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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:CFD-EIF3B

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CFD-EIF3B
	FusionPDB ID: 16087
	FusionGDB2.0 ID: 16087
		Hgene	Tgene
	Gene symbol	CFD	EIF3B
	Gene ID	200576	8662
	Gene name	phosphoinositide kinase, FYVE-type zinc finger containing	eukaryotic translation initiation factor 3 subunit B
	Synonyms	CFD\|FAB1\|HEL37\|PIP5K\|PIP5K3\|ZFYVE29	EIF3-ETA\|EIF3-P110\|EIF3-P116\|EIF3S9\|PRT1
	Cytomap	2q34	7p22.3
	Type of gene	protein-coding	protein-coding
	Description	1-phosphatidylinositol 3-phosphate 5-kinasePIPkin-IIIepididymis luminal protein 37phosphatidylinositol 3-phosphate 5-kinase type IIIphosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type IIIphosphoinositide kinase, FYVE finger containin	eukaryotic translation initiation factor 3 subunit Beukaryotic translation initiation factor 3 subunit 9eukaryotic translation initiation factor 3, subunit 9 (eta, 116kD)eukaryotic translation initiation factor 3, subunit 9 eta, 116kDaprt1 homolog
	Modification date	20200327	20200322
	UniProtAcc	Q9UEE9	P55884
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000327726, ENST00000592860,	ENST00000360876, ENST00000397011,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 1 X 3=9	16 X 22 X 8=2816
	# samples	4	22
	** MAII score	log2(4/9*10)=2.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(22/2816*10)=-3.67807190511264 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: CFD [Title/Abstract] AND EIF3B [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CFD(861956)-EIF3B(2411411), # samples:2
Anticipated loss of major functional domain due to fusion event.	CFD-EIF3B 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. CFD-EIF3B 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	EIF3B	GO:0006413	translational initiation	8995410\|17581632
Tgene	EIF3B	GO:0006446	regulation of translational initiation	8995410
Tgene	EIF3B	GO:0075522	IRES-dependent viral translational initiation	9573242
Tgene	EIF3B	GO:0075525	viral translational termination-reinitiation	21347434

Fusion gene breakpoints across CFD (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 EIF3B (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	ESCA	TCGA-L5-A88W	CFD	chr19	861956	+	EIF3B	chr7	2411411	+

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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)

ENST00000327726

CFD

chr19

861956

ENST00000360876

EIF3B

chr7

2411411

2237

852

135

1682

515

ENST00000327726

CFD

chr19

861956

ENST00000397011

EIF3B

chr7

2411411

2164

852

135

1682

515

ENST00000592860

CFD

chr19

861956

ENST00000360876

EIF3B

chr7

2411411

2021

636

1466

488

ENST00000592860

CFD

chr19

861956

ENST00000397011

EIF3B

chr7

2411411

1948

636

1466

488

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
ENST00000327726	ENST00000360876	CFD	chr19	861956	+	EIF3B	chr7	2411411	+	0.002455885	0.9975441
ENST00000327726	ENST00000397011	CFD	chr19	861956	+	EIF3B	chr7	2411411	+	0.002597558	0.99740237
ENST00000592860	ENST00000360876	CFD	chr19	861956	+	EIF3B	chr7	2411411	+	0.004099581	0.99590045
ENST00000592860	ENST00000397011	CFD	chr19	861956	+	EIF3B	chr7	2411411	+	0.004274832	0.99572515

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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

>16087_16087_1_CFD-EIF3B_CFD_chr19_861956_ENST00000327726_EIF3B_chr7_2411411_ENST00000360876_length(amino acids)=515AA_BP=239
MGRCPPGERPAPSTLIKAPPGPCLGQCLSHSGFTMHSWERLAVLVLLGAAACAAPPRGRILGGREAEAHARPYMASVQLNGAHLCGGVLV
AEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGT
LCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGVVTNFEIFRMREKQVPVDVVEMKETIIAFA
WEPNGSKFAVLHGEAPRISVSFYHVKNNGKIELIKMFDKQQANTIFWSPQGQFVVLAGLRSMNGALAFVDTSDCTVMNIAEHYMASDVEW
DPTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQLLWRPRPPTLLSQEQIKQIKKDLKKYSKIFEQKDRLSQSKASKELVER

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

>16087_16087_2_CFD-EIF3B_CFD_chr19_861956_ENST00000327726_EIF3B_chr7_2411411_ENST00000397011_length(amino acids)=515AA_BP=239
MGRCPPGERPAPSTLIKAPPGPCLGQCLSHSGFTMHSWERLAVLVLLGAAACAAPPRGRILGGREAEAHARPYMASVQLNGAHLCGGVLV
AEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGT
LCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGVVTNFEIFRMREKQVPVDVVEMKETIIAFA
WEPNGSKFAVLHGEAPRISVSFYHVKNNGKIELIKMFDKQQANTIFWSPQGQFVVLAGLRSMNGALAFVDTSDCTVMNIAEHYMASDVEW
DPTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQLLWRPRPPTLLSQEQIKQIKKDLKKYSKIFEQKDRLSQSKASKELVER

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

>16087_16087_3_CFD-EIF3B_CFD_chr19_861956_ENST00000592860_EIF3B_chr7_2411411_ENST00000360876_length(amino acids)=488AA_BP=212
MHSWERLAVLVLLGAAACGEEAWAWAAPPRGRILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAH
SLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPV
LDRATCNRRTHHDGAITERLMCAESNRRDSCKGVVTNFEIFRMREKQVPVDVVEMKETIIAFAWEPNGSKFAVLHGEAPRISVSFYHVKN
NGKIELIKMFDKQQANTIFWSPQGQFVVLAGLRSMNGALAFVDTSDCTVMNIAEHYMASDVEWDPTGRYVVTSVSWWSHKVDNAYWLWTF
QGRLLQKNNKDRFCQLLWRPRPPTLLSQEQIKQIKKDLKKYSKIFEQKDRLSQSKASKELVERRRTMMEDFRKYRKMAQELYMEQKNERL

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

>16087_16087_4_CFD-EIF3B_CFD_chr19_861956_ENST00000592860_EIF3B_chr7_2411411_ENST00000397011_length(amino acids)=488AA_BP=212
MHSWERLAVLVLLGAAACGEEAWAWAAPPRGRILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAH
SLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPV
LDRATCNRRTHHDGAITERLMCAESNRRDSCKGVVTNFEIFRMREKQVPVDVVEMKETIIAFAWEPNGSKFAVLHGEAPRISVSFYHVKN
NGKIELIKMFDKQQANTIFWSPQGQFVVLAGLRSMNGALAFVDTSDCTVMNIAEHYMASDVEWDPTGRYVVTSVSWWSHKVDNAYWLWTF
QGRLLQKNNKDRFCQLLWRPRPPTLLSQEQIKQIKKDLKKYSKIFEQKDRLSQSKASKELVERRRTMMEDFRKYRKMAQELYMEQKNERL

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

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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/chr19:861956/chr7:2411411)
- 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
CFD Q9UEE9	EIF3B P55884
FUNCTION: May play a role during embryogenesis. {ECO:0000250}.	FUNCTION: RNA-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis (PubMed:9388245, PubMed:17581632, PubMed:25849773, PubMed:27462815). The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S pre-initiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation (PubMed:9388245, PubMed:17581632). The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression (PubMed:25849773). {ECO:0000255\|HAMAP-Rule:MF_03001, ECO:0000269\|PubMed:17581632, ECO:0000269\|PubMed:25849773, ECO:0000269\|PubMed:27462815, ECO:0000269\|PubMed:9388245}.; FUNCTION: (Microbial infection) In case of FCV infection, plays a role in the ribosomal termination-reinitiation event leading to the translation of VP2 (PubMed:18056426). {ECO:0000269\|PubMed:18056426}.

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

EIF3B

chr19:861956

chr7:2411411

ENST00000360876

554_598

538.0

810.0

Repeat

Note=WD 6

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000360876

599_642

538.0

810.0

Repeat

Note=WD 7

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000360876

643_685

538.0

810.0

Repeat

Note=WD 8

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000397011

554_598

538.0

791.0

Repeat

Note=WD 6

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000397011

599_642

538.0

791.0

Repeat

Note=WD 7

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000397011

643_685

538.0

791.0

Repeat

Note=WD 8

- 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

CFD

chr19:861956

chr7:2411411

ENST00000327726

26_253

205.0

254.0

Domain

Peptidase S1

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000360876

185_268

538.0

810.0

Domain

RRM

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000397011

185_268

538.0

791.0

Domain

RRM

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000360876

285_324

538.0

810.0

Repeat

Note=WD 1

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000360876

325_365

538.0

810.0

Repeat

Note=WD 2

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000360876

366_425

538.0

810.0

Repeat

Note=WD 3

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000360876

426_489

538.0

810.0

Repeat

Note=WD 4

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000360876

490_553

538.0

810.0

Repeat

Note=WD 5

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000397011

285_324

538.0

791.0

Repeat

Note=WD 1

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000397011

325_365

538.0

791.0

Repeat

Note=WD 2

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000397011

366_425

538.0

791.0

Repeat

Note=WD 3

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000397011

426_489

538.0

791.0

Repeat

Note=WD 4

Tgene

EIF3B

chr19:861956

chr7:2411411

ENST00000397011

490_553

538.0

791.0

Repeat

Note=WD 5

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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
CFD
EIF3B

- 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 CFD-EIF3B

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 CFD-EIF3B

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