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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: 7439

FusionGeneSummary for CLN3_SIVA1

check button Fusion gene summary
Fusion gene informationFusion gene name: CLN3_SIVA1
Fusion gene ID: 7439
HgeneTgene
Gene symbol

CLN3

SIVA1

Gene ID

1201

10572

Gene nameCLN3, batteninSIVA1 apoptosis inducing factor
SynonymsBTN1|BTS|JNCLCD27BP|SIVA|Siva-1|Siva-2
Cytomap

16p12.1

14q32.33

Type of geneprotein-codingprotein-coding
Descriptionbatteninbatten disease proteinceroid-lipofuscinosis, neuronal 3apoptosis regulatory protein SivaCD27-binding (Siva) protein
Modification date2018052320180519
UniProtAcc

Q13286

O15304

Ensembl transtripts involved in fusion geneENST00000568224, ENST00000535392, 
ENST00000359984, ENST00000360019, 
ENST00000569430, ENST00000333496, 
ENST00000355477, ENST00000354630, 
ENST00000357806, ENST00000357857, 
ENST00000567963, ENST00000395653, 
ENST00000565316, ENST00000357076, 
ENST00000567160, 		ENST00000329967, 
ENST00000347067, 
Fusion gene scores* DoF score2 X 2 X 2=85 X 3 X 5=75
# samples 25
** MAII scorelog2(2/8*10)=1.32192809488736log2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLN3 [Title/Abstract] AND SIVA1 [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
HgeneCLN3

GO:0006672

ceramide metabolic process

15240864

HgeneCLN3

GO:0015809

arginine transport

16251196

HgeneCLN3

GO:0035752

lysosomal lumen pH elevation

10924275

HgeneCLN3

GO:0042987

amyloid precursor protein catabolic process

10924275

TgeneSIVA1

GO:0097191

extrinsic apoptotic signaling pathway

9177220


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
TCGALDOVTCGA-29-A5NZ-01ACLN3chr16

28497668

-SIVA1chr14

105225556

+
* 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
5CDS-intronENST00000568224ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000568224ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000535392ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000535392ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000359984ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000359984ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000360019ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000360019ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000569430ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000569430ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000333496ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000333496ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000355477ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000355477ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000354630ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000354630ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000357806ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000357806ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000357857ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000357857ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000567963ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000567963ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000395653ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000395653ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000565316ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
5CDS-intronENST00000565316ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000357076ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000357076ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000567160ENST00000329967CLN3chr16

28497668

-SIVA1chr14

105225556

+
intron-intronENST00000567160ENST00000347067CLN3chr16

28497668

-SIVA1chr14

105225556

+

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FusionProtFeatures for CLN3_SIVA1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CLN3

Q13286

SIVA1

O15304

Induces CD27-mediated apoptosis. Inhibits BCL2L1 isoformBcl-x(L) anti-apoptotic activity. Inhibits activation of NF-kappa-B and promotes T-cell receptor-mediated apoptosis.{ECO:0000269|PubMed:12011449, ECO:0000269|PubMed:14739602,ECO:0000269|PubMed:15034012, ECO:0000269|PubMed:15958577,ECO:0000269|PubMed:16491128}.

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 CLN3_SIVA1


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 CLN3_SIVA1


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
CLN3SBDS, COX15, IMMT, GCN1L1, KIAA0368, XPOT, PRKDC, ESYT2, HSD17B12, SEC61A2, ABCD3, SLC25A11, RPN2, AFG3L2, IRAK1, UNC45A, NUP205, XPO1, NUP93, ATG7, TRIP13, CYC1, DDX20, SIGMAR1, RIF1, AUP1, SLC25A10, VDAC2, GEMIN4, SFXN4, SLC25A22, TELO2, PHB, NPEPPS, FANCI, CCDC47, GANAB, CKAP4, DDOST, CAND1, CPT1A, ILVBL, TMPO, ELAVL1, KCNIP3, SLC25A4, SLC25A5, SLC25A6, SLC25A13, ATP2A2, PHGDH, SFXN3, SLC25A3, ARF4, TECR, DBH, SFXN1, TMEM33, PTPLAD1, LPHN2, DPM1, SLC25A1, SSR4, RPN1, XPO5, RCN2, CALU, FADS2, UQCRC2, SCAMP3, ERLIN2, ARF3, ATP1A1, ARF5, FKBP8, C19orf70, SAMM50, CDS2, STRA6, SEC61A1, EMD, ATP5L, FAR1, ARMC6, LPGAT1, SLC35B2, TFRC, CSE1L, PTH1R, RARS2, B3GALT2SIVA1CD27, LPAR2, S1PR4, PXMP2, TP53, MDM2, NEDD4, NEDD4L, XIAP, MAP3K7, APP, CDKN2A, UBE2D1, NGFRAP1, PCNA, TBXA2R, TRAF2, RAD18, TYK2, FOXP3, CD4, TCAP, MEFV, STMN1, CAMK2G, RHOU


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 CLN3_SIVA1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneSIVA1O15304DB01593ZincApoptosis regulatory protein Sivasmall moleculeapproved|investigational

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RelatedDiseases for CLN3_SIVA1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCLN3C0751383Juvenile Neuronal Ceroid Lipofuscinosis2ORPHANET;UNIPROT
HgeneCLN3C0038356Stomach Neoplasms1CTD_human
TgeneSIVA1C0010246Coxsackievirus Infections1CTD_human