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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: 15228

FusionGeneSummary for GPM6A_SCLT1

check button Fusion gene summary
Fusion gene informationFusion gene name: GPM6A_SCLT1
Fusion gene ID: 15228
HgeneTgene
Gene symbol

GPM6A

SCLT1

Gene ID

2823

132320

Gene nameglycoprotein M6Asodium channel and clathrin linker 1
SynonymsGPM6|M6ACAP-1A|CAP1A
Cytomap

4q34.2

4q28.2

Type of geneprotein-codingprotein-coding
Descriptionneuronal membrane glycoprotein M6-asodium channel and clathrin linker 1sodium channel-associated protein 1
Modification date2018052320180522
UniProtAcc

P51674

Q96NL6

Ensembl transtripts involved in fusion geneENST00000280187, ENST00000393658, 
ENST00000506894, ENST00000515090, 
ENST00000506219, 		ENST00000281142, 
ENST00000434680, ENST00000439369, 
ENST00000503215, ENST00000502495, 
ENST00000506368, ENST00000511426, 
ENST00000503401, 
Fusion gene scores* DoF score5 X 6 X 1=301 X 1 X 1=1
# samples 61
** MAII scorelog2(6/30*10)=1
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(1/1*10)=3.32192809488736
Context

PubMed: GPM6A [Title/Abstract] AND SCLT1 [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
HgeneGPM6A

GO:0001764

neuron migration

19298174

HgeneGPM6A

GO:0048863

stem cell differentiation

19298174


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
ChiTaRS3.1BF956714GPM6Achr4

176561949

+SCLT1chr4

129858004

-
* 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-3CDSENST00000280187ENST00000281142GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000280187ENST00000434680GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000280187ENST00000439369GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000280187ENST00000503215GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-5UTRENST00000280187ENST00000502495GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000280187ENST00000506368GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000280187ENST00000511426GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000280187ENST00000503401GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-3CDSENST00000393658ENST00000281142GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000393658ENST00000434680GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000393658ENST00000439369GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000393658ENST00000503215GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-5UTRENST00000393658ENST00000502495GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000393658ENST00000506368GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000393658ENST00000511426GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000393658ENST00000503401GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-3CDSENST00000506894ENST00000281142GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000506894ENST00000434680GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000506894ENST00000439369GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000506894ENST00000503215GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-5UTRENST00000506894ENST00000502495GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000506894ENST00000506368GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000506894ENST00000511426GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000506894ENST00000503401GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-3CDSENST00000515090ENST00000281142GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000515090ENST00000434680GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000515090ENST00000439369GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000515090ENST00000503215GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-5UTRENST00000515090ENST00000502495GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000515090ENST00000506368GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000515090ENST00000511426GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000515090ENST00000503401GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-3CDSENST00000506219ENST00000281142GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000506219ENST00000434680GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000506219ENST00000439369GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000506219ENST00000503215GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-5UTRENST00000506219ENST00000502495GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000506219ENST00000506368GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000506219ENST00000511426GPM6Achr4

176561949

+SCLT1chr4

129858004

-
intron-intronENST00000506219ENST00000503401GPM6Achr4

176561949

+SCLT1chr4

129858004

-

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FusionProtFeatures for GPM6A_SCLT1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
GPM6A

P51674

SCLT1

Q96NL6

Involved in neuronal differentiation, includingdifferentiation and migration of neuronal stem cells. Plays a rolein neuronal plasticity and is involved in neurite and filopodiaoutgrowth, filopodia motility and probably synapse formation.GPM6A-induced filopodia formation involves mitogen-activatedprotein kinase (MAPK) and Src signaling pathways. May be involvedin neuronal NGF-dependent Ca(2+) influx. May be involved inregulation of endocytosis and intracellular trafficking of G-protein-coupled receptors (GPCRs); enhances internalization andrecycling of mu-type opioid receptor.{ECO:0000269|PubMed:19298174}. Adapter protein that links SCN10A to clathrin. RegulatesSCN10A channel activity, possibly by promoting channelinternalization (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


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FusionGeneSequence for GPM6A_SCLT1


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 GPM6A_SCLT1


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 GPM6A_SCLT1


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 GPM6A_SCLT1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGPM6AC0036341Schizophrenia1PSYGENET