPS53	chr17	600658	-	ENST00000263073	SMG6	chr17	1989195	-	2974	422	137	1324	395
ENST00000571805	VPS53	chr17	600658	-	ENST00000354901	SMG6	chr17	1989195	-	2967	422	137	1324	395
ENST00000571805	VPS53	chr17	600658	-	ENST00000536871	SMG6	chr17	1989195	-	1412	422	137	1324	395
ENST00000401468	VPS53	chr17	600658	-	ENST00000544865	SMG6	chr17	1989195	-	2841	285	0	1187	395
ENST00000401468	VPS53	chr17	600658	-	ENST00000263073	SMG6	chr17	1989195	-	2837	285	0	1187	395
ENST00000401468	VPS53	chr17	600658	-	ENST00000354901	SMG6	chr17	1989195	-	2830	285	0	1187	395
ENST00000401468	VPS53	chr17	600658	-	ENST00000536871	SMG6	chr17	1989195	-	1275	285	0	1187	395

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
ENST00000437048	ENST00000544865	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002309583	0.99769044
ENST00000437048	ENST00000263073	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002289058	0.99771094
ENST00000437048	ENST00000354901	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002291078	0.9977089
ENST00000437048	ENST00000536871	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002099479	0.9979005
ENST00000291074	ENST00000544865	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002292679	0.99770725
ENST00000291074	ENST00000263073	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002277206	0.9977228
ENST00000291074	ENST00000354901	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002271684	0.9977283
ENST00000291074	ENST00000536871	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002094396	0.9979056
ENST00000571805	ENST00000544865	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002292276	0.9977077
ENST00000571805	ENST00000263073	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002276806	0.99772316
ENST00000571805	ENST00000354901	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002273695	0.99772626
ENST00000571805	ENST00000536871	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002114267	0.99788576
ENST00000401468	ENST00000544865	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002271668	0.9977283
ENST00000401468	ENST00000263073	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002262035	0.997738
ENST00000401468	ENST00000354901	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002256873	0.9977431
ENST00000401468	ENST00000536871	VPS53	chr17	600658	-	SMG6	chr17	1989195	-	0.002073856	0.9979261

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Fusion Amino Acid Sequences

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

>98490_98490_1_VPS53-SMG6_VPS53_chr17_600658_ENST00000291074_SMG6_chr17_1989195_ENST00000263073_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_2_VPS53-SMG6_VPS53_chr17_600658_ENST00000291074_SMG6_chr17_1989195_ENST00000354901_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_3_VPS53-SMG6_VPS53_chr17_600658_ENST00000291074_SMG6_chr17_1989195_ENST00000536871_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_4_VPS53-SMG6_VPS53_chr17_600658_ENST00000291074_SMG6_chr17_1989195_ENST00000544865_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_5_VPS53-SMG6_VPS53_chr17_600658_ENST00000401468_SMG6_chr17_1989195_ENST00000263073_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_6_VPS53-SMG6_VPS53_chr17_600658_ENST00000401468_SMG6_chr17_1989195_ENST00000354901_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_7_VPS53-SMG6_VPS53_chr17_600658_ENST00000401468_SMG6_chr17_1989195_ENST00000536871_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_8_VPS53-SMG6_VPS53_chr17_600658_ENST00000401468_SMG6_chr17_1989195_ENST00000544865_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_9_VPS53-SMG6_VPS53_chr17_600658_ENST00000437048_SMG6_chr17_1989195_ENST00000263073_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_10_VPS53-SMG6_VPS53_chr17_600658_ENST00000437048_SMG6_chr17_1989195_ENST00000354901_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_11_VPS53-SMG6_VPS53_chr17_600658_ENST00000437048_SMG6_chr17_1989195_ENST00000536871_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_12_VPS53-SMG6_VPS53_chr17_600658_ENST00000437048_SMG6_chr17_1989195_ENST00000544865_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_13_VPS53-SMG6_VPS53_chr17_600658_ENST00000571805_SMG6_chr17_1989195_ENST00000263073_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_14_VPS53-SMG6_VPS53_chr17_600658_ENST00000571805_SMG6_chr17_1989195_ENST00000354901_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_15_VPS53-SMG6_VPS53_chr17_600658_ENST00000571805_SMG6_chr17_1989195_ENST00000536871_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

>98490_98490_16_VPS53-SMG6_VPS53_chr17_600658_ENST00000571805_SMG6_chr17_1989195_ENST00000544865_length(amino acids)=395AA_BP=95
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVG
QDGRQVIAADCKRVTVLKYFLEALCGQEEPLLAFKGGKYVSVAPVPDTMGKEMGSQEGTRLEDEEEDVVIEDFEEDSEAEGSGGEDDIRE
LRAKKLALARKIAEQQRRQEKIQAVLEDHSQMRQMELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDH
RAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLR

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

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:2075952/chr17:565135)
- 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.

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

Hgene	Tgene
.	.
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: 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.

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.

- 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

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000263073

1197_1239

1119.0

1420.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000354901

1197_1239

211.0

512.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000354901

567_625

211.0

512.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000536871

1197_1239

211.0

512.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000536871

567_625

211.0

512.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000544865

1197_1239

1088.0

1389.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000263073

1246_1397

1119.0

1420.0

Domain

Note=PINc

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000354901

1246_1397

211.0

512.0

Domain

Note=PINc

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000536871

1246_1397

211.0

512.0

Domain

Note=PINc

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000544865

1246_1397

1088.0

1389.0

Domain

Note=PINc

- 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

Hgene

VPS53

chr17:600658

chr17:1989195

ENST00000291074

97_138

95.0

671.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

VPS53

chr17:600658

chr17:1989195

ENST00000437048

97_138

95.0

833.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

VPS53

chr17:600658

chr17:1989195

ENST00000571805

97_138

95.0

700.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000263073

163_193

1119.0

1420.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000263073

567_625

1119.0

1420.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000354901

163_193

211.0

512.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000536871

163_193

211.0

512.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000544865

163_193

1088.0

1389.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SMG6

chr17:600658

chr17:1989195

ENST00000544865

567_625

1088.0

1389.0

Coiled coil

Ontology_term=ECO:0000255

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Fusion Protein-Protein Interaction

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 from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
VPS53
SMG6

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner	Gene	Hbp	Tbp	ENST	Strand	BPexon	TotalExon	Protein feature loci	*BPloci	TotalLen	Interaction lost with
Tgene	SMG6	chr17:600658	chr17:1989195	ENST00000263073		12	19	114_503	1119.0	1420.0	telomeric DNA
Tgene	SMG6	chr17:600658	chr17:1989195	ENST00000354901		5	12	114_503	211.0	512.0	telomeric DNA
Tgene	SMG6	chr17:600658	chr17:1989195	ENST00000536871		4	11	114_503	211.0	512.0	telomeric DNA
Tgene	SMG6	chr17:600658	chr17:1989195	ENST00000544865		12	19	114_503	1088.0	1389.0	telomeric DNA

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Related Drugs to VPS53-SMG6

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to VPS53-SMG6

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source