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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:CBFB-NUTF2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CBFB-NUTF2
	FusionPDB ID: 13375
	FusionGDB2.0 ID: 13375
		Hgene	Tgene
	Gene symbol	CBFB	NUTF2
	Gene ID	865	10204
	Gene name	core-binding factor subunit beta	nuclear transport factor 2
	Synonyms	PEBP2B	NTF-2\|NTF2\|PP15
	Cytomap	16q22.1	16q22.1
	Type of gene	protein-coding	protein-coding
	Description	core-binding factor subunit betaCBF-betaPEA2-betaPEBP2-betaSL3-3 enhancer factor 1 beta subunitSL3-3 enhancer factor 1 subunit betaSL3/AKV core-binding factor beta subunitcore-binding factor beta subunitpolyomavirus enhancer binding protein 2, bet	nuclear transport factor 2placental protein 15
	Modification date	20200320	20200313
	UniProtAcc	Q13951	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000561924, ENST00000290858, ENST00000412916, ENST00000568858,	ENST00000219169, ENST00000568396, ENST00000569436,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	17 X 18 X 12=3672	12 X 9 X 6=648
	# samples	33	15
	** MAII score	log2(33/3672*10)=-3.47602812916799 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(15/648*10)=-2.11103131238874 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: CBFB [Title/Abstract] AND NUTF2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CBFB(67070658)-NUTF2(67902243), # samples:2
Anticipated loss of major functional domain due to fusion event.	CBFB-NUTF2 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. CBFB-NUTF2 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
Tgene	NUTF2	GO:0006606	protein import into nucleus	7744965\|10679025
Tgene	NUTF2	GO:0006611	protein export from nucleus	16449645

Fusion gene breakpoints across CBFB (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 NUTF2 (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	LUAD	TCGA-78-8660-01A	CBFB	chr16	67070658	+	NUTF2	chr16	67902243	+
ChimerDB4	LUAD	TCGA-78-8660	CBFB	chr16	67070658	+	NUTF2	chr16	67902242	+

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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)
ENST00000290858	CBFB	chr16	67070658	+	ENST00000219169	NUTF2	chr16	67902243	+	2482	543	261	827	188
ENST00000290858	CBFB	chr16	67070658	+	ENST00000569436	NUTF2	chr16	67902243	+	1238	543	261	827	188
ENST00000290858	CBFB	chr16	67070658	+	ENST00000568396	NUTF2	chr16	67902243	+	1238	543	261	827	188
ENST00000412916	CBFB	chr16	67070658	+	ENST00000219169	NUTF2	chr16	67902243	+	2384	445	163	729	188
ENST00000412916	CBFB	chr16	67070658	+	ENST00000569436	NUTF2	chr16	67902243	+	1140	445	163	729	188
ENST00000412916	CBFB	chr16	67070658	+	ENST00000568396	NUTF2	chr16	67902243	+	1140	445	163	729	188
ENST00000290858	CBFB	chr16	67070658	+	ENST00000219169	NUTF2	chr16	67902242	+	2482	543	261	827	188
ENST00000290858	CBFB	chr16	67070658	+	ENST00000569436	NUTF2	chr16	67902242	+	1238	543	261	827	188
ENST00000290858	CBFB	chr16	67070658	+	ENST00000568396	NUTF2	chr16	67902242	+	1238	543	261	827	188
ENST00000412916	CBFB	chr16	67070658	+	ENST00000219169	NUTF2	chr16	67902242	+	2384	445	163	729	188
ENST00000412916	CBFB	chr16	67070658	+	ENST00000569436	NUTF2	chr16	67902242	+	1140	445	163	729	188
ENST00000412916	CBFB	chr16	67070658	+	ENST00000568396	NUTF2	chr16	67902242	+	1140	445	163	729	188

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
ENST00000290858	ENST00000219169	CBFB	chr16	67070658	+	NUTF2	chr16	67902243	+	0.004257829	0.99574214
ENST00000290858	ENST00000569436	CBFB	chr16	67070658	+	NUTF2	chr16	67902243	+	0.005475971	0.994524
ENST00000290858	ENST00000568396	CBFB	chr16	67070658	+	NUTF2	chr16	67902243	+	0.005475971	0.994524
ENST00000412916	ENST00000219169	CBFB	chr16	67070658	+	NUTF2	chr16	67902243	+	0.005038908	0.99496114
ENST00000412916	ENST00000569436	CBFB	chr16	67070658	+	NUTF2	chr16	67902243	+	0.004547407	0.9954526
ENST00000412916	ENST00000568396	CBFB	chr16	67070658	+	NUTF2	chr16	67902243	+	0.004547407	0.9954526
ENST00000290858	ENST00000219169	CBFB	chr16	67070658	+	NUTF2	chr16	67902242	+	0.004257829	0.99574214
ENST00000290858	ENST00000569436	CBFB	chr16	67070658	+	NUTF2	chr16	67902242	+	0.005475971	0.994524
ENST00000290858	ENST00000568396	CBFB	chr16	67070658	+	NUTF2	chr16	67902242	+	0.005475971	0.994524
ENST00000412916	ENST00000219169	CBFB	chr16	67070658	+	NUTF2	chr16	67902242	+	0.005038908	0.99496114
ENST00000412916	ENST00000569436	CBFB	chr16	67070658	+	NUTF2	chr16	67902242	+	0.004547407	0.9954526
ENST00000412916	ENST00000568396	CBFB	chr16	67070658	+	NUTF2	chr16	67902242	+	0.004547407	0.9954526

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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

>13375_13375_1_CBFB-NUTF2_CBFB_chr16_67070658_ENST00000290858_NUTF2_chr16_67902242_ENST00000219169_length(amino acids)=188AA_BP=94
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLER
EAGKIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMF

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

>13375_13375_2_CBFB-NUTF2_CBFB_chr16_67070658_ENST00000290858_NUTF2_chr16_67902242_ENST00000568396_length(amino acids)=188AA_BP=94
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLER
EAGKIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMF

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

>13375_13375_3_CBFB-NUTF2_CBFB_chr16_67070658_ENST00000290858_NUTF2_chr16_67902242_ENST00000569436_length(amino acids)=188AA_BP=94
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLER
EAGKIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMF

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

>13375_13375_4_CBFB-NUTF2_CBFB_chr16_67070658_ENST00000290858_NUTF2_chr16_67902243_ENST00000219169_length(amino acids)=188AA_BP=94
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLER
EAGKIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMF

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

>13375_13375_5_CBFB-NUTF2_CBFB_chr16_67070658_ENST00000290858_NUTF2_chr16_67902243_ENST00000568396_length(amino acids)=188AA_BP=94
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLER
EAGKIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMF

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

>13375_13375_6_CBFB-NUTF2_CBFB_chr16_67070658_ENST00000290858_NUTF2_chr16_67902243_ENST00000569436_length(amino acids)=188AA_BP=94
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLER
EAGKIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMF

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

>13375_13375_7_CBFB-NUTF2_CBFB_chr16_67070658_ENST00000412916_NUTF2_chr16_67902242_ENST00000219169_length(amino acids)=188AA_BP=94
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLER
EAGKIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMF

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

>13375_13375_8_CBFB-NUTF2_CBFB_chr16_67070658_ENST00000412916_NUTF2_chr16_67902242_ENST00000568396_length(amino acids)=188AA_BP=94
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLER
EAGKIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMF

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

>13375_13375_9_CBFB-NUTF2_CBFB_chr16_67070658_ENST00000412916_NUTF2_chr16_67902242_ENST00000569436_length(amino acids)=188AA_BP=94
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLER
EAGKIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMF

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

>13375_13375_10_CBFB-NUTF2_CBFB_chr16_67070658_ENST00000412916_NUTF2_chr16_67902243_ENST00000219169_length(amino acids)=188AA_BP=94
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLER
EAGKIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMF

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

>13375_13375_11_CBFB-NUTF2_CBFB_chr16_67070658_ENST00000412916_NUTF2_chr16_67902243_ENST00000568396_length(amino acids)=188AA_BP=94
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLER
EAGKIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMF

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

>13375_13375_12_CBFB-NUTF2_CBFB_chr16_67070658_ENST00000412916_NUTF2_chr16_67902243_ENST00000569436_length(amino acids)=188AA_BP=94
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLER
EAGKIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMF

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

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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/chr16:67070658/chr16:67902243)
- 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
CBFB Q13951	.
FUNCTION: Forms the heterodimeric complex core-binding factor (CBF) with RUNX family proteins (RUNX1, RUNX2, and RUNX3). RUNX members modulate the transcription of their target genes through recognizing the core consensus binding sequence 5'-TGTGGT-3', or very rarely, 5'-TGCGGT-3', within their regulatory regions via their runt domain, while CBFB is a non-DNA-binding regulatory subunit that allosterically enhances the sequence-specific DNA-binding capacity of RUNX. The heterodimers bind to the core site of a number of enhancers and promoters, including murine leukemia virus, polyomavirus enhancer, T-cell receptor enhancers, LCK, IL3 and GM-CSF promoters. CBF complexes repress ZBTB7B transcription factor during cytotoxic (CD8+) T cell development. They bind to RUNX-binding sequence within the ZBTB7B locus acting as transcriptional silencer and allowing for cytotoxic T cell differentiation. {ECO:0000250\|UniProtKB:Q08024}.	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.

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

- 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

Tgene

NUTF2

chr16:67070658

chr16:67902242

ENST00000219169

10_121

33.0

128.0

Domain

NTF2

Tgene

NUTF2

chr16:67070658

chr16:67902242

ENST00000568396

10_121

33.0

128.0

Domain

NTF2

Tgene

NUTF2

chr16:67070658

chr16:67902242

ENST00000569436

10_121

33.0

128.0

Domain

NTF2

Tgene

NUTF2

chr16:67070658

chr16:67902243

ENST00000219169

10_121

33.0

128.0

Domain

NTF2

Tgene

NUTF2

chr16:67070658

chr16:67902243

ENST00000568396

10_121

33.0

128.0

Domain

NTF2

Tgene

NUTF2

chr16:67070658

chr16:67902243

ENST00000569436

10_121

33.0

128.0

Domain

NTF2

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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

CBFB

CHGB, RUNX1, MYOD1, RUNX3, COPRS, KMT2A, ELAVL1, CUL5, vif, nef, APOBEC3G, MYC, RAB2A, TCEB1, RNF7, TCEB2, RUNX2, ARL6IP6, SERPINB5, SLC25A32, TAS2R41, CRIP1, GALK1, PPIA, SOD1, NFATC1, GCHFR, G3BP1, CTNNB1, CBFA2T3, NKX2-1, IKZF3, IKZF1, AMBRA1, TRIM28, BAG3, BCL11B, CBFB, EMD, ETS1, HAX1, HLTF, HNRNPM, HSPBP1, PML, RBM14, TCF12, TCF7, TSC2, TUBA4A, ZBTB1, AKAP8L, ANXA1, HDAC3, IKZF2, SEC16A, TAF4, PDCD6IP, ARIH1, ARIH2, CUL2, DCAF11, NCOR1, NEDD8, RBX1, YTHDF2, PLEKHA4, CHRM5, BRD4, DDX58, ATG7, FBXW12, NIP7, HSPA1A, FCN3, FAM109A, LHFPL4, FOXF2, LRRC32, DUOXA2, VPS28, SMPDL3B, RP2, AQP12B, BTF3,

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
CBFB
NUTF2

- 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 CBFB-NUTF2

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 CBFB-NUTF2

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
Hgene	CBFB	C0023467	Leukemia, Myelocytic, Acute	2	CTD_human
Hgene	CBFB	C0023479	Acute myelomonocytic leukemia	2	CTD_human;ORPHANET
Hgene	CBFB	C0026998	Acute Myeloid Leukemia, M1	2	CTD_human
Hgene	CBFB	C1879321	Acute Myeloid Leukemia (AML-M2)	2	CTD_human
Hgene	CBFB	C0005941	Bone Diseases, Developmental	1	CTD_human
Hgene	CBFB	C0008925	Cleft Palate	1	CTD_human
Hgene	CBFB	C0018798	Congenital Heart Defects	1	CTD_human
Hgene	CBFB	C0029396	Heterotopic Ossification	1	CTD_human
Hgene	CBFB	C1837218	Cleft palate, isolated	1	CTD_human