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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:PRKAB2-RFWD2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PRKAB2-RFWD2
	FusionPDB ID: 68615
	FusionGDB2.0 ID: 68615
		Hgene	Tgene
	Gene symbol	PRKAB2	RFWD2
	Gene ID	5565	64326
	Gene name	protein kinase AMP-activated non-catalytic subunit beta 2	COP1 E3 ubiquitin ligase
	Synonyms	-	CFAP78\|FAP78\|RFWD2\|RNF200
	Cytomap	1q21.1	1q25.1-q25.2
	Type of gene	protein-coding	protein-coding
	Description	5'-AMP-activated protein kinase subunit beta-25'-AMP-activated protein kinase, beta-2 subunitAMP-activated protein kinase beta 2 non-catalytic subunitAMPK beta 2AMPK beta-2 chainAMPK subunit beta-2protein kinase, AMP-activated, beta 2 non-catalytic	E3 ubiquitin-protein ligase COP1E3 ubiquitin-protein ligase RFWD2RING finger protein 200RING-type E3 ubiquitin transferase RFWD2constitutive photomorphogenesis protein 1 homologconstitutive photomorphogenic protein 1putative ubiquitin ligase COP1ri
	Modification date	20200327	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000254101, ENST00000425272, ENST00000496858,	ENST00000308769, ENST00000367669,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 3 X 2=18	28 X 17 X 12=5712
	# samples	3	27
	** MAII score	log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(27/5712*10)=-4.40296466697827 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PRKAB2 [Title/Abstract] AND RFWD2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PRKAB2(146638424)-RFWD2(176118212), # samples:1
Anticipated loss of major functional domain due to fusion event.	PRKAB2-RFWD2 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. PRKAB2-RFWD2 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. PRKAB2-RFWD2 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. PRKAB2-RFWD2 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	RFWD2	GO:0010212	response to ionizing radiation	19805145

Fusion gene breakpoints across PRKAB2 (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 RFWD2 (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
ChiTaRS5.0	N/A	DA824273	PRKAB2	chr1	146638424	-	RFWD2	chr1	176118212	-

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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)
ENST00000254101	PRKAB2	chr1	146638424	-	ENST00000367669	RFWD2	chr1	176118212	-	2312	556	61	1989	642
ENST00000254101	PRKAB2	chr1	146638424	-	ENST00000308769	RFWD2	chr1	176118212	-	1930	556	61	1929	623
ENST00000425272	PRKAB2	chr1	146638424	-	ENST00000367669	RFWD2	chr1	176118212	-	2068	312	54	1745	563
ENST00000425272	PRKAB2	chr1	146638424	-	ENST00000308769	RFWD2	chr1	176118212	-	1686	312	54	1685	543

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
ENST00000254101	ENST00000367669	PRKAB2	chr1	146638424	-	RFWD2	chr1	176118212	-	0.001060138	0.9989398
ENST00000254101	ENST00000308769	PRKAB2	chr1	146638424	-	RFWD2	chr1	176118212	-	0.001928871	0.99807113
ENST00000425272	ENST00000367669	PRKAB2	chr1	146638424	-	RFWD2	chr1	176118212	-	0.000280897	0.9997191
ENST00000425272	ENST00000308769	PRKAB2	chr1	146638424	-	RFWD2	chr1	176118212	-	0.000907379	0.9990926

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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

>68615_68615_1_PRKAB2-RFWD2_PRKAB2_chr1_146638424_ENST00000254101_RFWD2_chr1_176118212_ENST00000308769_length(amino acids)=623AA_BP=165
MQNSHHISGPWRRERIARGGPRRAAAMGNTTSDRVSGERHGAKAARSEGAGGHAPGKEHKIMVGSTDDPSVFSLPDSKLPGDKEFVSWQQ
DLEDSVKPTQQARPTVIRWSEGGKEVFISGSFNNWSTKIPLIKSHNDFVAILDLPEGEHQYKFFVDGQWVHDPSEESHAAQLQILMEFLK
VARRNKREEMSGLYSPVSEDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGSSQTKKQPWYNSTLASRRKRLTAHFEDLEQCYFSTRMSRI
SDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASDLYNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDTVIQDAVDIHYPENEMTC
NSKISCISWSSYHKNLLASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKLWSTNLDNSVASIEAKANVC
CVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRKAVSYAKFVSGEEIVSASTDSQLKLWNVGKPYCLRSFKGHINEKNFVGLA

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

>68615_68615_2_PRKAB2-RFWD2_PRKAB2_chr1_146638424_ENST00000254101_RFWD2_chr1_176118212_ENST00000367669_length(amino acids)=642AA_BP=165
MQNSHHISGPWRRERIARGGPRRAAAMGNTTSDRVSGERHGAKAARSEGAGGHAPGKEHKIMVGSTDDPSVFSLPDSKLPGDKEFVSWQQ
DLEDSVKPTQQARPTVIRWSEGGKEVFISGSFNNWSTKIPLIKSHNDFVAILDLPEGEHQYKFFVDGQWVHDPSEESHAAQLQILMEFLK
VARRNKREQLEQIQKELSVLEEDIKRVEEMSGLYSPVSEDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGSSQTKKQPWYNSTLASRRKR
LTAHFEDLEQCYFSTRMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASDLYNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYE
YDTVIQDAVDIHYPENEMTCNSKISCISWSSYHKNLLASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVK
LWSTNLDNSVASIEAKANVCCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRKAVSYAKFVSGEEIVSASTDSQLKLWNVGK
PYCLRSFKGHINEKNFVGLASNGDYIACGSENNSLYLYYKGLSKTLLTFKFDTVKSVLDKDRKEDDTNEFVSAVCWRALPDGESNVLIAA

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

>68615_68615_3_PRKAB2-RFWD2_PRKAB2_chr1_146638424_ENST00000425272_RFWD2_chr1_176118212_ENST00000308769_length(amino acids)=543AA_BP=86
MQPWETPPATGCPGSATAPRLHAPRAQAAMPRGRSTRSWWGVRTTPACSASLTPSHNDFVAILDLPEGEHQYKFFVDGQWVHDPSEESHA
AQLQILMEFLKVARRNKREEMSGLYSPVSEDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGSSQTKKQPWYNSTLASRRKRLTAHFEDLE
QCYFSTRMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASDLYNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDTVIQDAV
DIHYPENEMTCNSKISCISWSSYHKNLLASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKLWSTNLDNS
VASIEAKANVCCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRKAVSYAKFVSGEEIVSASTDSQLKLWNVGKPYCLRSFKG
HINEKNFVGLASNGDYIACGSENNSLYLYYKGLSKTLLTFKFDTVKSVLDKDRKEDDTNEFVSAVCWRALPDGESNVLIAANSQGTIKVL

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

>68615_68615_4_PRKAB2-RFWD2_PRKAB2_chr1_146638424_ENST00000425272_RFWD2_chr1_176118212_ENST00000367669_length(amino acids)=563AA_BP=86
MQPWETPPATGCPGSATAPRLHAPRAQAAMPRGRSTRSWWGVRTTPACSASLTPSHNDFVAILDLPEGEHQYKFFVDGQWVHDPSEESHA
AQLQILMEFLKVARRNKREQLEQIQKELSVLEEDIKRVEEMSGLYSPVSEDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGSSQTKKQPW
YNSTLASRRKRLTAHFEDLEQCYFSTRMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASDLYNGSSIVSSIEFDRDCDYFAI
AGVTKKIKVYEYDTVIQDAVDIHYPENEMTCNSKISCISWSSYHKNLLASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLMDPKL
LASGSDDAKVKLWSTNLDNSVASIEAKANVCCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRKAVSYAKFVSGEEIVSAST
DSQLKLWNVGKPYCLRSFKGHINEKNFVGLASNGDYIACGSENNSLYLYYKGLSKTLLTFKFDTVKSVLDKDRKEDDTNEFVSAVCWRAL

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

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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/chr1:146638424/chr1:176118212)
- 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
.	.
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.	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

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000308769

419_458

250.0

708.0

Repeat

Note=WD 1

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000308769

468_508

250.0

708.0

Repeat

Note=WD 2

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000308769

511_551

250.0

708.0

Repeat

Note=WD 3

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000308769

553_593

250.0

708.0

Repeat

Note=WD 4

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000308769

597_635

250.0

708.0

Repeat

Note=WD 5

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000308769

638_677

250.0

708.0

Repeat

Note=WD 6

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000308769

691_729

250.0

708.0

Repeat

Note=WD 7

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000367669

419_458

254.0

732.0

Repeat

Note=WD 1

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000367669

468_508

254.0

732.0

Repeat

Note=WD 2

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000367669

511_551

254.0

732.0

Repeat

Note=WD 3

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000367669

553_593

254.0

732.0

Repeat

Note=WD 4

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000367669

597_635

254.0

732.0

Repeat

Note=WD 5

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000367669

638_677

254.0

732.0

Repeat

Note=WD 6

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000367669

691_729

254.0

732.0

Repeat

Note=WD 7

- 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

RFWD2

chr1:146638424

chr1:176118212

ENST00000308769

233_301

250.0

708.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000367669

233_301

254.0

732.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000308769

2_110

250.0

708.0

Compositional bias

Note=Ser-rich

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000367669

2_110

254.0

732.0

Compositional bias

Note=Ser-rich

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000308769

109_113

250.0

708.0

Motif

Note=Nuclear localization signal 1

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000308769

195_206

250.0

708.0

Motif

Note=Nuclear localization signal 2

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000308769

235_245

250.0

708.0

Motif

Nuclear export signal

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000367669

109_113

254.0

732.0

Motif

Note=Nuclear localization signal 1

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000367669

195_206

254.0

732.0

Motif

Note=Nuclear localization signal 2

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000367669

235_245

254.0

732.0

Motif

Nuclear export signal

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000308769

136_174

250.0

708.0

Zinc finger

RING-type

Tgene

RFWD2

chr1:146638424

chr1:176118212

ENST00000367669

136_174

254.0

732.0

Zinc finger

RING-type

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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
PRKAB2
RFWD2

- 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 PRKAB2-RFWD2

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 PRKAB2-RFWD2

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