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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:ZNHIT3-WDR60 (FusionGDB2 ID:102434)

Fusion Gene Summary for ZNHIT3-WDR60

Fusion gene summary

Fusion gene information	Fusion gene name: ZNHIT3-WDR60
	Fusion gene ID: 102434
		Hgene	Tgene
	Gene symbol	ZNHIT3	WDR60
	Gene ID	9326	55112
	Gene name	zinc finger HIT-type containing 3	WD repeat domain 60
	Synonyms	Hit1\|PEHO\|TRIP3	CFAP163\|DIC6\|FAP163\|SRPS6\|SRTD8
	Cytomap	17q12	7q36.3
	Type of gene	protein-coding	protein-coding
	Description	zinc finger HIT domain-containing protein 3HNF-4a coactivatorTR-interacting protein 3TRIP-3thyroid hormone receptor interactor 3thyroid receptor interacting protein 3zinc finger, HIT domain containing 3zinc finger, HIT type 3	WD repeat-containing protein 60testicular secretory protein Li 66
	Modification date	20200313	20200313
	UniProtAcc	.	.
	Ensembl transtripts involved in fusion gene	ENST00000490126, ENST00000225410, ENST00000588253, ENST00000592616, ENST00000590858,	ENST00000407559,
Fusion gene scores	* DoF score	2 X 2 X 2=8	5 X 6 X 4=120
	# samples	2	6
	** MAII score	log2(2/8*10)=1.32192809488736	log2(6/120*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: ZNHIT3 [Title/Abstract] AND WDR60 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	ZNHIT3(34842810)-WDR60(158715068), # samples:3
Anticipated loss of major functional domain due to fusion event.

* 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 ZNHIT3 (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 WDR60 (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	BLCA	TCGA-FD-A6TG-01A	ZNHIT3	chr17	34842810	+	WDR60	chr7	158715068	+
ChimerDB4	BLCA	TCGA-FD-A6TG-01A	ZNHIT3	chr17	34842810	+	WDR60	chr7	158715068	+
ChimerDB4	BLCA	TCGA-FD-A6TG-01A	ZNHIT3	chr17	34842810	-	WDR60	chr7	158715068	+

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Fusion Gene ORF analysis for ZNHIT3-WDR60

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	ENST00000490126	ENST00000407559	ZNHIT3	chr17	34842810	+	WDR60	chr7	158715068	+
In-frame	ENST00000225410	ENST00000407559	ZNHIT3	chr17	34842810	+	WDR60	chr7	158715068	+
intron-3CDS	ENST00000588253	ENST00000407559	ZNHIT3	chr17	34842810	+	WDR60	chr7	158715068	+
In-frame	ENST00000592616	ENST00000407559	ZNHIT3	chr17	34842810	+	WDR60	chr7	158715068	+
intron-3CDS	ENST00000590858	ENST00000407559	ZNHIT3	chr17	34842810	+	WDR60	chr7	158715068	+

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)

ENST00000225410

ZNHIT3

chr17

34842810

ENST00000407559

WDR60

chr7

158715068

1873

183

1462

465

ENST00000592616

ZNHIT3

chr17

34842810

ENST00000407559

WDR60

chr7

158715068

1813

123

1402

465

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
ENST00000225410	ENST00000407559	ZNHIT3	chr17	34842810	+	WDR60	chr7	158715068	+	0.023267655	0.9767323
ENST00000592616	ENST00000407559	ZNHIT3	chr17	34842810	+	WDR60	chr7	158715068	+	0.023242174	0.9767578

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Fusion Genomic Features for ZNHIT3-WDR60

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)
ZNHIT3	chr17	34842810	+	WDR60	chr7	158715067	+	4.44E-06	0.9999956
ZNHIT3	chr17	34842810	+	WDR60	chr7	158715067	+	4.44E-06	0.9999956

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 ZNHIT3-WDR60

Go to
FGviewer for the breakpoints of chr17:34842810-chr7:158715068
.
- 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
.	.
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.

- 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

Hgene

ZNHIT3

chr17:34842810

chr7:158715068

ENST00000225410

11_42

39.333333333333336

156.0

Zinc finger

HIT-type

Tgene

WDR60

chr17:34842810

chr7:158715068

ENST00000407559

694_734

640.3333333333334

1067.0

Repeat

WD 1

Tgene

WDR60

chr17:34842810

chr7:158715068

ENST00000407559

775_821

640.3333333333334

1067.0

Repeat

WD 2

Tgene

WDR60

chr17:34842810

chr7:158715068

ENST00000407559

907_947

640.3333333333334

1067.0

Repeat

WD 3

Tgene

WDR60

chr17:34842810

chr7:158715068

ENST00000407559

952_992

640.3333333333334

1067.0

Repeat

WD 4

- 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

Tgene

WDR60

chr17:34842810

chr7:158715068

ENST00000407559

473_552

640.3333333333334

1067.0

Region

Binding to the DYNLT2B-DYNLT1/DYNLT3 dimer

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Fusion Gene Sequence for ZNHIT3-WDR60

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.

>In-frame_ENST00000225410_ENST00000407559_TCGA-FD-A6TG-01A_ZNHIT3_chr17_34842810_+_WDR60_chr7_158715068_length(transcript)=1873nt_BP=183nt
GCACGCGGGCGCGGCTGCGTGAGAGGCGCGCGGCGGCGCAGTAAACAGTCTCCTTCCACAAAACCATGGCGTCGCTCAAATGTAGCACCG
TCGTCTGCGTGATCTGCTTGGAGAAGCCCAAATACCGCTGTCCAGCCTGCCGCGTGCCCTACTGCTCGGTAGTCTGCTTCCGGAAGCACA
AAGATCGAAAAGTATCCTCCTTGCACACCTCCCGAGTTCAGAGGCAGATGGTGGTCTCCGTTCACGACTTACCCGAGAAGAGCTTTGTGC
CCCTGCTGGACAGCAAATACGTCCTCTGTGTGTGGGATATTTGGCAGCCTTCAGGGCCACAGAAAGTTCTGATATGTGAGTCCCAGGTCA
CGTGTTGCTGCTTGAGCCCTTTGAAAGCATTTTTACTGTTTGCCGGAACAGCGCACGGCTCAGTTGTCGTCTGGGATTTGAGAGAAGACT
CAAGGCTGCATTACTCTGTGACGCTGAGCGATGGCTTCTGGACGTTCCGGACCGCCACGTTTTCCACCGATGGAATCCTTACCTCAGTAA
ACCACCGAAGCCCTCTTCAAGCAGTAGAACCTATCTCAACGTCCGTCCACAAAAAGCAGAGCTTTGTGCTTTCACCCTTTTCTACTCAAG
AAGAAATGTCAGGTTTGTCCTTCCACATCGCTTCCTTGGATGAGAGTGGGGTTCTCAATGTATGGGTGGTTGTTGAATTACCAAAGGCAG
ACATCGCAGGTTCAATAAGTGATTTAGGTCTGATGCCTGGAGGGAGGGTCAAGCTGGTACATAGTGCTCTGATCCAGTTGGGTGACAGTC
TTTCCCATAAAGGTAATGAATTTTGGGGCACTACACAAACACTGAATGTTAAATTTCTGCCTTCAGATCCTAATCACTTTATTATTGGCA
CAGACATGGGTCTCATAAGCCATGGCACAAGACAAGATTTGAGAGTGGCTCCCAAACTATTCAAACCTCAGCAACATGGTATAAGACCAG
TGAAAGTTAATGTCATTGATTTTTCACCATTTGGAGAACCAATATTTTTGGCCGGCTGTTCGGACGGAAGCATCAGGCTGCACCAGCTGA
GCTCCGCGTTTCCGCTCCTGCAGTGGGACAGCAGCACGGACAGCCATGCGGTCACCGGCCTGCAGTGGTCCCCAACCAGGCCTGCCGTGT
TCCTGGTGCAGGACGACACATCCAACATCTACATCTGGGACCTCCTCCAGAGCGATCTGGGTCCTGTCGCCAAACAGCAGGTCTCCCCCA
ACAGGCTGGTGGCCATGGCTGCGGTGGGTGAGCCTGAGAAGGCTGGTGGCAGCTTCCTGGCCCTGGTGCTGGCCAGGGCGTCTGGCTCCA
TCGACATCCAGCACCTGAAGAGGCGGTGGGCGGCCCCGGAGGTGGACGAGTGCAACAGGCTGCGTCTGCTTTTGCAGGAAGCCCTGTGGC
CAGAGGGAAAACTGCACAAGTAGCGGGTGTGGCTGAGAGGACCGCGTTTCTGTAATGACCCAGATTTAAAAGACATAAGGTGGATAATTC
TACATTTGTGTGCAAGTATATTTATGTATATAGACTATGTATATTCTGTATATAATTTATTTTACATGAATATGTCTTTGGTATTCCCAG
TAAATAGATGACTACTTTTGAGTGGAAACAAAGAACATTCTAGCATTTACAAAACTTCCAGGGGAATGTAGAGCCACGTCCAGGGTGCTC
TTTTCTGAGAGTATTTCGAGTTATTTTTAGAACAGTTTAAATATTGTCACATTACTGCTAGATTTTAAACAGCCTACCATGAAAATGTAT

>In-frame_ENST00000225410_ENST00000407559_TCGA-FD-A6TG-01A_ZNHIT3_chr17_34842810_+_WDR60_chr7_158715068_length(amino acids)=465AA_start in transcript=65_stop in transcript=1462
MASLKCSTVVCVICLEKPKYRCPACRVPYCSVVCFRKHKDRKVSSLHTSRVQRQMVVSVHDLPEKSFVPLLDSKYVLCVWDIWQPSGPQK
VLICESQVTCCCLSPLKAFLLFAGTAHGSVVVWDLREDSRLHYSVTLSDGFWTFRTATFSTDGILTSVNHRSPLQAVEPISTSVHKKQSF
VLSPFSTQEEMSGLSFHIASLDESGVLNVWVVVELPKADIAGSISDLGLMPGGRVKLVHSALIQLGDSLSHKGNEFWGTTQTLNVKFLPS
DPNHFIIGTDMGLISHGTRQDLRVAPKLFKPQQHGIRPVKVNVIDFSPFGEPIFLAGCSDGSIRLHQLSSAFPLLQWDSSTDSHAVTGLQ
WSPTRPAVFLVQDDTSNIYIWDLLQSDLGPVAKQQVSPNRLVAMAAVGEPEKAGGSFLALVLARASGSIDIQHLKRRWAAPEVDECNRLR

--------------------------------------------------------------
>In-frame_ENST00000592616_ENST00000407559_TCGA-FD-A6TG-01A_ZNHIT3_chr17_34842810_+_WDR60_chr7_158715068_length(transcript)=1813nt_BP=123nt
AAACCATGGCGTCGCTCAAATGTAGCACCGTCGTCTGCGTGATCTGCTTGGAGAAGCCCAAATACCGCTGTCCAGCCTGCCGCGTGCCCT
ACTGCTCGGTAGTCTGCTTCCGGAAGCACAAAGATCGAAAAGTATCCTCCTTGCACACCTCCCGAGTTCAGAGGCAGATGGTGGTCTCCG
TTCACGACTTACCCGAGAAGAGCTTTGTGCCCCTGCTGGACAGCAAATACGTCCTCTGTGTGTGGGATATTTGGCAGCCTTCAGGGCCAC
AGAAAGTTCTGATATGTGAGTCCCAGGTCACGTGTTGCTGCTTGAGCCCTTTGAAAGCATTTTTACTGTTTGCCGGAACAGCGCACGGCT
CAGTTGTCGTCTGGGATTTGAGAGAAGACTCAAGGCTGCATTACTCTGTGACGCTGAGCGATGGCTTCTGGACGTTCCGGACCGCCACGT
TTTCCACCGATGGAATCCTTACCTCAGTAAACCACCGAAGCCCTCTTCAAGCAGTAGAACCTATCTCAACGTCCGTCCACAAAAAGCAGA
GCTTTGTGCTTTCACCCTTTTCTACTCAAGAAGAAATGTCAGGTTTGTCCTTCCACATCGCTTCCTTGGATGAGAGTGGGGTTCTCAATG
TATGGGTGGTTGTTGAATTACCAAAGGCAGACATCGCAGGTTCAATAAGTGATTTAGGTCTGATGCCTGGAGGGAGGGTCAAGCTGGTAC
ATAGTGCTCTGATCCAGTTGGGTGACAGTCTTTCCCATAAAGGTAATGAATTTTGGGGCACTACACAAACACTGAATGTTAAATTTCTGC
CTTCAGATCCTAATCACTTTATTATTGGCACAGACATGGGTCTCATAAGCCATGGCACAAGACAAGATTTGAGAGTGGCTCCCAAACTAT
TCAAACCTCAGCAACATGGTATAAGACCAGTGAAAGTTAATGTCATTGATTTTTCACCATTTGGAGAACCAATATTTTTGGCCGGCTGTT
CGGACGGAAGCATCAGGCTGCACCAGCTGAGCTCCGCGTTTCCGCTCCTGCAGTGGGACAGCAGCACGGACAGCCATGCGGTCACCGGCC
TGCAGTGGTCCCCAACCAGGCCTGCCGTGTTCCTGGTGCAGGACGACACATCCAACATCTACATCTGGGACCTCCTCCAGAGCGATCTGG
GTCCTGTCGCCAAACAGCAGGTCTCCCCCAACAGGCTGGTGGCCATGGCTGCGGTGGGTGAGCCTGAGAAGGCTGGTGGCAGCTTCCTGG
CCCTGGTGCTGGCCAGGGCGTCTGGCTCCATCGACATCCAGCACCTGAAGAGGCGGTGGGCGGCCCCGGAGGTGGACGAGTGCAACAGGC
TGCGTCTGCTTTTGCAGGAAGCCCTGTGGCCAGAGGGAAAACTGCACAAGTAGCGGGTGTGGCTGAGAGGACCGCGTTTCTGTAATGACC
CAGATTTAAAAGACATAAGGTGGATAATTCTACATTTGTGTGCAAGTATATTTATGTATATAGACTATGTATATTCTGTATATAATTTAT
TTTACATGAATATGTCTTTGGTATTCCCAGTAAATAGATGACTACTTTTGAGTGGAAACAAAGAACATTCTAGCATTTACAAAACTTCCA
GGGGAATGTAGAGCCACGTCCAGGGTGCTCTTTTCTGAGAGTATTTCGAGTTATTTTTAGAACAGTTTAAATATTGTCACATTACTGCTA
GATTTTAAACAGCCTACCATGAAAATGTATCTTAATGAACTATTTTCTTATGCATAAAGTATGTGAACACATGTCTAAATTAAAAGGAAT

>In-frame_ENST00000592616_ENST00000407559_TCGA-FD-A6TG-01A_ZNHIT3_chr17_34842810_+_WDR60_chr7_158715068_length(amino acids)=465AA_start in transcript=5_stop in transcript=1402
MASLKCSTVVCVICLEKPKYRCPACRVPYCSVVCFRKHKDRKVSSLHTSRVQRQMVVSVHDLPEKSFVPLLDSKYVLCVWDIWQPSGPQK
VLICESQVTCCCLSPLKAFLLFAGTAHGSVVVWDLREDSRLHYSVTLSDGFWTFRTATFSTDGILTSVNHRSPLQAVEPISTSVHKKQSF
VLSPFSTQEEMSGLSFHIASLDESGVLNVWVVVELPKADIAGSISDLGLMPGGRVKLVHSALIQLGDSLSHKGNEFWGTTQTLNVKFLPS
DPNHFIIGTDMGLISHGTRQDLRVAPKLFKPQQHGIRPVKVNVIDFSPFGEPIFLAGCSDGSIRLHQLSSAFPLLQWDSSTDSHAVTGLQ
WSPTRPAVFLVQDDTSNIYIWDLLQSDLGPVAKQQVSPNRLVAMAAVGEPEKAGGSFLALVLARASGSIDIQHLKRRWAAPEVDECNRLR

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

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Fusion Gene PPI Analysis for ZNHIT3-WDR60

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 ZNHIT3-WDR60

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 ZNHIT3-WDR60

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	ZNHIT3	C0025958	Microcephaly	1	GENOMICS_ENGLAND
Hgene	ZNHIT3	C1850055	PEHO syndrome	1	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	WDR60	C0265275	Jeune thoracic dystrophy	4	GENOMICS_ENGLAND;ORPHANET
Tgene	WDR60	C3809691	SHORT-RIB THORACIC DYSPLASIA 8 WITH OR WITHOUT POLYDACTYLY	4	GENOMICS_ENGLAND;UNIPROT
Tgene	WDR60	C0152427	Polydactyly	1	GENOMICS_ENGLAND
Tgene	WDR60	C0432197	Short rib-polydactyly syndrome, Verma-Naumoff type	1	ORPHANET