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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:CRYZ-VPS13D (FusionGDB2 ID:HG1429TG55187)

Fusion Gene Summary for CRYZ-VPS13D

Fusion gene summary

Fusion gene information	Fusion gene name: CRYZ-VPS13D
	Fusion gene ID: hg1429tg55187
		Hgene	Tgene
	Gene symbol	CRYZ	VPS13D
	Gene ID	1429	55187
	Gene name	crystallin zeta	vacuolar protein sorting 13 homolog D
	Synonyms	-	SCAR4
	Cytomap	('CRYZ')('VPS13D') 1p31.1	1p36.22-p36.21
	Type of gene	protein-coding	protein-coding
	Description	quinone oxidoreductaseNADPH:quinone reductasecrystallin, zeta (quinone reductase)epididymis secretory sperm binding protein	vacuolar protein sorting-associated protein 13Dvacuolar protein sorting 13D
	Modification date	20200313	20200313
	UniProtAcc	Q08257	.
	Ensembl transtripts involved in fusion gene	ENST00000340866, ENST00000370871, ENST00000417775, ENST00000370872, ENST00000492102,
Fusion gene scores	* DoF score	3 X 4 X 3=36	8 X 10 X 5=400
	# samples	4	11
	** MAII score	log2(4/36*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(11/400*10)=-1.86249647625006 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: CRYZ [Title/Abstract] AND VPS13D [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	CRYZ(75184893)-VPS13D(12475140), # samples:2
Anticipated loss of major functional domain due to fusion event.	CRYZ-VPS13D seems lost the major protein functional domain in Tgene partner, which is a essential 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
Hgene	CRYZ	GO:0042178	xenobiotic catabolic process	17497241

Fusion gene information
* 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	OV	TCGA-61-2095-01A	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
ChimerDB4	OV	TCGA-61-2095	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+

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Fusion Gene ORF analysis for CRYZ-VPS13D

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
5CDS-3UTR	ENST00000340866	ENST00000496628	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
5CDS-3UTR	ENST00000340866	ENST00000496628	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
5CDS-3UTR	ENST00000340866	ENST00000543766	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
5CDS-3UTR	ENST00000340866	ENST00000543766	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
5CDS-3UTR	ENST00000370871	ENST00000496628	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
5CDS-3UTR	ENST00000370871	ENST00000496628	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
5CDS-3UTR	ENST00000370871	ENST00000543766	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
5CDS-3UTR	ENST00000370871	ENST00000543766	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
5CDS-3UTR	ENST00000417775	ENST00000496628	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
5CDS-3UTR	ENST00000417775	ENST00000496628	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
5CDS-3UTR	ENST00000417775	ENST00000543766	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
5CDS-3UTR	ENST00000417775	ENST00000543766	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
5CDS-intron	ENST00000340866	ENST00000471923	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
5CDS-intron	ENST00000340866	ENST00000471923	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
5CDS-intron	ENST00000340866	ENST00000543710	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
5CDS-intron	ENST00000340866	ENST00000543710	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
5CDS-intron	ENST00000370871	ENST00000471923	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
5CDS-intron	ENST00000370871	ENST00000471923	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
5CDS-intron	ENST00000370871	ENST00000543710	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
5CDS-intron	ENST00000370871	ENST00000543710	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
5CDS-intron	ENST00000417775	ENST00000471923	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
5CDS-intron	ENST00000417775	ENST00000471923	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
5CDS-intron	ENST00000417775	ENST00000543710	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
5CDS-intron	ENST00000417775	ENST00000543710	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
Frame-shift	ENST00000340866	ENST00000356315	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
Frame-shift	ENST00000340866	ENST00000356315	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
Frame-shift	ENST00000340866	ENST00000358136	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
Frame-shift	ENST00000340866	ENST00000358136	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
Frame-shift	ENST00000370871	ENST00000356315	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
Frame-shift	ENST00000370871	ENST00000356315	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
Frame-shift	ENST00000370871	ENST00000358136	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
Frame-shift	ENST00000370871	ENST00000358136	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
Frame-shift	ENST00000417775	ENST00000356315	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
Frame-shift	ENST00000417775	ENST00000356315	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
Frame-shift	ENST00000417775	ENST00000358136	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
Frame-shift	ENST00000417775	ENST00000358136	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
intron-3CDS	ENST00000370872	ENST00000356315	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
intron-3CDS	ENST00000370872	ENST00000356315	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
intron-3CDS	ENST00000370872	ENST00000358136	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
intron-3CDS	ENST00000370872	ENST00000358136	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
intron-3CDS	ENST00000492102	ENST00000356315	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
intron-3CDS	ENST00000492102	ENST00000356315	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
intron-3CDS	ENST00000492102	ENST00000358136	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
intron-3CDS	ENST00000492102	ENST00000358136	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
intron-3UTR	ENST00000370872	ENST00000496628	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
intron-3UTR	ENST00000370872	ENST00000496628	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
intron-3UTR	ENST00000370872	ENST00000543766	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
intron-3UTR	ENST00000370872	ENST00000543766	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
intron-3UTR	ENST00000492102	ENST00000496628	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
intron-3UTR	ENST00000492102	ENST00000496628	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
intron-3UTR	ENST00000492102	ENST00000543766	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
intron-3UTR	ENST00000492102	ENST00000543766	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
intron-intron	ENST00000370872	ENST00000471923	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
intron-intron	ENST00000370872	ENST00000471923	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
intron-intron	ENST00000370872	ENST00000543710	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
intron-intron	ENST00000370872	ENST00000543710	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
intron-intron	ENST00000492102	ENST00000471923	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
intron-intron	ENST00000492102	ENST00000471923	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+
intron-intron	ENST00000492102	ENST00000543710	CRYZ	chr1	75184893	-	VPS13D	chr1	12475140	+
intron-intron	ENST00000492102	ENST00000543710	CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+

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 CRYZ-VPS13D

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)
CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+	1.13E-06	0.9999988
CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+	1.13E-06	0.9999988
CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+	1.13E-06	0.9999988
CRYZ	chr1	75184892	-	VPS13D	chr1	12475139	+	1.13E-06	0.9999988

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 CRYZ-VPS13D

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:75184893/:12475140)
- 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
CRYZ Q08257	.
FUNCTION: Does not have alcohol dehydrogenase activity. Binds NADP and acts through a one-electron transfer process. Orthoquinones, such as 1,2-naphthoquinone or 9,10-phenanthrenequinone, are the best substrates (in vitro). May act in the detoxification of xenobiotics. Interacts with (AU)-rich elements (ARE) in the 3'-UTR of target mRNA species. Enhances the stability of mRNA coding for BCL2. NADPH binding interferes with mRNA binding. {ECO:0000269\|PubMed:17497241, ECO:0000269\|PubMed:20103721}.	FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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

- 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

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Fusion Gene Sequence for CRYZ-VPS13D

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 CRYZ-VPS13D

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 CRYZ-VPS13D

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
Hgene	CRYZ	Q08257	DB00266	Dicoumarol	Inhibitor	Small molecule	Approved

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Related Diseases for CRYZ-VPS13D

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Tgene		C1846492	SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 4	2	CTD_human;GENOMICS_ENGLAND;UNIPROT
Tgene		C0043094	Weight Gain	1	CTD_human

Fusion Gene Studies in Kim Lab

Fusion gene:CRYZ-VPS13D (FusionGDB2 ID:HG1429TG55187)

Fusion Gene Summary for CRYZ-VPS13D

Fusion Gene ORF analysis for CRYZ-VPS13D

Fusion Genomic Features for CRYZ-VPS13D

Fusion Protein Features for CRYZ-VPS13D

Fusion Gene Sequence for CRYZ-VPS13D

Fusion Gene PPI Analysis for CRYZ-VPS13D

Related Drugs for CRYZ-VPS13D

Related Diseases for CRYZ-VPS13D

Fusion Gene Studies
in Kim Lab