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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: 19495

FusionGeneSummary for LAS1L_SDC3

check button Fusion gene summary
Fusion gene informationFusion gene name: LAS1L_SDC3
Fusion gene ID: 19495
HgeneTgene
Gene symbol

LAS1L

SDC3

Gene ID

81887

9672

Gene nameLAS1 like, ribosome biogenesis factorsyndecan 3
SynonymsLas1-like|WTS|dJ475B7.2SDCN|SYND3
Cytomap

Xq12

1p35.2

Type of geneprotein-codingprotein-coding
Descriptionribosomal biogenesis protein LAS1Lprotein LAS1 homologsyndecan-3N-syndecansyndecan neural typesyndecan proteoglycan 3
Modification date2018052320180523
UniProtAcc

Q9Y4W2

O75056

Ensembl transtripts involved in fusion geneENST00000374807, ENST00000374811, 
ENST00000374804, ENST00000312391, 
ENST00000336798, ENST00000339394, 
ENST00000471567, 
Fusion gene scores* DoF score2 X 2 X 2=88 X 8 X 5=320
# samples 211
** MAII scorelog2(2/8*10)=1.32192809488736log2(11/320*10)=-1.5405683813627
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LAS1L [Title/Abstract] AND SDC3 [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

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
ChiTaRS3.1BF935530LAS1LchrX

64739256

+SDC3chr1

31345192

+
* 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
intron-3UTRENST00000374807ENST00000336798LAS1LchrX

64739256

+SDC3chr1

31345192

+
intron-intronENST00000374807ENST00000339394LAS1LchrX

64739256

+SDC3chr1

31345192

+
intron-intronENST00000374807ENST00000471567LAS1LchrX

64739256

+SDC3chr1

31345192

+
intron-3UTRENST00000374811ENST00000336798LAS1LchrX

64739256

+SDC3chr1

31345192

+
intron-intronENST00000374811ENST00000339394LAS1LchrX

64739256

+SDC3chr1

31345192

+
intron-intronENST00000374811ENST00000471567LAS1LchrX

64739256

+SDC3chr1

31345192

+
intron-3UTRENST00000374804ENST00000336798LAS1LchrX

64739256

+SDC3chr1

31345192

+
intron-intronENST00000374804ENST00000339394LAS1LchrX

64739256

+SDC3chr1

31345192

+
intron-intronENST00000374804ENST00000471567LAS1LchrX

64739256

+SDC3chr1

31345192

+
intron-3UTRENST00000312391ENST00000336798LAS1LchrX

64739256

+SDC3chr1

31345192

+
intron-intronENST00000312391ENST00000339394LAS1LchrX

64739256

+SDC3chr1

31345192

+
intron-intronENST00000312391ENST00000471567LAS1LchrX

64739256

+SDC3chr1

31345192

+

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FusionProtFeatures for LAS1L_SDC3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LAS1L

Q9Y4W2

SDC3

O75056

Involved in the biogenesis of the 60S ribosomal subunit.Required for maturation of the 28S rRNA. Functions as a componentof the Five Friends of Methylated CHTOP (5FMC) complex; the 5FMCcomplex is recruited to ZNF148 by methylated CHTOP, leading todesumoylation of ZNF148 and subsequent transactivation of ZNF148target genes. {ECO:0000269|PubMed:20647540,ECO:0000269|PubMed:22872859}. Cell surface proteoglycan that may bear heparan sulfate(By similarity). May have a role in the organization of cell shapeby affecting the actin cytoskeleton, possibly by transferringsignals from the cell surface in a sugar-dependent mechanism.{ECO:0000250, ECO:0000269|PubMed:11527150}.

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 LAS1L_SDC3


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 LAS1L_SDC3


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


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 LAS1L_SDC3


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 LAS1L_SDC3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource