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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:HGS-BAIAP2 (FusionGDB2 ID:36247)

Fusion Gene Summary for HGS-BAIAP2

Fusion gene summary

Fusion gene information	Fusion gene name: HGS-BAIAP2
	Fusion gene ID: 36247
		Hgene	Tgene
	Gene symbol	HGS	BAIAP2
	Gene ID	9146	10458
	Gene name	hepatocyte growth factor-regulated tyrosine kinase substrate	BAR/IMD domain containing adaptor protein 2
	Synonyms	HRS	BAP2\|FLAF3\|IRSP53\|WAML
	Cytomap	17q25.3	17q25.3
	Type of gene	protein-coding	protein-coding
	Description	hepatocyte growth factor-regulated tyrosine kinase substratehuman growth factor-regulated tyrosine kinase substrateprotein pp110	brain-specific angiogenesis inhibitor 1-associated protein 2BAI1 associated protein 2IRS-58IRSp53/58WASP and MIM likefas ligand-associated factor 3insulin receptor substrate of 53 kDainsulin receptor substrate p53/p58insulin receptor substrate pro
	Modification date	20200327	20200327
	UniProtAcc	O14964	Q6UXY1
	Ensembl transtripts involved in fusion gene	ENST00000329138,	ENST00000321300, ENST00000435091, ENST00000575245, ENST00000321280, ENST00000416299, ENST00000428708, ENST00000573894, ENST00000575712, ENST00000392411,
Fusion gene scores	* DoF score	7 X 9 X 5=315	17 X 10 X 8=1360
	# samples	9	18
	** MAII score	log2(9/315*10)=-1.8073549220576 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(18/1360*10)=-2.91753783980803 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: HGS [Title/Abstract] AND BAIAP2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	HGS(79658601)-BAIAP2(79089570), # 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)

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	HGS	GO:0046426	negative regulation of JAK-STAT cascade	12444102

Fusion gene breakpoints across HGS (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 BAIAP2 (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	STAD	TCGA-BR-4357-01A	HGS	chr17	79658601	-	BAIAP2	chr17	79089570	+

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Fusion Gene ORF analysis for HGS-BAIAP2

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
5CDS-3UTR	ENST00000329138	ENST00000321300	HGS	chr17	79658601	-	BAIAP2	chr17	79089570	+
5CDS-3UTR	ENST00000329138	ENST00000435091	HGS	chr17	79658601	-	BAIAP2	chr17	79089570	+
5CDS-3UTR	ENST00000329138	ENST00000575245	HGS	chr17	79658601	-	BAIAP2	chr17	79089570	+
5CDS-intron	ENST00000329138	ENST00000321280	HGS	chr17	79658601	-	BAIAP2	chr17	79089570	+
5CDS-intron	ENST00000329138	ENST00000416299	HGS	chr17	79658601	-	BAIAP2	chr17	79089570	+
5CDS-intron	ENST00000329138	ENST00000428708	HGS	chr17	79658601	-	BAIAP2	chr17	79089570	+
5CDS-intron	ENST00000329138	ENST00000573894	HGS	chr17	79658601	-	BAIAP2	chr17	79089570	+
5CDS-intron	ENST00000329138	ENST00000575712	HGS	chr17	79658601	-	BAIAP2	chr17	79089570	+
In-frame	ENST00000329138	ENST00000392411	HGS	chr17	79658601	-	BAIAP2	chr17	79089570	+

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)

ENST00000329138

HGS

chr17

79658601

ENST00000392411

BAIAP2

chr17

79089570

1006

797

962

168

264

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
ENST00000329138	ENST00000392411	HGS	chr17	79658601	-	BAIAP2	chr17	79089570	+	0.002721733	0.9972783

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Fusion Genomic Features for HGS-BAIAP2

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)

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 HGS-BAIAP2

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:79658601/chr17:79089570)
- 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
HGS O14964	BAIAP2 Q6UXY1
FUNCTION: Involved in intracellular signal transduction mediated by cytokines and growth factors. When associated with STAM, it suppresses DNA signaling upon stimulation by IL-2 and GM-CSF. Could be a direct effector of PI3-kinase in vesicular pathway via early endosomes and may regulate trafficking to early and late endosomes by recruiting clathrin. May concentrate ubiquitinated receptors within clathrin-coated regions. Involved in down-regulation of receptor tyrosine kinase via multivesicular body (MVBs) when complexed with STAM (ESCRT-0 complex). The ESCRT-0 complex binds ubiquitin and acts as sorting machinery that recognizes ubiquitinated receptors and transfers them to further sequential lysosomal sorting/trafficking processes. May contribute to the efficient recruitment of SMADs to the activin receptor complex. Involved in receptor recycling via its association with the CART complex, a multiprotein complex required for efficient transferrin receptor recycling but not for EGFR degradation.	FUNCTION: Phosphoinositides-binding protein that induces the formation of planar or gently curved membrane structures. Binds to phosphoinositides, including to phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) headgroups. There seems to be no clear preference for a specific phosphoinositide (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.

- 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

Hgene

HGS

chr17:79658601

chr17:79089570

ENST00000329138

15_143

220

778.0

Domain

VHS

Hgene

HGS

chr17:79658601

chr17:79089570

ENST00000329138

160_220

220

778.0

Zinc finger

FYVE-type

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000321280

132_153

522.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000575712

132_153

513.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000321280

1_250

522.0

Domain

IMD

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000321280

374_437

522.0

Domain

SH3

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000575712

1_250

513.0

Domain

IMD

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000575712

374_437

513.0

Domain

SH3

- 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

Hgene

HGS

chr17:79658601

chr17:79089570

ENST00000329138

346_394

220

778.0

Compositional bias

Note=Pro-rich

Hgene

HGS

chr17:79658601

chr17:79089570

ENST00000329138

505_772

220

778.0

Compositional bias

Note=Gln-rich

Hgene

HGS

chr17:79658601

chr17:79089570

ENST00000329138

258_277

220

778.0

Domain

UIM

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000321300

132_153

511

553.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000428708

132_153

511

535.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000435091

132_153

527

623.6666666666666

Coiled coil

Ontology_term=ECO:0000255

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000321300

1_250

511

553.0

Domain

IMD

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000321300

374_437

511

553.0

Domain

SH3

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000428708

1_250

511

535.0

Domain

IMD

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000428708

374_437

511

535.0

Domain

SH3

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000435091

1_250

527

623.6666666666666

Domain

IMD

Tgene

BAIAP2

chr17:79658601

chr17:79089570

ENST00000435091

374_437

527

623.6666666666666

Domain

SH3

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Fusion Gene Sequence for HGS-BAIAP2

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.

>36247_36247_1_HGS-BAIAP2_HGS_chr17_79658601_ENST00000329138_BAIAP2_chr17_79089570_ENST00000392411_length(transcript)=1006nt_BP=797nt
CCTCGCGGCTCTAGGGCCGGCGCGGTGACGTGCGCGTGCGCGCACTGGAGGGAAAAGGCGGAAGCGGAAGTCGGGGGGCGCGCCAGCTCG
TAGCAGGGGAGCGCCCGCGGCGTCGGGTTTGGGCTGGAGGTCGCCATGGGGCGAGGCAGCGGCACCTTCGAGCGTCTCCTAGACAAGGCG
ACCAGCCAGCTCCTGTTGGAGACAGATTGGGAGTCCATTTTGCAGATCTGCGACCTGATCCGCCAAGGGGACACACAAGCAAAATATGCT
GTGAATTCCATCAAGAAGAAAGTCAACGACAAGAACCCACACGTCGCCTTGTATGCCCTGGAGGTCATGGAATCTGTGGTAAAGAACTGT
GGCCAGACAGTTCATGATGAGGTGGCCAACAAGCAGACCATGGAGGAGCTGAAGGACCTGCTGAAGAGACAAGTGGAGGTAAACGTCCGT
AACAAGATCCTGTACCTGATCCAGGCCTGGGCGCATGCCTTCCGGAACGAGCCCAAGTACAAGGTGGTCCAGGACACCTACCAGATCATG
AAGGTGGAGGGGCACGTCTTTCCAGAATTCAAAGAGAGCGATGCCATGTTTGCTGCCGAGAGAGCCCCAGACTGGGTGGACGCTGAGGAA
TGCCACCGCTGCAGGGTGCAGTTCGGGGTGATGACCCGTAAGCACCACTGCCGGGCGTGTGGGCAGATATTCTGTGGAAAGTGTTCTTCC
AAGTACTCCACCATCCCCAAGTTTGGCATCGAGAAGGAGGTGCGCGTGTGTGAGCCCTGCTACGAGCAGCTGAACAGGAATCCCTTTGCC
CACGTCCAGCTGAAGCCGACAGTGACCAACGACAGGTCTGCCCCCCTCCTCAGCTGATGGCCACATCTGCAGTGCTGCCCATCTGGTGGC
TTCCCCCGCCCTTCCCATGTAGCCTGTTCTGTCATCATCTGTGCGTTCCTGTGTAGAGAACATCCAGGCCCCGGCTGCCTGGTCTTGCCC

>36247_36247_1_HGS-BAIAP2_HGS_chr17_79658601_ENST00000329138_BAIAP2_chr17_79089570_ENST00000392411_length(amino acids)=264AA_BP=0
MFSTQERTDDDRTGYMGRAGEATRWAALQMWPSAEEGGRPVVGHCRLQLDVGKGIPVQLLVAGLTHAHLLLDAKLGDGGVLGRTLSTEYL
PTRPAVVLTGHHPELHPAAVAFLSVHPVWGSLGSKHGIALFEFWKDVPLHLHDLVGVLDHLVLGLVPEGMRPGLDQVQDLVTDVYLHLSL

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

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Fusion Gene PPI Analysis for HGS-BAIAP2

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
Hgene	HGS	chr17:79658601	chr17:79089570	ENST00000329138	-	8	22	480_777	220.66666666666666	778.0	NF2
Hgene	HGS	chr17:79658601	chr17:79089570	ENST00000329138	-	8	22	445_543	220.66666666666666	778.0	SNAP25 and TRAK2
Hgene	HGS	chr17:79658601	chr17:79089570	ENST00000329138	-	8	22	225_543	220.66666666666666	778.0	SNX1
Hgene	HGS	chr17:79658601	chr17:79089570	ENST00000329138	-	8	22	454_572	220.66666666666666	778.0	STAM

- 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 HGS-BAIAP2

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 HGS-BAIAP2

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source