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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:FKBP1A-CDS2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: FKBP1A-CDS2
	FusionPDB ID: 30463
	FusionGDB2.0 ID: 30463
		Hgene	Tgene
	Gene symbol	FKBP1A	CDS2
	Gene ID	2280	8760
	Gene name	FKBP prolyl isomerase 1A	CDP-diacylglycerol synthase 2
	Synonyms	FKBP-12\|FKBP-1A\|FKBP1\|FKBP12\|PKC12\|PKCI2\|PPIASE	-
	Cytomap	20p13	20p12.3
	Type of gene	protein-coding	protein-coding
	Description	peptidyl-prolyl cis-trans isomerase FKBP1A12 kDa FK506-binding protein12 kDa FKBPFK506 binding protein 1A, 12kDaFK506 binding protein12FK506-binding protein 1FK506-binding protein 12FK506-binding protein 1AFK506-binding protein, T-cell, 12-kDFKBP	phosphatidate cytidylyltransferase 2CDP-DAG synthase 2CDP-DG synthase 2CDP-DG synthetase 2CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2CDP-diglyceride diphosphorylase 2CDP-diglyceride pyrophosphorylase 2CDP-diglyceride synthase
	Modification date	20200313	20200327
	UniProtAcc	P62942	O95674
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000381715, ENST00000381719, ENST00000381724, ENST00000400137, ENST00000439640, ENST00000460490,	ENST00000379070, ENST00000535100, ENST00000379062, ENST00000460006,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 6 X 5=180	10 X 11 X 7=770
	# samples	7	13
	** MAII score	log2(7/180*10)=-1.36257007938471 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(13/770*10)=-2.56634682255381 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: FKBP1A [Title/Abstract] AND CDS2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	FKBP1A(1373478)-CDS2(5169713), # samples:3
Anticipated loss of major functional domain due to fusion event.	FKBP1A-CDS2 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. FKBP1A-CDS2 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. FKBP1A-CDS2 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. FKBP1A-CDS2 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene 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)

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	FKBP1A	GO:0000413	protein peptidyl-prolyl isomerization	1696686
Hgene	FKBP1A	GO:0007183	SMAD protein complex assembly	16720724
Hgene	FKBP1A	GO:0031398	positive regulation of protein ubiquitination	16720724
Hgene	FKBP1A	GO:0032092	positive regulation of protein binding	18346205
Hgene	FKBP1A	GO:0032515	negative regulation of phosphoprotein phosphatase activity	7592869
Hgene	FKBP1A	GO:0032925	regulation of activin receptor signaling pathway	16720724
Hgene	FKBP1A	GO:0051280	negative regulation of release of sequestered calcium ion into cytosol	12443530
Hgene	FKBP1A	GO:0060314	regulation of ryanodine-sensitive calcium-release channel activity	7592869
Hgene	FKBP1A	GO:0060315	negative regulation of ryanodine-sensitive calcium-release channel activity	12443530
Hgene	FKBP1A	GO:0097435	supramolecular fiber organization	18346205
Hgene	FKBP1A	GO:1990000	amyloid fibril formation	18346205

Fusion gene breakpoints across FKBP1A (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 CDS2 (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	HNSC	TCGA-CV-6937-01A	FKBP1A	chr20	1373478	-	CDS2	chr20	5169713	+
ChimerDB4	HNSC	TCGA-CV-6937	FKBP1A	chr20	1373477	-	CDS2	chr20	5169712	+
ChimerDB4	HNSC	TCGA-CV-6937	FKBP1A	chr20	1373478	-	CDS2	chr20	5169713	+

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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)
ENST00000400137	FKBP1A	chr20	1373478	-	ENST00000460006	CDS2	chr20	5169713	+	8259	249	503	0	168
ENST00000400137	FKBP1A	chr20	1373478	-	ENST00000379062	CDS2	chr20	5169713	+	736	249	503	0	168
ENST00000381724	FKBP1A	chr20	1373478	-	ENST00000460006	CDS2	chr20	5169713	+	8215	205	7519	7938	139
ENST00000381724	FKBP1A	chr20	1373478	-	ENST00000379062	CDS2	chr20	5169713	+	692	205	145	561	138
ENST00000381715	FKBP1A	chr20	1373478	-	ENST00000460006	CDS2	chr20	5169713	+	8139	129	7443	7862	139
ENST00000381715	FKBP1A	chr20	1373478	-	ENST00000379062	CDS2	chr20	5169713	+	616	129	69	485	138
ENST00000400137	FKBP1A	chr20	1373477	-	ENST00000460006	CDS2	chr20	5169712	+	8259	249	503	0	168
ENST00000400137	FKBP1A	chr20	1373477	-	ENST00000379062	CDS2	chr20	5169712	+	736	249	503	0	168
ENST00000381724	FKBP1A	chr20	1373477	-	ENST00000460006	CDS2	chr20	5169712	+	8215	205	7519	7938	139
ENST00000381724	FKBP1A	chr20	1373477	-	ENST00000379062	CDS2	chr20	5169712	+	692	205	145	561	138
ENST00000381715	FKBP1A	chr20	1373477	-	ENST00000460006	CDS2	chr20	5169712	+	8139	129	7443	7862	139
ENST00000381715	FKBP1A	chr20	1373477	-	ENST00000379062	CDS2	chr20	5169712	+	616	129	69	485	138

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
ENST00000400137	ENST00000460006	FKBP1A	chr20	1373478	-	CDS2	chr20	5169713	+	0.63490695	0.365093
ENST00000400137	ENST00000379062	FKBP1A	chr20	1373478	-	CDS2	chr20	5169713	+	0.02750951	0.97249055
ENST00000381724	ENST00000460006	FKBP1A	chr20	1373478	-	CDS2	chr20	5169713	+	0.63171375	0.3682862
ENST00000381724	ENST00000379062	FKBP1A	chr20	1373478	-	CDS2	chr20	5169713	+	0.027346047	0.9726539
ENST00000381715	ENST00000460006	FKBP1A	chr20	1373478	-	CDS2	chr20	5169713	+	0.6335957	0.3664043
ENST00000381715	ENST00000379062	FKBP1A	chr20	1373478	-	CDS2	chr20	5169713	+	0.02025719	0.9797428
ENST00000400137	ENST00000460006	FKBP1A	chr20	1373477	-	CDS2	chr20	5169712	+	0.63490695	0.365093
ENST00000400137	ENST00000379062	FKBP1A	chr20	1373477	-	CDS2	chr20	5169712	+	0.02750951	0.97249055
ENST00000381724	ENST00000460006	FKBP1A	chr20	1373477	-	CDS2	chr20	5169712	+	0.63171375	0.3682862
ENST00000381724	ENST00000379062	FKBP1A	chr20	1373477	-	CDS2	chr20	5169712	+	0.027346047	0.9726539
ENST00000381715	ENST00000460006	FKBP1A	chr20	1373477	-	CDS2	chr20	5169712	+	0.6335957	0.3664043
ENST00000381715	ENST00000379062	FKBP1A	chr20	1373477	-	CDS2	chr20	5169712	+	0.02025719	0.9797428

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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

>30463_30463_1_FKBP1A-CDS2_FKBP1A_chr20_1373477_ENST00000381715_CDS2_chr20_5169712_ENST00000379062_length(amino acids)=138AA_BP=20
MSPQGAPSPSAARPAWCTTPKTVRMYPFQIHSIALSTFASLIGPFGGFFASGFKRAFKIKDFANTIPGHGGIMDRFDCQYLMATFVNVYI

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

>30463_30463_2_FKBP1A-CDS2_FKBP1A_chr20_1373477_ENST00000381715_CDS2_chr20_5169712_ENST00000460006_length(amino acids)=139AA_BP=
MGSPSVEGSWEPWWFFFFFWFFFFDRAVDILLNSILRICLTKKFPNTERASPPALGSCLCWECQASHGTHHCQCLCLPEVSRVCPGSVSS

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

>30463_30463_3_FKBP1A-CDS2_FKBP1A_chr20_1373477_ENST00000381724_CDS2_chr20_5169712_ENST00000379062_length(amino acids)=138AA_BP=20
MSPQGAPSPSAARPAWCTTPKTVRMYPFQIHSIALSTFASLIGPFGGFFASGFKRAFKIKDFANTIPGHGGIMDRFDCQYLMATFVNVYI

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

>30463_30463_4_FKBP1A-CDS2_FKBP1A_chr20_1373477_ENST00000381724_CDS2_chr20_5169712_ENST00000460006_length(amino acids)=139AA_BP=
MGSPSVEGSWEPWWFFFFFWFFFFDRAVDILLNSILRICLTKKFPNTERASPPALGSCLCWECQASHGTHHCQCLCLPEVSRVCPGSVSS

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

>30463_30463_5_FKBP1A-CDS2_FKBP1A_chr20_1373477_ENST00000400137_CDS2_chr20_5169712_ENST00000379062_length(amino acids)=168AA_BP=1
MLNQFAWVRASDKTGDVYIDKGGHQILAVKAIHDASMARNGIGKVFDFKGSFESTCEESSKGANERGKGGESDAVNLEGVHPDRFRCSAP

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

>30463_30463_6_FKBP1A-CDS2_FKBP1A_chr20_1373477_ENST00000400137_CDS2_chr20_5169712_ENST00000460006_length(amino acids)=168AA_BP=1
MLNQFAWVRASDKTGDVYIDKGGHQILAVKAIHDASMARNGIGKVFDFKGSFESTCEESSKGANERGKGGESDAVNLEGVHPDRFRCSAP

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

>30463_30463_7_FKBP1A-CDS2_FKBP1A_chr20_1373478_ENST00000381715_CDS2_chr20_5169713_ENST00000379062_length(amino acids)=138AA_BP=20
MSPQGAPSPSAARPAWCTTPKTVRMYPFQIHSIALSTFASLIGPFGGFFASGFKRAFKIKDFANTIPGHGGIMDRFDCQYLMATFVNVYI

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

>30463_30463_8_FKBP1A-CDS2_FKBP1A_chr20_1373478_ENST00000381715_CDS2_chr20_5169713_ENST00000460006_length(amino acids)=139AA_BP=
MGSPSVEGSWEPWWFFFFFWFFFFDRAVDILLNSILRICLTKKFPNTERASPPALGSCLCWECQASHGTHHCQCLCLPEVSRVCPGSVSS

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

>30463_30463_9_FKBP1A-CDS2_FKBP1A_chr20_1373478_ENST00000381724_CDS2_chr20_5169713_ENST00000379062_length(amino acids)=138AA_BP=20
MSPQGAPSPSAARPAWCTTPKTVRMYPFQIHSIALSTFASLIGPFGGFFASGFKRAFKIKDFANTIPGHGGIMDRFDCQYLMATFVNVYI

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

>30463_30463_10_FKBP1A-CDS2_FKBP1A_chr20_1373478_ENST00000381724_CDS2_chr20_5169713_ENST00000460006_length(amino acids)=139AA_BP=
MGSPSVEGSWEPWWFFFFFWFFFFDRAVDILLNSILRICLTKKFPNTERASPPALGSCLCWECQASHGTHHCQCLCLPEVSRVCPGSVSS

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

>30463_30463_11_FKBP1A-CDS2_FKBP1A_chr20_1373478_ENST00000400137_CDS2_chr20_5169713_ENST00000379062_length(amino acids)=168AA_BP=1
MLNQFAWVRASDKTGDVYIDKGGHQILAVKAIHDASMARNGIGKVFDFKGSFESTCEESSKGANERGKGGESDAVNLEGVHPDRFRCSAP

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

>30463_30463_12_FKBP1A-CDS2_FKBP1A_chr20_1373478_ENST00000400137_CDS2_chr20_5169713_ENST00000460006_length(amino acids)=168AA_BP=1
MLNQFAWVRASDKTGDVYIDKGGHQILAVKAIHDASMARNGIGKVFDFKGSFESTCEESSKGANERGKGGESDAVNLEGVHPDRFRCSAP

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

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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/chr20:1373478/chr20:5169713)
- 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
FKBP1A P62942	CDS2 O95674
FUNCTION: Keeps in an inactive conformation TGFBR1, the TGF-beta type I serine/threonine kinase receptor, preventing TGF-beta receptor activation in absence of ligand. Recruits SMAD7 to ACVR1B which prevents the association of SMAD2 and SMAD3 with the activin receptor complex, thereby blocking the activin signal. May modulate the RYR1 calcium channel activity. PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. {ECO:0000269\|PubMed:16720724, ECO:0000269\|PubMed:1696686, ECO:0000269\|PubMed:1701173, ECO:0000269\|PubMed:9233797}.	FUNCTION: Catalyzes the conversion of phosphatidic acid (PA) to CDP-diacylglycerol (CDP-DAG), an essential intermediate in the synthesis of phosphatidylglycerol, cardiolipin and phosphatidylinositol (PubMed:25375833). Exhibits specificity for the nature of the acyl chains at the sn-1 and sn-2 positions in the substrate, PA and the preferred acyl chain composition is 1-stearoyl-2-arachidonoyl-sn-phosphatidic acid (PubMed:25375833). Plays an important role in regulating the growth and maturation of lipid droplets which are storage organelles at the center of lipid and energy homeostasis (PubMed:26946540, PubMed:31548309). {ECO:0000269\|PubMed:25375833, ECO:0000269\|PubMed:26946540, ECO:0000269\|PubMed:31548309}.

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

CDS2

chr20:1373477

chr20:5169712

ENST00000460006

340_360

327.0

446.0

Transmembrane

Helical

Tgene

CDS2

chr20:1373478

chr20:5169713

ENST00000460006

340_360

327.0

446.0

Transmembrane

Helical

- 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

FKBP1A

chr20:1373477

chr20:5169712

ENST00000381719

20_108

28.333333333333332

109.0

Domain

PPIase FKBP-type

Hgene

FKBP1A

chr20:1373477

chr20:5169712

ENST00000400137

20_108

28.333333333333332

446.0

Domain

PPIase FKBP-type

Hgene

FKBP1A

chr20:1373478

chr20:5169713

ENST00000381719

20_108

28.333333333333332

109.0

Domain

PPIase FKBP-type

Hgene

FKBP1A

chr20:1373478

chr20:5169713

ENST00000400137

20_108

28.333333333333332

446.0

Domain

PPIase FKBP-type

Tgene

CDS2

chr20:1373477

chr20:5169712

ENST00000460006

132_152

327.0

446.0

Transmembrane

Helical

Tgene

CDS2

chr20:1373477

chr20:5169712

ENST00000460006

166_186

327.0

446.0

Transmembrane

Helical

Tgene

CDS2

chr20:1373477

chr20:5169712

ENST00000460006

213_233

327.0

446.0

Transmembrane

Helical

Tgene

CDS2

chr20:1373477

chr20:5169712

ENST00000460006

262_282

327.0

446.0

Transmembrane

Helical

Tgene

CDS2

chr20:1373477

chr20:5169712

ENST00000460006

79_99

327.0

446.0

Transmembrane

Helical

Tgene

CDS2

chr20:1373478

chr20:5169713

ENST00000460006

132_152

327.0

446.0

Transmembrane

Helical

Tgene

CDS2

chr20:1373478

chr20:5169713

ENST00000460006

166_186

327.0

446.0

Transmembrane

Helical

Tgene

CDS2

chr20:1373478

chr20:5169713

ENST00000460006

213_233

327.0

446.0

Transmembrane

Helical

Tgene

CDS2

chr20:1373478

chr20:5169713

ENST00000460006

262_282

327.0

446.0

Transmembrane

Helical

Tgene

CDS2

chr20:1373478

chr20:5169713

ENST00000460006

79_99

327.0

446.0

Transmembrane

Helical

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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 >>>177_FKBP1A_1373478_CDS2_5169713_ranked_0.pdb	FKBP1A	1373477	1373478	ENST00000379062	CDS2	chr20	5169713	+	MLNQFAWVRASDKTGDVYIDKGGHQILAVKAIHDASMARNGIGKVFDFKGSFESTCEESSKGANERGKGGESDAVNLEGVHPDRFRCSAP	168

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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.

FKBP1A_pLDDT.png

CDS2_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
FKBP1A
CDS2

- 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

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Related Drugs to FKBP1A-CDS2

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 FKBP1A-CDS2

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