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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: 36833

FusionGeneSummary for SV2A_LIMCH1

check button Fusion gene summary
Fusion gene informationFusion gene name: SV2A_LIMCH1
Fusion gene ID: 36833
HgeneTgene
Gene symbol

SV2A

LIMCH1

Gene ID

9900

22998

Gene namesynaptic vesicle glycoprotein 2ALIM and calponin homology domains 1
SynonymsSV2LIMCH1A|LMO7B
Cytomap

1q21.2

4p13

Type of geneprotein-codingprotein-coding
Descriptionsynaptic vesicle glycoprotein 2ALIM and calponin homology domains-containing protein 1
Modification date2018052320180519
UniProtAcc

Q7L0J3

Q9UPQ0

Ensembl transtripts involved in fusion geneENST00000369146, ENST00000369145, 
ENST00000513024, ENST00000509638, 
ENST00000508501, ENST00000512946, 
ENST00000313860, ENST00000512632, 
ENST00000512820, ENST00000503057, 
ENST00000511496, ENST00000514096, 
ENST00000509277, ENST00000396595, 
ENST00000381753, ENST00000509454, 
ENST00000515785, 
Fusion gene scores* DoF score5 X 5 X 1=2510 X 10 X 6=600
# samples 510
** MAII scorelog2(5/25*10)=1
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(10/600*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SV2A [Title/Abstract] AND LIMCH1 [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
ChiTaRS3.1AA582263SV2Achr1

149875217

+LIMCH1chr4

41643447

+
* 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-intronENST00000369146ENST00000513024SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000509638SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000508501SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000512946SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000313860SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000512632SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000512820SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000503057SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000511496SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000514096SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000509277SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000396595SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000381753SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000509454SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369146ENST00000515785SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000513024SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000509638SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000508501SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000512946SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000313860SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000512632SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000512820SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000503057SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000511496SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000514096SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000509277SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000396595SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000381753SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000509454SV2Achr1

149875217

+LIMCH1chr4

41643447

+
intron-intronENST00000369145ENST00000515785SV2Achr1

149875217

+LIMCH1chr4

41643447

+

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FusionProtFeatures for SV2A_LIMCH1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SV2A

Q7L0J3

LIMCH1

Q9UPQ0

Plays a role in the control of regulated secretion inneural and endocrine cells, enhancing selectively low-frequencyneurotransmission. Positively regulates vesicle fusion bymaintaining the readily releasable pool of secretory vesicles (Bysimilarity). {ECO:0000250}.

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 SV2A_LIMCH1


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 SV2A_LIMCH1


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 SV2A_LIMCH1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneSV2AQ7L0J3DB01202LevetiracetamSynaptic vesicle glycoprotein 2Asmall moleculeapproved|investigational
HgeneSV2AQ7L0J3DB05541BrivaracetamSynaptic vesicle glycoprotein 2Asmall moleculeapproved|investigational

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RelatedDiseases for SV2A_LIMCH1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSV2AC0036341Schizophrenia1PSYGENET
TgeneLIMCH1C0236969Substance-Related Disorders1CTD_human
TgeneLIMCH1C0345967Malignant mesothelioma1CTD_human