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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:ITFG1-PHKB (FusionGDB2 ID:40202)

Fusion Gene Summary for ITFG1-PHKB

Fusion gene summary

Fusion gene information	Fusion gene name: ITFG1-PHKB
	Fusion gene ID: 40202
		Hgene	Tgene
	Gene symbol	ITFG1	PHKB
	Gene ID	81533	5257
	Gene name	integrin alpha FG-GAP repeat containing 1	phosphorylase kinase regulatory subunit beta
	Synonyms	2310047C21Rik\|CDA08\|LNKN-1\|TIP	-
	Cytomap	16q12.1	16q12.1
	Type of gene	protein-coding	protein-coding
	Description	T-cell immunomodulatory proteinLINKINintegrin-alpha FG-GAP repeat-containing protein 1	phosphorylase b kinase regulatory subunit betaphosphorylase kinase beta-subunitphosphorylase kinase subunit betaphosphorylase kinase, beta
	Modification date	20200313	20200313
	UniProtAcc	Q8TB96	.
	Ensembl transtripts involved in fusion gene	ENST00000568047, ENST00000320640, ENST00000544001,	ENST00000566044, ENST00000455779, ENST00000299167, ENST00000323584, ENST00000567402,
Fusion gene scores	* DoF score	9 X 9 X 5=405	13 X 17 X 9=1989
	# samples	9	15
	** MAII score	log2(9/405*10)=-2.16992500144231 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(15/1989*10)=-3.72900887033786 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: ITFG1 [Title/Abstract] AND PHKB [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	ITFG1(47462715)-PHKB(47531310), # samples:1 PHKB(47644831)-ITFG1(47347734), # samples:1
Anticipated loss of major functional domain due to fusion event.	ITFG1-PHKB seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. ITFG1-PHKB 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

Fusion gene breakpoints across ITFG1 (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 PHKB (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	Non-Cancer	TCGA-CG-5721-11A	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+

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Fusion Gene ORF analysis for ITFG1-PHKB

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
intron-3CDS	ENST00000568047	ENST00000566044	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
intron-3CDS	ENST00000568047	ENST00000455779	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
intron-3CDS	ENST00000568047	ENST00000299167	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
intron-3CDS	ENST00000568047	ENST00000323584	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
intron-3UTR	ENST00000568047	ENST00000567402	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
In-frame	ENST00000320640	ENST00000566044	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
In-frame	ENST00000320640	ENST00000455779	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
In-frame	ENST00000320640	ENST00000299167	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
In-frame	ENST00000320640	ENST00000323584	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
5CDS-3UTR	ENST00000320640	ENST00000567402	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
Frame-shift	ENST00000544001	ENST00000566044	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
Frame-shift	ENST00000544001	ENST00000455779	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
Frame-shift	ENST00000544001	ENST00000299167	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
Frame-shift	ENST00000544001	ENST00000323584	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+
5CDS-3UTR	ENST00000544001	ENST00000567402	ITFG1	chr16	47462715	-	PHKB	chr16	47531310	+

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)

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

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Fusion Genomic Features for ITFG1-PHKB

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)
ITFG1	chr16	47462714	-	PHKB	chr16	47531309	+	4.06E-05	0.99995947
ITFG1	chr16	47462714	-	PHKB	chr16	47531309	+	4.06E-05	0.99995947

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 ITFG1-PHKB

Go to
FGviewer for the breakpoints of chr16:47462715-chr16:47531310
.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
ITFG1 Q8TB96	.
FUNCTION: Modulator of T-cell function. Has a protective effect in graft versus host disease model (By similarity). {ECO:0000250}.	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.

- 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

Tgene

PHKB

chr16:47462715

chr16:47531310

ENST00000299167

768_795

25.333333333333332

1094.0

Region

Calmodulin-binding

Tgene

PHKB

chr16:47462715

chr16:47531310

ENST00000299167

920_951

25.333333333333332

1094.0

Region

Calmodulin-binding

Tgene

PHKB

chr16:47462715

chr16:47531310

ENST00000323584

768_795

25.333333333333332

1094.0

Region

Calmodulin-binding

Tgene

PHKB

chr16:47462715

chr16:47531310

ENST00000323584

920_951

25.333333333333332

1094.0

Region

Calmodulin-binding

Tgene

PHKB

chr16:47462715

chr16:47531310

ENST00000455779

768_795

18.333333333333332

1087.0

Region

Calmodulin-binding

Tgene

PHKB

chr16:47462715

chr16:47531310

ENST00000455779

920_951

18.333333333333332

1087.0

Region

Calmodulin-binding

Tgene

PHKB

chr16:47462715

chr16:47531310

ENST00000566044

768_795

18.333333333333332

1087.0

Region

Calmodulin-binding

Tgene

PHKB

chr16:47462715

chr16:47531310

ENST00000566044

920_951

18.333333333333332

1087.0

Region

Calmodulin-binding

- 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

ITFG1

chr16:47462715

chr16:47531310

ENST00000320640

258_293

218.33333333333334

613.0

Repeat

Note=FG-GAP%3B atypical

Hgene

ITFG1

chr16:47462715

chr16:47531310

ENST00000320640

567_587

218.33333333333334

613.0

Transmembrane

Helical

Tgene

PHKB

chr16:47462715

chr16:47531310

ENST00000299167

7_29

25.333333333333332

1094.0

Region

Calmodulin-binding

Tgene

PHKB

chr16:47462715

chr16:47531310

ENST00000323584

7_29

25.333333333333332

1094.0

Region

Calmodulin-binding

Tgene

PHKB

chr16:47462715

chr16:47531310

ENST00000455779

7_29

18.333333333333332

1087.0

Region

Calmodulin-binding

Tgene

PHKB

chr16:47462715

chr16:47531310

ENST00000566044

7_29

18.333333333333332

1087.0

Region

Calmodulin-binding

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Fusion Gene Sequence for ITFG1-PHKB

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.

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Fusion Gene PPI Analysis for ITFG1-PHKB

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

- 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 ITFG1-PHKB

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 ITFG1-PHKB

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Tgene	PHKB	C0543514	Glycogen Storage Disease IXB	2	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	PHKB	C0017919	Glycogen Storage Disease	1	GENOMICS_ENGLAND