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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 41661

FusionGeneSummary for VRK2_CHSY1

check button Fusion gene summary
Fusion gene informationFusion gene name: VRK2_CHSY1
Fusion gene ID: 41661
HgeneTgene
Gene symbol

VRK2

CHSY1

Gene ID

7444

22856

Gene namevaccinia related kinase 2chondroitin sulfate synthase 1
Synonyms-CHSY|CSS1|ChSy-1|TPBS
Cytomap

2p16.1

15q26.3

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase VRK2vaccinia virus B1R-related kinase 2chondroitin sulfate synthase 1N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase 1N-acetylgalactosaminyltransferase IIcarbohydrate synthase 1chondroitin glucuronyltransferase 1chondroitin glucuronyltransferase IIchondroitin synthase
Modification date2018052720180519
UniProtAcc

Q86Y07

Q86X52

Ensembl transtripts involved in fusion geneENST00000435505, ENST00000417641, 
ENST00000478687, ENST00000412104, 
ENST00000340157, ENST00000440705, 
ENST00000254190, ENST00000543813, 
Fusion gene scores* DoF score3 X 3 X 2=183 X 2 X 3=18
# samples 33
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: VRK2 [Title/Abstract] AND CHSY1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneVRK2

GO:0046777

protein autophosphorylation

14645249|16704422

TgeneCHSY1

GO:0030206

chondroitin sulfate biosynthetic process

11514575


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVBRCATCGA-E9-A1NF-01AVRK2chr2

58276102

+CHSY1chr15

101719185

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shiftENST00000435505ENST00000254190VRK2chr2

58276102

+CHSY1chr15

101719185

-
5CDS-5UTRENST00000435505ENST00000543813VRK2chr2

58276102

+CHSY1chr15

101719185

-
Frame-shiftENST00000417641ENST00000254190VRK2chr2

58276102

+CHSY1chr15

101719185

-
5CDS-5UTRENST00000417641ENST00000543813VRK2chr2

58276102

+CHSY1chr15

101719185

-
intron-3CDSENST00000478687ENST00000254190VRK2chr2

58276102

+CHSY1chr15

101719185

-
intron-5UTRENST00000478687ENST00000543813VRK2chr2

58276102

+CHSY1chr15

101719185

-
Frame-shiftENST00000412104ENST00000254190VRK2chr2

58276102

+CHSY1chr15

101719185

-
5CDS-5UTRENST00000412104ENST00000543813VRK2chr2

58276102

+CHSY1chr15

101719185

-
Frame-shiftENST00000340157ENST00000254190VRK2chr2

58276102

+CHSY1chr15

101719185

-
5CDS-5UTRENST00000340157ENST00000543813VRK2chr2

58276102

+CHSY1chr15

101719185

-
Frame-shiftENST00000440705ENST00000254190VRK2chr2

58276102

+CHSY1chr15

101719185

-
5CDS-5UTRENST00000440705ENST00000543813VRK2chr2

58276102

+CHSY1chr15

101719185

-

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FusionProtFeatures for VRK2_CHSY1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
VRK2

Q86Y07

CHSY1

Q86X52

Has both beta-1,3-glucuronic acid and beta-1,4-N-acetylgalactosamine transferase activity. Transfers glucuronicacid (GlcUA) from UDP-GlcUA and N-acetylgalactosamine (GalNAc)from UDP-GalNAc to the non-reducing end of the elongatingchondroitin polymer. Involved in the negative control ofosteogenesis likely through the modulation of NOTCH signaling.{ECO:0000269|PubMed:11514575, ECO:0000269|PubMed:21129727}.

check buttonRetention 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for VRK2_CHSY1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for VRK2_CHSY1


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
VRK2CDC42, TP53, LNX1, MAPK8IP1, MAPK8IP2, MAP3K7, MAP2K7, MAPK8, LMNA, CCT4, TCP1, CCT2, RBX1, ILK, FAM187B, SPINT2, SRPRB, FAF2, TCTN2, TCTN3, EVC2, TMEM17, TMEM216, TMEM67, LDHD, CTDNEP1, TMPRSS3, ZNRF4CHSY1ELAVL1, HLA-DPA1, PEX19, PLAUR, DCN, SDF4, SLC39A4, PTCH1, PON2, GOLT1B, FOXN3, CHSY3, CSGALNACT2, ATP2B2, SCGB2A2, KCNA10, SLC39A12


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for VRK2_CHSY1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for VRK2_CHSY1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneVRK2C0036341Schizophrenia2PSYGENET
TgeneCHSY1C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneCHSY1C1854466Temtamy preaxial brachydactyly syndrome1ORPHANET;UNIPROT