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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:DEAF1-SH3GL1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: DEAF1-SH3GL1
	FusionPDB ID: 22126
	FusionGDB2.0 ID: 22126
		Hgene	Tgene
	Gene symbol	DEAF1	SH3GL1
	Gene ID	10522	6455
	Gene name	DEAF1 transcription factor	SH3 domain containing GRB2 like 1, endophilin A2
	Synonyms	MRD24\|NUDR\|SPN\|ZMYND5	CNSA1\|EEN\|SH3D2B\|SH3P8
	Cytomap	11p15.5	19p13.3
	Type of gene	protein-coding	protein-coding
	Description	deformed epidermal autoregulatory factor 1 homolognuclear DEAF-1-related transcriptional regulatorsuppressinzinc finger MYND domain-containing protein 5	endophilin-A2EEN fusion partner of MLLSH3 domain protein 2BSH3 domain-containing GRB2-like protein 1SH3-containing Grb-2-like 1 proteinSH3-domain GRB2-like 1endophilin-2extra 11-19 leukemia fusionextra eleven-nineteen leukemia fusion gene protein
	Modification date	20200313	20200313
	UniProtAcc	O75398	Q99961
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000382409, ENST00000338675, ENST00000525904,	ENST00000269886, ENST00000417295, ENST00000598564,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 5 X 4=120	10 X 6 X 9=540
	# samples	8	10
	** MAII score	log2(8/120*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/540*10)=-2.43295940727611 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: DEAF1 [Title/Abstract] AND SH3GL1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	DEAF1(686858)-SH3GL1(4366991), # samples:2
Anticipated loss of major functional domain due to fusion event.	DEAF1-SH3GL1 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. DEAF1-SH3GL1 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. DEAF1-SH3GL1 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. DEAF1-SH3GL1 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
Hgene	DEAF1	GO:0000122	negative regulation of transcription by RNA polymerase II	24726472
Hgene	DEAF1	GO:0033599	regulation of mammary gland epithelial cell proliferation	18826651
Hgene	DEAF1	GO:0045892	negative regulation of transcription, DNA-templated	24726472
Hgene	DEAF1	GO:0045893	positive regulation of transcription, DNA-templated	24726472

Fusion gene breakpoints across DEAF1 (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 SH3GL1 (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	BLCA	TCGA-XF-AAMZ-01A	DEAF1	chr11	686858	-	SH3GL1	chr19	4366991	-
ChimerDB4	BLCA	TCGA-XF-AAMZ	DEAF1	chr11	686858	-	SH3GL1	chr19	4366991	-

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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)
ENST00000382409	DEAF1	chr11	686858	-	ENST00000269886	SH3GL1	chr19	4366991	-	3581	1289	485	2350	621
ENST00000382409	DEAF1	chr11	686858	-	ENST00000598564	SH3GL1	chr19	4366991	-	3388	1289	485	2158	557
ENST00000382409	DEAF1	chr11	686858	-	ENST00000417295	SH3GL1	chr19	4366991	-	2491	1289	485	2206	573

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
ENST00000382409	ENST00000269886	DEAF1	chr11	686858	-	SH3GL1	chr19	4366991	-	0.012877779	0.98712224
ENST00000382409	ENST00000598564	DEAF1	chr11	686858	-	SH3GL1	chr19	4366991	-	0.012320465	0.9876795
ENST00000382409	ENST00000417295	DEAF1	chr11	686858	-	SH3GL1	chr19	4366991	-	0.010277053	0.98972297

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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

>22126_22126_1_DEAF1-SH3GL1_DEAF1_chr11_686858_ENST00000382409_SH3GL1_chr19_4366991_ENST00000269886_length(amino acids)=621AA_BP=17
MEDSDSAAKQLGLAEAAAVAAAAAVAAAAAAAAGGEAEEPVLSRDEDSEEDADSEAERETPRVTAVAVMAAEPGHMDMGAEALPGPDEAA
AAAAFAEVTTVTVANVGAAADNVFTTSVANAASISGHVLSGRTALQIGDSLNTEKATLIVVHTDGSIVETTGLKGPAAPLTPGPQSPPTP
LAPGQEKGGTKYNWDPSVYDSELPVRCRNISGTLYKNRLGSGGRGRCIKQGENWYSPTEFEAMAGRASSKDWKRSIRYAGRPLQCLIQLV
SEKVGGAEGTKLDDDFKEMEKKVDVTSKAVTEVLARTIEYLQPNPASRAKLTMLNTVSKIRGQVKNPGYPQSEGLLGECMIRHGKELGGE
SNFGDALLDAGESMKRLAEVKDSLDIEVKQNFIDPLQNLCEKDLKEIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFEESKEVA
ETSMHNLLETDIEQVSQLSALVDAQLDYHRQAVQILDELAEKLKRRMREASSRPKREYKPKPREPFDLGEPEQSNGGFPCTTAPKIAASS

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

>22126_22126_2_DEAF1-SH3GL1_DEAF1_chr11_686858_ENST00000382409_SH3GL1_chr19_4366991_ENST00000417295_length(amino acids)=573AA_BP=17
MEDSDSAAKQLGLAEAAAVAAAAAVAAAAAAAAGGEAEEPVLSRDEDSEEDADSEAERETPRVTAVAVMAAEPGHMDMGAEALPGPDEAA
AAAAFAEVTTVTVANVGAAADNVFTTSVANAASISGHVLSGRTALQIGDSLNTEKATLIVVHTDGSIVETTGLKGPAAPLTPGPQSPPTP
LAPGQEKGGTKYNWDPSVYDSELPVRCRNISGTLYKNRLGSGGRGRCIKQGENWYSPTEFEAMAGRASSKDWKRSIRYAGRPLQCLIQLV
SEKVGGAEGTKLDDDFKEMEKKVDVTSKAVTEVLARTIEYLQPNPGDALLDAGESMKRLAEVKDSLDIEVKQNFIDPLQNLCEKDLKEIQ
HHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFEESKEVAETSMHNLLETDIEQVSQLSALVDAQLDYHRQAVQILDELAEKLKRRMR
EASSRPKREYKPKPREPFDLGEPEQSNGGFPCTTAPKIAASSSFRSSDKPIRTPSRSMPPLDQPSCKALYDFEPENDGELGFHEGDVITL

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

>22126_22126_3_DEAF1-SH3GL1_DEAF1_chr11_686858_ENST00000382409_SH3GL1_chr19_4366991_ENST00000598564_length(amino acids)=557AA_BP=17
MEDSDSAAKQLGLAEAAAVAAAAAVAAAAAAAAGGEAEEPVLSRDEDSEEDADSEAERETPRVTAVAVMAAEPGHMDMGAEALPGPDEAA
AAAAFAEVTTVTVANVGAAADNVFTTSVANAASISGHVLSGRTALQIGDSLNTEKATLIVVHTDGSIVETTGLKGPAAPLTPGPQSPPTP
LAPGQEKGGTKYNWDPSVYDSELPVRCRNISGTLYKNRLGSGGRGRCIKQGENWYSPTEFEAMAGRASSKDWKRSIRYAGRPLQCLIQLV
SEKVGGAEGTKLDDDFKEMEKKVDVTSKAVTEVLARTIEYLQPNPASRAKLTMLNTVSKIRGQNLCEKDLKEIQHHLKKLEGRRLDFDYK
KKRQGKIPDEELRQALEKFEESKEVAETSMHNLLETDIEQVSQLSALVDAQLDYHRQAVQILDELAEKLKRRMREASSRPKREYKPKPRE
PFDLGEPEQSNGGFPCTTAPKIAASSSFRSSDKPIRTPSRSMPPLDQPSCKALYDFEPENDGELGFHEGDVITLTNQIDENWYEGMLDGQ

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

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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/chr11:686858/chr19:4366991)
- 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
DEAF1 O75398	SH3GL1 Q99961
FUNCTION: Transcription factor that binds to sequence with multiple copies of 5'-TTC[CG]G-3' present in its own promoter and that of the HNRPA2B1 gene. Down-regulates transcription of these genes. Binds to the retinoic acid response element (RARE) 5'-AGGGTTCACCGAAAGTTCA-3'. Activates the proenkephalin gene independently of promoter binding, probably through protein-protein interaction. When secreted, behaves as an inhibitor of cell proliferation, by arresting cells in the G0 or G1 phase. Required for neural tube closure and skeletal patterning. Regulates epithelial cell proliferation and side-branching in the mammary gland. Controls the expression of peripheral tissue antigens in pancreatic lymph nodes. Isoform 1 displays greater transcriptional activity than isoform 4. Isoform 4 may inhibit transcriptional activity of isoform 1 by interacting with isoform 1 and retaining it in the cytoplasm. Transcriptional activator of EIF4G3. {ECO:0000269\|PubMed:10521432, ECO:0000269\|PubMed:11427895, ECO:0000269\|PubMed:11705868, ECO:0000269\|PubMed:18826651, ECO:0000269\|PubMed:19668219, ECO:0000269\|PubMed:24726472}.	FUNCTION: Implicated in endocytosis. May recruit other proteins to membranes with high curvature (By similarity). {ECO:0000250}.

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

Hgene

DEAF1

chr11:686858

chr19:4366991

ENST00000382409

2_122

268.0

566.0

Compositional bias

Note=Ala-rich

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000269886

145_250

15.0

369.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000417295

145_250

15.0

321.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000598564

145_250

15.0

305.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000269886

18_249

15.0

369.0

Domain

BAR

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000269886

306_365

15.0

369.0

Domain

SH3

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000417295

18_249

15.0

321.0

Domain

BAR

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000417295

306_365

15.0

321.0

Domain

SH3

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000598564

18_249

15.0

305.0

Domain

BAR

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000598564

306_365

15.0

305.0

Domain

SH3

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000269886

60_87

15.0

369.0

Region

Required for dimerization upon membrane association

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000417295

60_87

15.0

321.0

Region

Required for dimerization upon membrane association

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000598564

60_87

15.0

305.0

Region

Required for dimerization upon membrane association

- 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

DEAF1

chr11:686858

chr19:4366991

ENST00000338675

2_122

491.0

Compositional bias

Note=Ala-rich

Hgene

DEAF1

chr11:686858

chr19:4366991

ENST00000338675

383_439

491.0

Compositional bias

Note=Pro-rich

Hgene

DEAF1

chr11:686858

chr19:4366991

ENST00000382409

383_439

268.0

566.0

Compositional bias

Note=Pro-rich

Hgene

DEAF1

chr11:686858

chr19:4366991

ENST00000338675

193_273

491.0

Domain

SAND

Hgene

DEAF1

chr11:686858

chr19:4366991

ENST00000382409

193_273

268.0

566.0

Domain

SAND

Hgene

DEAF1

chr11:686858

chr19:4366991

ENST00000338675

301_316

491.0

Motif

Nuclear localization signal

Hgene

DEAF1

chr11:686858

chr19:4366991

ENST00000382409

301_316

268.0

566.0

Motif

Nuclear localization signal

Hgene

DEAF1

chr11:686858

chr19:4366991

ENST00000338675

504_540

491.0

Zinc finger

MYND-type

Hgene

DEAF1

chr11:686858

chr19:4366991

ENST00000382409

504_540

268.0

566.0

Zinc finger

MYND-type

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000269886

1_21

15.0

369.0

Region

Membrane-binding amphipathic helix

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000417295

1_21

15.0

321.0

Region

Membrane-binding amphipathic helix

Tgene

SH3GL1

chr11:686858

chr19:4366991

ENST00000598564

1_21

15.0

305.0

Region

Membrane-binding amphipathic helix

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>1305_DEAF1_686858_SH3GL1_4366991_1305_DEAF1_686858_SH3GL1_4366991_ranked_0.pdb	DEAF1	686858	686858	ENST00000417295	SH3GL1	chr19	4366991	-	MEDSDSAAKQLGLAEAAAVAAAAAVAAAAAAAAGGEAEEPVLSRDEDSEEDADSEAERETPRVTAVAVMAAEPGHMDMGAEALPGPDEAA AAAAFAEVTTVTVANVGAAADNVFTTSVANAASISGHVLSGRTALQIGDSLNTEKATLIVVHTDGSIVETTGLKGPAAPLTPGPQSPPTP LAPGQEKGGTKYNWDPSVYDSELPVRCRNISGTLYKNRLGSGGRGRCIKQGENWYSPTEFEAMAGRASSKDWKRSIRYAGRPLQCLIQLV SEKVGGAEGTKLDDDFKEMEKKVDVTSKAVTEVLARTIEYLQPNPASRAKLTMLNTVSKIRGQVKNPGYPQSEGLLGECMIRHGKELGGE SNFGDALLDAGESMKRLAEVKDSLDIEVKQNFIDPLQNLCEKDLKEIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFEESKEVA ETSMHNLLETDIEQVSQLSALVDAQLDYHRQAVQILDELAEKLKRRMREASSRPKREYKPKPREPFDLGEPEQSNGGFPCTTAPKIAASS	621

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

DEAF1_pLDDT.png

SH3GL1_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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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
DEAF1
SH3GL1

- 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
Hgene	DEAF1	chr11:686858	chr19:4366991	ENST00000338675	-	1	11	403_478	0	491.0	LMO4
Hgene	DEAF1	chr11:686858	chr19:4366991	ENST00000382409	-	5	12	403_478	268.0	566.0	LMO4

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Related Drugs to DEAF1-SH3GL1

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

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to DEAF1-SH3GL1

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