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	Kinase Fusion Gene Summary
	Kinase Fusion Gene Sample Information
	Kinase Fusion ORF Analysis
	Kinase Fusion Amino Acid Sequences
	Multiple Sequence Alignment of All Fusion Protein Isoforms
	Kinase Fusion Protein Functional Features
	Kinase Fusion Protein Structures
	Comparison of Fusion Protein Isoforms
	Comparison of Fusion Protein Sequences/Structures with Known Sequences/Structures from PDB
	pLDDT Scores and Difference Analysis of pLDDT Scores Between the Active Sites (Best) and Non-Active Sites.
	Ramachandran Plot of Kinase Fusion Protein Structure
	Potential Active Site Information
	Virtual Screening Results
	Kinase-Substrate Information
	Related Drugs with This Kinase Fusion Protein
	Related Disease with This Kinase Fusion Protein
	Clinical Trials of the Found Drugs/Small Molecules

Kinase Fusion Gene:ATE1_FGFR2

Kinase Fusion Protein Summary

Kinase Fusion gene summary

Kinase Fusion partner gene information	Kinase Fusion gene name: ATE1_FGFR2
	KinaseFusionDB ID: KFG465
	FusionGDB2.0 ID: KFG465
		Hgene	Tgene
	Gene symbol	ATE1	FGFR2
	Gene ID	11101	2263
	Gene name	arginyltransferase 1	fibroblast growth factor receptor 2
	Synonyms	-	BBDS\|BEK\|BFR-1\|CD332\|CEK3\|CFD1\|ECT1\|JWS\|K-SAM\|KGFR\|TK14\|TK25
	Cytomap	10q26.13	10q26.13
	Type of gene	protein-coding	protein-coding
	Description	arginyl-tRNA--protein transferase 1R-transferase 1arginine-tRNA--protein transferase 1arginyl-tRNA-protein transferase	fibroblast growth factor receptor 2BEK fibroblast growth factor receptorbacteria-expressed kinasekeratinocyte growth factor receptorprotein tyrosine kinase, receptor like 14
	Modification date	20240407	20240416
	UniProtAcc	O95260	P21802
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000224652, ENST00000369040, ENST00000369043, ENST00000535655, ENST00000540606, ENST00000543447, ENST00000481784,	ENST00000359354, ENST00000478859, ENST00000490349, ENST00000346997, ENST00000351936, ENST00000356226, ENST00000357555, ENST00000358487, ENST00000360144, ENST00000369056, ENST00000369059, ENST00000369060, ENST00000369061, ENST00000457416,
Context (manual curation of fusion genes in KinaseFusionDB)	PubMed: ATE1 [Title/Abstract] AND FGFR2 [Title/Abstract] AND fusion [Title/Abstract] Molecular heterogeneity in the novel fusion gene APIP-FGFR2: Diversity of genomic breakpoints in gastric cancer with high-level amplifications at 11p13 and 10q26 (pmid: 28123544)
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	FGFR2(123298106)-ATE1(123503373), # samples:2 FGFR2(123353223)-ATE1(123503373), # samples:2 ATE1(123549684)-FGFR2(123263455), # samples:1

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	FGFR2	GO:0008284	positive regulation of cell population proliferation	8663044
Tgene	FGFR2	GO:0008543	fibroblast growth factor receptor signaling pathway	8663044\|15629145
Tgene	FGFR2	GO:0018108	peptidyl-tyrosine phosphorylation	15629145\|16844695
Tgene	FGFR2	GO:0046777	protein autophosphorylation	15629145

Kinase Fusion gene breakpoints across ATE1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Kinase Fusion gene breakpoints across FGFR2 (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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Kinase Fusion Gene Sample Information

Kinase Fusion gene information.

Kinase Fusion gene information from four resources (ChiTars 5.0, ChimerDB 4.0, COSMIC, and CCLE)
* 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	Sample	Hgene	Hchr	Hbp	Tgene	Tchr	Tbp
ChimerDB4	TCGA-BR-8080-01A	ATE1	chr10	123549684	FGFR2	chr10	123263455

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Kinase Fusion ORF Analysis

Kinase Fusion information from ORFfinder translation from full-length transcript sequence from KinaseFusionDB.

Henst

Tenst

Hgene

Hchr

Hbp

Tgene

Tchr

Tbp

Seq length
(transcript)

Seq length
(amino acids)

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Kinase Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from KinaseFusionDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>Henst_Tenst_Hgene_Hchr_Hbp_Tgene_Tchr_Tbp_length(fusion AA)_AAseq

Multiple Sequence Alignment of All Fusion Protein Isoforms

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Kinase 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/:123298106/:123503373)
- 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
ATE1 O95260	FGFR2 P21802
FUNCTION: Involved in the post-translational conjugation of arginine to the N-terminal aspartate or glutamate of a protein. This arginylation is required for degradation of the protein via the ubiquitin pathway. Does not arginylate cysteine residues. {ECO:0000250\|UniProtKB:Q9Z2A5}.	FUNCTION: Tyrosine-protein kinase that acts as a cell-surface receptor for fibroblast growth factors and plays an essential role in the regulation of cell proliferation, differentiation, migration and apoptosis, and in the regulation of embryonic development. Required for normal embryonic patterning, trophoblast function, limb bud development, lung morphogenesis, osteogenesis and skin development. Plays an essential role in the regulation of osteoblast differentiation, proliferation and apoptosis, and is required for normal skeleton development. Promotes cell proliferation in keratinocytes and immature osteoblasts, but promotes apoptosis in differentiated osteoblasts. Phosphorylates PLCG1, FRS2 and PAK4. Ligand binding leads to the activation of several signaling cascades. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate. Phosphorylation of FRS2 triggers recruitment of GRB2, GAB1, PIK3R1 and SOS1, and mediates activation of RAS, MAPK1/ERK2, MAPK3/ERK1 and the MAP kinase signaling pathway, as well as of the AKT1 signaling pathway. FGFR2 signaling is down-regulated by ubiquitination, internalization and degradation. Mutations that lead to constitutive kinase activation or impair normal FGFR2 maturation, internalization and degradation lead to aberrant signaling. Over-expressed FGFR2 promotes activation of STAT1. {ECO:0000269\|PubMed:12529371, ECO:0000269\|PubMed:15190072, ECO:0000269\|PubMed:15629145, ECO:0000269\|PubMed:16384934, ECO:0000269\|PubMed:16597617, ECO:0000269\|PubMed:17311277, ECO:0000269\|PubMed:17623664, ECO:0000269\|PubMed:18374639, ECO:0000269\|PubMed:19103595, ECO:0000269\|PubMed:19387476, ECO:0000269\|PubMed:19410646, ECO:0000269\|PubMed:21596750, ECO:0000269\|PubMed:8663044}.

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 domain in the 5'-partner of fusion protein (protein functional feature from UniProt).

Partner

Hgeneene

Hbp

Tgeneene

Tbp

ENST

BPexon

TotalExon

Protein feature loci

BPloci

TotalLen

Feature

Note

- Retained domain in the 3'-partner of fusion protein (protein functional feature from UniProt).

Partner

Hgeneene

Hbp

Tgeneene

Tbp

ENST

BPexon

TotalExon

Protein feature loci

BPloci

TotalLen

Feature

Note

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Kinase-Substrate Information of ATE1_FGFR2

Phosphorylation target of the kinase
(phosphosite, 03-17-2024)

Kinase	Kinase UniProt Acc	Kinase species	Substrate	Substrate UniProt Acc	Substrate phosphorylated residues	Substrate phosphorylated sites (+/-7AA)	Domain
FGFR2	P21802	human	FGFR2	P21802	Y769	TLTTNEEyLDLSQPL
FGFR2	P21802	human	CTNNB1	P35222	Y142	AVVNLINyQDDAELA
FGFR2	P21802	human	PTEN	P60484	Y240	RREDKFMyFEFPQPL	PTEN_C2
FGFR2	P21802	human	GLO1	Q04760	Y136	GIAVPDVysACkRFE	Glyoxalase
FGFR2	P21802	human	TFRC	P02786	Y20	FGGEPLsytRFsLAR
FGFR2	P21802	human	GRB2	P62993	Y160	QVPQQPtyVQALFDF

Biological Network Integration of This Kinase and Substrates
(GeneMANIA website)

Enriched GO biological processes of the phosphorylation target genes of the kinase

Kinase	GOID	GO term	P.adjust
FGFR2	ID	Description	0.00e+00
FGFR2	GO:0008543	fibroblast growth factor receptor signaling pathway	7.81e-04
FGFR2	GO:0030316	osteoclast differentiation	7.81e-04
FGFR2	GO:0044344	cellular response to fibroblast growth factor stimulus	7.81e-04
FGFR2	GO:0060742	epithelial cell differentiation involved in prostate gland development	7.81e-04
FGFR2	GO:0021761	limbic system development	7.81e-04
FGFR2	GO:0071774	response to fibroblast growth factor	7.81e-04
FGFR2	GO:0001704	formation of primary germ layer	7.81e-04
FGFR2	GO:0060670	branching involved in labyrinthine layer morphogenesis	7.81e-04
FGFR2	GO:0060572	morphogenesis of an epithelial bud	9.34e-04
FGFR2	GO:0097091	synaptic vesicle clustering	9.61e-04
FGFR2	GO:0048660	regulation of smooth muscle cell proliferation	1.18e-03
FGFR2	GO:0048659	smooth muscle cell proliferation	1.18e-03
FGFR2	GO:0001837	epithelial to mesenchymal transition	1.18e-03
FGFR2	GO:0061138	morphogenesis of a branching epithelium	1.23e-03
FGFR2	GO:0060713	labyrinthine layer morphogenesis	1.23e-03
FGFR2	GO:0007369	gastrulation	1.26e-03
FGFR2	GO:0060571	morphogenesis of an epithelial fold	1.26e-03
FGFR2	GO:0001763	morphogenesis of a branching structure	1.26e-03
FGFR2	GO:0002053	positive regulation of mesenchymal cell proliferation	1.26e-03
FGFR2	GO:0060669	embryonic placenta morphogenesis	1.40e-03
FGFR2	GO:0060441	epithelial tube branching involved in lung morphogenesis	1.61e-03
FGFR2	GO:0002573	myeloid leukocyte differentiation	1.61e-03
FGFR2	GO:0051091	positive regulation of DNA-binding transcription factor activity	1.62e-03
FGFR2	GO:0010464	regulation of mesenchymal cell proliferation	1.62e-03
FGFR2	GO:0033002	muscle cell proliferation	1.62e-03
FGFR2	GO:0031069	hair follicle morphogenesis	1.62e-03
FGFR2	GO:0048762	mesenchymal cell differentiation	1.80e-03
FGFR2	GO:0010092	specification of animal organ identity	1.80e-03
FGFR2	GO:0048730	epidermis morphogenesis	1.83e-03
FGFR2	GO:0010463	mesenchymal cell proliferation	2.43e-03
FGFR2	GO:0060428	lung epithelium development	2.43e-03
FGFR2	GO:0060711	labyrinthine layer development	2.58e-03
FGFR2	GO:0060070	canonical Wnt signaling pathway	2.59e-03
FGFR2	GO:0035987	endodermal cell differentiation	2.62e-03
FGFR2	GO:0048546	digestive tract morphogenesis	2.62e-03
FGFR2	GO:0060485	mesenchyme development	2.62e-03
FGFR2	GO:0030850	prostate gland development	2.64e-03
FGFR2	GO:0060688	regulation of morphogenesis of a branching structure	2.78e-03
FGFR2	GO:0060425	lung morphogenesis	2.85e-03
FGFR2	GO:0097479	synaptic vesicle localization	2.85e-03
FGFR2	GO:0001706	endoderm formation	3.21e-03
FGFR2	GO:0001701	in utero embryonic development	3.84e-03
FGFR2	GO:0045453	bone resorption	3.84e-03
FGFR2	GO:0001655	urogenital system development	3.84e-03
FGFR2	GO:0048645	animal organ formation	3.84e-03
FGFR2	GO:0051090	regulation of DNA-binding transcription factor activity	3.84e-03
FGFR2	GO:0030900	forebrain development	3.84e-03
FGFR2	GO:0051347	positive regulation of transferase activity	3.96e-03
FGFR2	GO:1904888	cranial skeletal system development	4.12e-03

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Related Drugs to ATE1_FGFR2

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

Hgene

Tgene

Drug

Source

PMID

Distribution of the number of studies mentioning ATE1-FGFR2 and kinase inhibitors the PubMed Abstract (04-01-2024)

Fusion gene - drug pair 1

Fusion gene - drug pair 2

PMID

Publication date

DOI

Study title

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Related Diseases to ATE1_FGFR2

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

Hgene

Tgene

Disease

Source

PMID

Related diseases from the literature mentioned this fusion gene and drug.
(PubMed, 04-01-2024)

MeSH ID

MeSH term

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Tgene	FGFR2	C2931196	Craniofacial dysostosis type 1	23	CTD_human;GENOMICS_ENGLAND;UNIPROT
Tgene	FGFR2	C0220658	Pfeiffer Syndrome	21	CTD_human;GENOMICS_ENGLAND;UNIPROT
Tgene	FGFR2	C0001193	Apert syndrome	19	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	FGFR2	C0795998	JACKSON-WEISS SYNDROME	10	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	FGFR2	C0175699	Saethre-Chotzen Syndrome	8	CTD_human;GENOMICS_ENGLAND;ORPHANET
Tgene	FGFR2	C1852406	Cutis Gyrata Syndrome of Beare And Stevenson	8	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	FGFR2	C2936791	Antley-Bixler Syndrome, Autosomal Dominant	7	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	FGFR2	C1510455	Acrocephalosyndactylia	6	CTD_human;ORPHANET
Tgene	FGFR2	C0265269	Lacrimoauriculodentodigital syndrome	5	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	FGFR2	C0010278	Craniosynostosis	4	CTD_human;GENOMICS_ENGLAND
Tgene	FGFR2	C1863389	Apert-Crouzon Disease	4	CTD_human
Tgene	FGFR2	C1865070	SCAPHOCEPHALY, MAXILLARY RETRUSION, AND MENTAL RETARDATION	4	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	FGFR2	C0006142	Malignant neoplasm of breast	3	CTD_human;UNIPROT
Tgene	FGFR2	C0030044	Acrocephaly	3	CTD_human
Tgene	FGFR2	C0036341	Schizophrenia	3	PSYGENET
Tgene	FGFR2	C0221356	Brachycephaly	3	CTD_human
Tgene	FGFR2	C0265534	Scaphycephaly	3	CTD_human
Tgene	FGFR2	C0265535	Trigonocephaly	3	CTD_human
Tgene	FGFR2	C0376634	Craniofacial Abnormalities	3	CTD_human
Tgene	FGFR2	C0678222	Breast Carcinoma	3	CTD_human
Tgene	FGFR2	C1257931	Mammary Neoplasms, Human	3	CTD_human
Tgene	FGFR2	C1458155	Mammary Neoplasms	3	CTD_human
Tgene	FGFR2	C1833340	Synostotic Posterior Plagiocephaly	3	CTD_human
Tgene	FGFR2	C1860819	Metopic synostosis	3	CTD_human
Tgene	FGFR2	C2931150	Synostotic Anterior Plagiocephaly	3	CTD_human
Tgene	FGFR2	C3281247	BENT BONE DYSPLASIA SYNDROME	3	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	FGFR2	C4551902	Craniosynostosis, Type 1	3	CTD_human
Tgene	FGFR2	C4704874	Mammary Carcinoma, Human	3	CTD_human
Tgene	FGFR2	C0008925	Cleft Palate	2	CTD_human
Tgene	FGFR2	C0011570	Mental Depression	2	PSYGENET
Tgene	FGFR2	C0011581	Depressive disorder	2	PSYGENET
Tgene	FGFR2	C0024623	Malignant neoplasm of stomach	2	CGI;CTD_human
Tgene	FGFR2	C0038356	Stomach Neoplasms	2	CGI;CTD_human
Tgene	FGFR2	C1708349	Hereditary Diffuse Gastric Cancer	2	CTD_human
Tgene	FGFR2	C1837218	Cleft palate, isolated	2	CTD_human

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Clinical Trials of the Found Drugs/Small Molecules

Statistics of the Clinical Trials of the Found Kinase Inibitors from clinicaltrials.gov (06-17-2024)

Clinical Trials from clinicaltrials.gov (06-17-2024)

Fusion Gene

Kinase Inhibitor

NCT ID

Study Status

Phases

Disease

# Enrolment

Date