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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:SS18-ZNF521

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SS18-ZNF521
FusionPDB ID: 86696
FusionGDB2.0 ID: 86696
HgeneTgene
Gene symbol

SS18

ZNF521

Gene ID

6760

25925

Gene nameSS18 subunit of BAF chromatin remodeling complexzinc finger protein 521
SynonymsSSXT|SYTEHZF|Evi3
Cytomap

18q11.2

18q11.2

Type of geneprotein-codingprotein-coding
Descriptionprotein SSXTSS18, nBAF chromatin remodeling complex subunitsynovial sarcoma translocated to X chromosome proteinsynovial sarcoma translocation, chromosome 18synovial sarcoma, translocated to X chromosomezinc finger protein 521LYST-interacting protein 3early hematopoietic zinc finger protein
Modification date2020032920200313
UniProtAcc

O75177

.
Ensembl transtripts involved in fusion geneENST idsENST00000269137, ENST00000415083, 
ENST00000542420, ENST00000542743, 
ENST00000545952, ENST00000539849, 
ENST00000585241, 		ENST00000579111, 
ENST00000361524, ENST00000538137, 
ENST00000584787, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score24 X 33 X 8=633613 X 10 X 9=1170
# samples 3815
** MAII scorelog2(38/6336*10)=-4.05950101174866
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/1170*10)=-2.96347412397489
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: SS18 [Title/Abstract] AND ZNF521 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SS18(23667465)-ZNF521(22672045), # samples:2
Anticipated loss of major functional domain due to fusion event.SS18-ZNF521 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.
SS18-ZNF521 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.
SS18-ZNF521 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.
SS18-ZNF521 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.
SS18-ZNF521 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
SS18-ZNF521 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
SS18-ZNF521 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
SS18-ZNF521 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
HgeneSS18

GO:0045944

positive regulation of transcription by RNA polymerase II

15919756


check buttonFusion gene breakpoints across SS18 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across ZNF521 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4SARCTCGA-DX-A48K-01ASS18chr18

23667465

-ZNF521chr18

22672045

-
ChimerDB4SARCTCGA-DX-AATS-01ASS18chr18

23658040

-ZNF521chr18

22672045

-
ChimerDB4SARCTCGA-DX-AATS-01ASS18chr18

23667465

-ZNF521chr18

22672045

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000542420SS18chr1823658040-ENST00000361524ZNF521chr1822672045-134828454925697
ENST00000542420SS18chr1823658040-ENST00000584787ZNF521chr1822672045-84928454925697
ENST00000542420SS18chr1823658040-ENST00000538137ZNF521chr1822672045-68128454925697

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
ENST00000542420ENST00000361524SS18chr1823658040-ZNF521chr1822672045-0.364989670.6350103
ENST00000542420ENST00000584787SS18chr1823658040-ZNF521chr1822672045-0.162743450.83725655
ENST00000542420ENST00000538137SS18chr1823658040-ZNF521chr1822672045-0.089129740.9108703

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Fusion Amino Acid Sequences


check button 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

>86696_86696_1_SS18-ZNF521_SS18_chr18_23658040_ENST00000542420_ZNF521_chr18_22672045_ENST00000361524_length(amino acids)=97AA_BP=6
MGHCMILQLCLEEKLLWTLCTVIDLVFLSMGRENMLLQLVCLNKYCKADWTLEGASHPFEAVLYQVALEFGRRVKGLAAEFAFMVQSFIA

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

>86696_86696_2_SS18-ZNF521_SS18_chr18_23658040_ENST00000542420_ZNF521_chr18_22672045_ENST00000538137_length(amino acids)=97AA_BP=6
MGHCMILQLCLEEKLLWTLCTVIDLVFLSMGRENMLLQLVCLNKYCKADWTLEGASHPFEAVLYQVALEFGRRVKGLAAEFAFMVQSFIA

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

>86696_86696_3_SS18-ZNF521_SS18_chr18_23658040_ENST00000542420_ZNF521_chr18_22672045_ENST00000584787_length(amino acids)=97AA_BP=6
MGHCMILQLCLEEKLLWTLCTVIDLVFLSMGRENMLLQLVCLNKYCKADWTLEGASHPFEAVLYQVALEFGRRVKGLAAEFAFMVQSFIA

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

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Fusion Protein Functional Features


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/chr18:23667465/chr18:22672045)
- 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
SS18

O75177

.
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: 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.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSS18chr18:23658040chr18:22672045ENST00000269137-31050_5377.0388.0MotifSH2-binding
HgeneSS18chr18:23658040chr18:22672045ENST00000415083-31150_5377.0419.0MotifSH2-binding
TgeneZNF521chr18:23658040chr18:22672045ENST00000361524481225_12471219.33333333333331312.0Zinc fingerC2H2-type 28
TgeneZNF521chr18:23658040chr18:22672045ENST00000361524481256_12791219.33333333333331312.0Zinc fingerC2H2-type 29
TgeneZNF521chr18:23658040chr18:22672045ENST00000361524481286_13091219.33333333333331312.0Zinc fingerC2H2-type 30
TgeneZNF521chr18:23658040chr18:22672045ENST00000538137481225_12471219.33333333333331312.0Zinc fingerC2H2-type 28
TgeneZNF521chr18:23658040chr18:22672045ENST00000538137481256_12791219.33333333333331312.0Zinc fingerC2H2-type 29
TgeneZNF521chr18:23658040chr18:22672045ENST00000538137481286_13091219.33333333333331312.0Zinc fingerC2H2-type 30

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSS18chr18:23658040chr18:22672045ENST00000269137-310175_41877.0388.0Compositional biasNote=Gln-rich
HgeneSS18chr18:23658040chr18:22672045ENST00000269137-31095_9977.0388.0Compositional biasNote=Poly-Pro
HgeneSS18chr18:23658040chr18:22672045ENST00000415083-311175_41877.0419.0Compositional biasNote=Gln-rich
HgeneSS18chr18:23658040chr18:22672045ENST00000415083-31195_9977.0419.0Compositional biasNote=Poly-Pro
HgeneSS18chr18:23658040chr18:22672045ENST00000269137-310374_37777.0388.0MotifSH2-binding
HgeneSS18chr18:23658040chr18:22672045ENST00000269137-310392_40177.0388.0MotifSH3-binding
HgeneSS18chr18:23658040chr18:22672045ENST00000269137-310413_41677.0388.0MotifSH2-binding
HgeneSS18chr18:23658040chr18:22672045ENST00000415083-311374_37777.0419.0MotifSH2-binding
HgeneSS18chr18:23658040chr18:22672045ENST00000415083-311392_40177.0419.0MotifSH3-binding
HgeneSS18chr18:23658040chr18:22672045ENST00000415083-311413_41677.0419.0MotifSH2-binding
HgeneSS18chr18:23658040chr18:22672045ENST00000269137-3102_18677.0388.0RegionNote=Transcriptional activation
HgeneSS18chr18:23658040chr18:22672045ENST00000269137-310344_36977.0388.0RegionNote=2 X 13 AA imperfect tandem repeats
HgeneSS18chr18:23658040chr18:22672045ENST00000415083-3112_18677.0419.0RegionNote=Transcriptional activation
HgeneSS18chr18:23658040chr18:22672045ENST00000415083-311344_36977.0419.0RegionNote=2 X 13 AA imperfect tandem repeats
HgeneSS18chr18:23658040chr18:22672045ENST00000269137-310344_35677.0388.0RepeatNote=1
HgeneSS18chr18:23658040chr18:22672045ENST00000269137-310357_36977.0388.0RepeatNote=2
HgeneSS18chr18:23658040chr18:22672045ENST00000415083-311344_35677.0419.0RepeatNote=1
HgeneSS18chr18:23658040chr18:22672045ENST00000415083-311357_36977.0419.0RepeatNote=2
TgeneZNF521chr18:23658040chr18:22672045ENST00000361524481020_10421219.33333333333331312.0Zinc fingerC2H2-type 24
TgeneZNF521chr18:23658040chr18:22672045ENST00000361524481065_10831219.33333333333331312.0Zinc fingerC2H2-type 25%3B degenerate
TgeneZNF521chr18:23658040chr18:22672045ENST00000361524481138_11611219.33333333333331312.0Zinc fingerC2H2-type 26
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448118_1401219.33333333333331312.0Zinc fingerC2H2-type 2
TgeneZNF521chr18:23658040chr18:22672045ENST00000361524481195_12171219.33333333333331312.0Zinc fingerC2H2-type 27
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448146_1681219.33333333333331312.0Zinc fingerC2H2-type 3
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448174_1961219.33333333333331312.0Zinc fingerC2H2-type 4
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448202_2241219.33333333333331312.0Zinc fingerC2H2-type 5
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448246_2691219.33333333333331312.0Zinc fingerC2H2-type 6
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448281_3041219.33333333333331312.0Zinc fingerC2H2-type 7
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448310_3321219.33333333333331312.0Zinc fingerC2H2-type 8
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448405_4291219.33333333333331312.0Zinc fingerC2H2-type 9%3B degenerate
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448437_4601219.33333333333331312.0Zinc fingerC2H2-type 10
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448477_5001219.33333333333331312.0Zinc fingerC2H2-type 11
TgeneZNF521chr18:23658040chr18:22672045ENST000003615244847_671219.33333333333331312.0Zinc fingerC2H2-type 1%3B degenerate
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448513_5361219.33333333333331312.0Zinc fingerC2H2-type 12
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448560_5851219.33333333333331312.0Zinc fingerC2H2-type 13%3B atypical
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448634_6561219.33333333333331312.0Zinc fingerC2H2-type 14
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448664_6861219.33333333333331312.0Zinc fingerC2H2-type 15
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448694_7171219.33333333333331312.0Zinc fingerC2H2-type 16
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448722_7451219.33333333333331312.0Zinc fingerC2H2-type 17
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448752_7751219.33333333333331312.0Zinc fingerC2H2-type 18
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448783_8051219.33333333333331312.0Zinc fingerC2H2-type 19
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448809_8321219.33333333333331312.0Zinc fingerC2H2-type 20
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448886_9081219.33333333333331312.0Zinc fingerC2H2-type 21%3B degenerate
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448930_9521219.33333333333331312.0Zinc fingerC2H2-type 22
TgeneZNF521chr18:23658040chr18:22672045ENST0000036152448959_9811219.33333333333331312.0Zinc fingerC2H2-type 23
TgeneZNF521chr18:23658040chr18:22672045ENST00000538137481020_10421219.33333333333331312.0Zinc fingerC2H2-type 24
TgeneZNF521chr18:23658040chr18:22672045ENST00000538137481065_10831219.33333333333331312.0Zinc fingerC2H2-type 25%3B degenerate
TgeneZNF521chr18:23658040chr18:22672045ENST00000538137481138_11611219.33333333333331312.0Zinc fingerC2H2-type 26
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748118_1401219.33333333333331312.0Zinc fingerC2H2-type 2
TgeneZNF521chr18:23658040chr18:22672045ENST00000538137481195_12171219.33333333333331312.0Zinc fingerC2H2-type 27
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748146_1681219.33333333333331312.0Zinc fingerC2H2-type 3
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748174_1961219.33333333333331312.0Zinc fingerC2H2-type 4
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748202_2241219.33333333333331312.0Zinc fingerC2H2-type 5
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748246_2691219.33333333333331312.0Zinc fingerC2H2-type 6
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748281_3041219.33333333333331312.0Zinc fingerC2H2-type 7
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748310_3321219.33333333333331312.0Zinc fingerC2H2-type 8
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748405_4291219.33333333333331312.0Zinc fingerC2H2-type 9%3B degenerate
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748437_4601219.33333333333331312.0Zinc fingerC2H2-type 10
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748477_5001219.33333333333331312.0Zinc fingerC2H2-type 11
TgeneZNF521chr18:23658040chr18:22672045ENST000005381374847_671219.33333333333331312.0Zinc fingerC2H2-type 1%3B degenerate
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748513_5361219.33333333333331312.0Zinc fingerC2H2-type 12
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748560_5851219.33333333333331312.0Zinc fingerC2H2-type 13%3B atypical
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748634_6561219.33333333333331312.0Zinc fingerC2H2-type 14
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748664_6861219.33333333333331312.0Zinc fingerC2H2-type 15
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748694_7171219.33333333333331312.0Zinc fingerC2H2-type 16
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748722_7451219.33333333333331312.0Zinc fingerC2H2-type 17
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748752_7751219.33333333333331312.0Zinc fingerC2H2-type 18
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748783_8051219.33333333333331312.0Zinc fingerC2H2-type 19
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748809_8321219.33333333333331312.0Zinc fingerC2H2-type 20
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748886_9081219.33333333333331312.0Zinc fingerC2H2-type 21%3B degenerate
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748930_9521219.33333333333331312.0Zinc fingerC2H2-type 22
TgeneZNF521chr18:23658040chr18:22672045ENST0000053813748959_9811219.33333333333331312.0Zinc fingerC2H2-type 23


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors
SS18SMARCA2, SMARCB1, EP300, MLLT10, GRB2, Bcl7b, SMARCD1, RBM14, YWHAG, ELAVL1, CUL3, CST11, ATF2, TLE1, SMARCA5, HDAC1, HDAC2, EED, SUZ12, EZH2, SS18, NFKBID, DPF3, DPF2, SMARCE1, ARID1B, ARID1A, PHF10, SMARCC2, SMARCC1, GLTSCR1, SMARCD3, SMARCD2, SMARCA4, ARID2, DPF1, ACTL6A, ACTL6B, BCL7A, BCL7C, BCL7B, BRD9, CDKN1A, NEFM, RAB5C, SYNCRIP, Wash, FUS, DDIT3, FLI1, nsp13ab, BRD3, NR3C1, SS18L1, BRD7, PBRM1, ACTC1, STK11IP, DDX58, UBQLN2, PTPRR, T, ELF5, ERG, ETV4, FOS, GATA2, GCM1, HNF4A, IRF1, IRF4, KLF3, KLF5, LHX2, MYOD1, PAX7, SOX17, SOX2, SP7,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
SS18all structure
ZNF521


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to SS18-ZNF521


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

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Related Diseases to SS18-ZNF521


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

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSS18C0039101synovial sarcoma2CTD_human;ORPHANET