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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: 20312

FusionGeneSummary for LSAMP_CCDC58

check button Fusion gene summary
Fusion gene informationFusion gene name: LSAMP_CCDC58
Fusion gene ID: 20312
HgeneTgene
Gene symbol

LSAMP

CCDC58

Gene ID

4045

131076

Gene namelimbic system associated membrane proteincoiled-coil domain containing 58
SynonymsIGLON3|LAMP-
Cytomap

3q13.31

3q21.1

Type of geneprotein-codingprotein-coding
Descriptionlimbic system-associated membrane proteinIgLON family member 3coiled-coil domain-containing protein 58
Modification date2018052220180519
UniProtAcc

Q13449

Q4VC31

Ensembl transtripts involved in fusion geneENST00000539563, ENST00000490035, 
ENST00000498645, 
ENST00000291458, 
ENST00000497726, ENST00000466854, 
ENST00000479899, 
Fusion gene scores* DoF score6 X 7 X 4=1684 X 2 X 3=24
# samples 84
** MAII scorelog2(8/168*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: LSAMP [Title/Abstract] AND CCDC58 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationTumor suppressor gene involved fusion gene, in-frame but not retained their domain.
* 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
TCGARVSARCTCGA-SG-A6Z4-01ALSAMPchr3

117716029

-CCDC58chr3

122081874

-
* 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
In-frameENST00000539563ENST00000291458LSAMPchr3

117716029

-CCDC58chr3

122081874

-
In-frameENST00000539563ENST00000497726LSAMPchr3

117716029

-CCDC58chr3

122081874

-
5CDS-5UTRENST00000539563ENST00000466854LSAMPchr3

117716029

-CCDC58chr3

122081874

-
5CDS-5UTRENST00000539563ENST00000479899LSAMPchr3

117716029

-CCDC58chr3

122081874

-
intron-3CDSENST00000490035ENST00000291458LSAMPchr3

117716029

-CCDC58chr3

122081874

-
intron-3CDSENST00000490035ENST00000497726LSAMPchr3

117716029

-CCDC58chr3

122081874

-
intron-5UTRENST00000490035ENST00000466854LSAMPchr3

117716029

-CCDC58chr3

122081874

-
intron-5UTRENST00000490035ENST00000479899LSAMPchr3

117716029

-CCDC58chr3

122081874

-
intron-3CDSENST00000498645ENST00000291458LSAMPchr3

117716029

-CCDC58chr3

122081874

-
intron-3CDSENST00000498645ENST00000497726LSAMPchr3

117716029

-CCDC58chr3

122081874

-
intron-5UTRENST00000498645ENST00000466854LSAMPchr3

117716029

-CCDC58chr3

122081874

-
intron-5UTRENST00000498645ENST00000479899LSAMPchr3

117716029

-CCDC58chr3

122081874

-

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FusionProtFeatures for LSAMP_CCDC58


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

Q13449

CCDC58

Q4VC31

Mediates selective neuronal growth and axon targeting.Contributes to the guidance of developing axons and remodeling ofmature circuits in the limbic system. Essential for normal growthof the hyppocampal mossy fiber projection (By similarity).{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
HgeneLSAMPchr3:117716029chr3:122081874ENST00000490035-17132_214-167339DomainNote=Ig-like C2-type 2
HgeneLSAMPchr3:117716029chr3:122081874ENST00000490035-17219_304-167339DomainNote=Ig-like C2-type 3
HgeneLSAMPchr3:117716029chr3:122081874ENST00000490035-1729_122-167339DomainNote=Ig-like C2-type 1
TgeneCCDC58chr3:117716029chr3:122081874ENST00000291458-2582_120108145Coiled coilOntology_term=ECO:0000255


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FusionGeneSequence for LSAMP_CCDC58


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.
>In-frame_LSAMP_ENST00000539563_chr3_117716029_-_CCDC58_ENST00000291458_chr3_122081874_-_59aa

>In-frame_LSAMP_ENST00000539563_chr3_117716029_-_CCDC58_ENST00000497726_chr3_122081874_-_59aa


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_LSAMP_ENST00000539563_chr3_117716029_-_CCDC58_ENST00000291458_chr3_122081874_-_178nt
ATGAGGACCTACTGGCTGCACAGCGTCTGGGTGCTGGGCTTTTTCCTGTCCCTCTTCTCATTGCAAGTTGAAATGGATGCAGTCAGAACT

>In-frame_LSAMP_ENST00000539563_chr3_117716029_-_CCDC58_ENST00000497726_chr3_122081874_-_178nt
ATGAGGACCTACTGGCTGCACAGCGTCTGGGTGCTGGGCTTTTTCCTGTCCCTCTTCTCATTGCAAGTTGAAATGGATGCAGTCAGAACT


* Fusion transcript sequences (Full-length transcript).
>In-frame_LSAMP_ENST00000539563_chr3_117716029_-_CCDC58_ENST00000291458_chr3_122081874_-_456nt
ATGAGGACCTACTGGCTGCACAGCGTCTGGGTGCTGGGCTTTTTCCTGTCCCTCTTCTCATTGCAAGTTGAAATGGATGCAGTCAGAACT
GAATGTTGAAGAAGTGGTAAATGACAGGAGCTGGAAGGTGTTTAATGAACGCTGCCGAATTCACTTCAAGCCTCCAAAGAATGAATAAAG
AGAGATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAGGACTGGGTCATCTCATAAGAGCTAAGCATGACAGATATCAACAGGGCGGGC
TTTCTAGGATGATTTCTGAGCCAACAGTCCAAGACCTTTTGTTGATTTCAGCCCCACTTAGCCAAGACCTCAAGTATAAATAATTCTGAT
AATTATGGAGAAATCAACTGCTATTTTATACTGATTCTGTAAAAAAAAAAAAAAAAAATTTTTGTAACTATTAAAATAATTTTCTGACTC

>In-frame_LSAMP_ENST00000539563_chr3_117716029_-_CCDC58_ENST00000497726_chr3_122081874_-_447nt
ATGAGGACCTACTGGCTGCACAGCGTCTGGGTGCTGGGCTTTTTCCTGTCCCTCTTCTCATTGCAAGTTGAAATGGATGCAGTCAGAACT
GAATGTTGAAGAAGTGGTAAATGACAGGAGCTGGAAGGTGTTTAATGAACGCTGCCGAATTCACTTCAAGCCTCCAAAGAATGAATAAAG
AGAGATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAGGACTGGGTCATCTCATAAGAGCTAAGCATGACAGATATCAACAGGGCGGGC
TTTCTAGGATGATTTCTGAGCCAACAGTCCAAGACCTTTTGTTGATTTCAGCCCCACTTAGCCAAGACCTCAAGTATAAATAATTCTGAT


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FusionGenePPI for LSAMP_CCDC58


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
LSAMPNTM, LSAMP, NEGR1, DNAAF2CCDC58ELAVL1, SHMT2, FUBP1, GNB2L1, HSPA9, TIAL1, UBE2D2, PCBP2, PITPNA, STAMBP, CCDC58, DNAJC19, AFG3L2, MTFMT, PAM16, CYCS, ECH1


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 LSAMP_CCDC58


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 LSAMP_CCDC58


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLSAMPC0036341Schizophrenia1PSYGENET
HgeneLSAMPC0041696Unipolar Depression1PSYGENET
HgeneLSAMPC1269683Major Depressive Disorder1PSYGENET