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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:GPM6A-SCLT1 (FusionGDB2 ID:34194)

Fusion Gene Summary for GPM6A-SCLT1

check button Fusion gene summary
Fusion gene informationFusion gene name: GPM6A-SCLT1
Fusion gene ID: 34194
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 date2020031320200313
UniProtAcc

P51674

.
Ensembl transtripts involved in fusion geneENST00000280187, ENST00000393658, 
ENST00000506894, ENST00000515090, 
ENST00000506219, 		ENST00000281142, 
ENST00000434680, ENST00000439369, 
ENST00000503215, ENST00000502495, 
ENST00000506368, ENST00000511426, 
ENST00000503401, 
Fusion gene scores* DoF score6 X 7 X 1=425 X 5 X 3=75
# samples 75
** MAII scorelog2(7/42*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

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

Most frequent breakpointGPM6A(176561949)-SCLT1(129858004), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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 buttonFusion gene breakpoints across GPM6A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across SCLT1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS5.0N/ABF956714GPM6Achr4

176561949

+SCLT1chr4

129858004

-


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Fusion Gene ORF analysis for GPM6A-SCLT1

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

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for GPM6A-SCLT1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for GPM6A-SCLT1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

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

P51674

.
FUNCTION: Involved in neuronal differentiation, including differentiation and migration of neuronal stem cells. Plays a role in neuronal plasticity and is involved in neurite and filopodia outgrowth, filopodia motility and probably synapse formation. GPM6A-induced filopodia formation involves mitogen-activated protein kinase (MAPK) and Src signaling pathways. May be involved in neuronal NGF-dependent Ca(2+) influx. May be involved in regulation of endocytosis and intracellular trafficking of G-protein-coupled receptors (GPCRs); enhances internalization and recycling of mu-type opioid receptor. {ECO:0000269|PubMed:19298174}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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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Fusion Gene Sequence for GPM6A-SCLT1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis 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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Related Drugs for GPM6A-SCLT1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for GPM6A-SCLT1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGPM6AC0036341Schizophrenia1PSYGENET
HgeneGPM6AC2239176Liver carcinoma1CTD_human
TgeneSCLT1C0403553Renal dysplasia and retinal aplasia (disorder)3GENOMICS_ENGLAND
TgeneSCLT1C0029294Orofaciodigital Syndromes1GENOMICS_ENGLAND