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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: 20318

FusionGeneSummary for LSM10_CLSTN1

check button Fusion gene summary
Fusion gene informationFusion gene name: LSM10_CLSTN1
Fusion gene ID: 20318
HgeneTgene
Gene symbol

LSM10

CLSTN1

Gene ID

84967

22883

Gene nameLSM10, U7 small nuclear RNA associatedcalsyntenin 1
SynonymsMST074|MSTP074ALC-ALPHA|CDHR12|CST-1|CSTN1|PIK3CD|XB31alpha|alcalpha1|alcalpha2
Cytomap

1p34.3

1p36.22

Type of geneprotein-codingprotein-coding
DescriptionU7 snRNA-associated Sm-like protein LSm10U7 snRNP-specific Sm-like protein LSM10calsyntenin-1alcadein-alphaalzheimer-related cadherin-like proteincadherin-related family member 12non-classical cadherin XB31alpha
Modification date2018051920180523
UniProtAcc

Q969L4

O94985

Ensembl transtripts involved in fusion geneENST00000476041, ENST00000315732, 
ENST00000377298, ENST00000361311, 
ENST00000377288, ENST00000477264, 
Fusion gene scores* DoF score1 X 1 X 1=15 X 5 X 3=75
# samples 17
** MAII scorelog2(1/1*10)=3.32192809488736log2(7/75*10)=-0.0995356735509144
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LSM10 [Title/Abstract] AND CLSTN1 [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
TCGALDBRCATCGA-AQ-A04J-01ALSM10chr1

36859367

-CLSTN1chr1

9790763

-
* 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
5UTR-3CDSENST00000476041ENST00000377298LSM10chr1

36859367

-CLSTN1chr1

9790763

-
5UTR-3CDSENST00000476041ENST00000361311LSM10chr1

36859367

-CLSTN1chr1

9790763

-
5UTR-3CDSENST00000476041ENST00000377288LSM10chr1

36859367

-CLSTN1chr1

9790763

-
5UTR-5UTRENST00000476041ENST00000477264LSM10chr1

36859367

-CLSTN1chr1

9790763

-
intron-3CDSENST00000315732ENST00000377298LSM10chr1

36859367

-CLSTN1chr1

9790763

-
intron-3CDSENST00000315732ENST00000361311LSM10chr1

36859367

-CLSTN1chr1

9790763

-
intron-3CDSENST00000315732ENST00000377288LSM10chr1

36859367

-CLSTN1chr1

9790763

-
intron-5UTRENST00000315732ENST00000477264LSM10chr1

36859367

-CLSTN1chr1

9790763

-

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FusionProtFeatures for LSM10_CLSTN1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LSM10

Q969L4

CLSTN1

O94985

Appears to function in the U7 snRNP complex that isinvolved in histone 3'-end processing. Increases U7 snRNA levelsbut not histone 3'-end pre-mRNA processing activity, whenoverexpressed. Required for cell cycle progression from G1 to Sphases. Binds specifically to U7 snRNA. Binds to the downstreamcleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependentmanner. {ECO:0000269|PubMed:16914750}. Induces KLC1 association with vesicles and functions asa cargo in axonal anterograde transport. Complex formation withAPBA2 and APP, stabilizes APP metabolism and enhances APBA2-mediated suppression of beta-APP40 secretion, due to theretardation of intracellular APP maturation. In complex with APBA2and C99, a C-terminal APP fragment, abolishes C99 interaction withPSEN1 and thus APP C99 cleavage by gamma-secretase, most probablythrough stabilization of the direct interaction between APBA2 andAPP. The intracellular fragment AlcICD suppresses APBB1-dependenttransactivation stimulated by APP C-terminal intracellularfragment (AICD), most probably by competing with AICD for APBB1-binding. May modulate calcium-mediated postsynaptic signals (Bysimilarity). {ECO:0000250, ECO:0000269|PubMed:12972431}.

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 LSM10_CLSTN1


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 LSM10_CLSTN1


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
LSM10LSM3, ZNF473, CLNS1A, SMN1, MOV10, NXF1, TGS1, SNRPF, LSM6, SNRPGCLSTN1APBA2, APP, PSEN1, TRIP12, SETDB1, SLK, MCM3AP, BAHCC1, MDM2, TM2D3, PVRIG, GINM1, CD96, CHST8, DEFA5, SCGB1D1, APBA3, PCDHA4, SLAMF1, CDCP1, LYPD5, GML, MGAT4C, ADAM33, LRRTM1, P2RX5, PCDH20, TRIM25


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 LSM10_CLSTN1


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 LSM10_CLSTN1


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