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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:SQSTM1-GRIA1 (FusionGDB2 ID:85614)

Fusion Gene Summary for SQSTM1-GRIA1

check button Fusion gene summary
Fusion gene informationFusion gene name: SQSTM1-GRIA1
Fusion gene ID: 85614
HgeneTgene
Gene symbol

SQSTM1

GRIA1

Gene ID

8878

2890

Gene namesequestosome 1glutamate ionotropic receptor AMPA type subunit 1
SynonymsA170|DMRV|FTDALS3|NADGP|OSIL|PDB3|ZIP3|p60|p62|p62BGLUH1|GLUR1|GLURA|GluA1|HBGR1
Cytomap

5q35.3

5q33.2

Type of geneprotein-codingprotein-coding
Descriptionsequestosome-1EBI3-associated protein of 60 kDaEBI3-associated protein p60EBIAPautophagy receptor p62oxidative stress induced likephosphotyrosine independent ligand for the Lck SH2 domain p62phosphotyrosine-independent ligand for the Lck SH2 domainglutamate receptor 1AMPA 1AMPA-selective glutamate receptor 1gluR-1gluR-AgluR-K1glutamate receptor, ionotropic, AMPA 1
Modification date2020032720200329
UniProtAcc.

P42261

Ensembl transtripts involved in fusion geneENST00000376929, ENST00000506690, 
ENST00000389805, ENST00000402874, 
ENST00000510187, ENST00000360718, 
ENST00000285900, ENST00000518142, 
ENST00000340592, ENST00000521843, 
ENST00000448073, ENST00000518783, 
ENST00000518862, 
Fusion gene scores* DoF score29 X 23 X 12=80044 X 4 X 3=48
# samples 334
** MAII scorelog2(33/8004*10)=-4.60018323765993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SQSTM1 [Title/Abstract] AND GRIA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSQSTM1(179233591)-GRIA1(153077604), # samples:2
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
HgeneSQSTM1

GO:0006914

autophagy

20452972

HgeneSQSTM1

GO:0007032

endosome organization

27368102

HgeneSQSTM1

GO:0031397

negative regulation of protein ubiquitination

20452972

HgeneSQSTM1

GO:0061635

regulation of protein complex stability

25127057

HgeneSQSTM1

GO:1905719

protein localization to perinuclear region of cytoplasm

27368102


check buttonFusion gene breakpoints across SQSTM1 (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 GRIA1 (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
ChimerDB4LUADTCGA-95-A4VK-01ASQSTM1chr5

179233591

+GRIA1chr5

153077604

+
ChimerDB4LUADTCGA-95-A4VK-01ASQSTM1chr5

179233591

-GRIA1chr5

153077604

+


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Fusion Gene ORF analysis for SQSTM1-GRIA1

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-3CDSENST00000376929ENST00000285900SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
5UTR-3CDSENST00000376929ENST00000518142SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
5UTR-3CDSENST00000376929ENST00000340592SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
5UTR-3CDSENST00000376929ENST00000521843SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
5UTR-3CDSENST00000376929ENST00000448073SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
5UTR-3CDSENST00000376929ENST00000518783SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
5UTR-intronENST00000376929ENST00000518862SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000506690ENST00000285900SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000506690ENST00000518142SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000506690ENST00000340592SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000506690ENST00000521843SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000506690ENST00000448073SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000506690ENST00000518783SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-intronENST00000506690ENST00000518862SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000389805ENST00000285900SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000389805ENST00000518142SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000389805ENST00000340592SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000389805ENST00000521843SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000389805ENST00000448073SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000389805ENST00000518783SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-intronENST00000389805ENST00000518862SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000402874ENST00000285900SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000402874ENST00000518142SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000402874ENST00000340592SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000402874ENST00000521843SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000402874ENST00000448073SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000402874ENST00000518783SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-intronENST00000402874ENST00000518862SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000510187ENST00000285900SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000510187ENST00000518142SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000510187ENST00000340592SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000510187ENST00000521843SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000510187ENST00000448073SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000510187ENST00000518783SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-intronENST00000510187ENST00000518862SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000360718ENST00000285900SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000360718ENST00000518142SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000360718ENST00000340592SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000360718ENST00000521843SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000360718ENST00000448073SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-3CDSENST00000360718ENST00000518783SQSTM1chr5

179233591

+GRIA1chr5

153077604

+
intron-intronENST00000360718ENST00000518862SQSTM1chr5

179233591

+GRIA1chr5

153077604

+

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 SQSTM1-GRIA1


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)
SQSTM1chr5179233591+GRIA1chr5153077603+0.0050348260.99496514
SQSTM1chr5179233591+GRIA1chr5153077603+0.0050348260.99496514

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 SQSTM1-GRIA1


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
.GRIA1

P42261

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.FUNCTION: Ionotropic glutamate receptor. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L-glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. In the presence of CACNG4 or CACNG7 or CACNG8, shows resensitization which is characterized by a delayed accumulation of current flux upon continued application of glutamate. {ECO:0000269|PubMed:20805473, ECO:0000269|PubMed:21172611}.

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 SQSTM1-GRIA1


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 SQSTM1-GRIA1


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 SQSTM1-GRIA1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneGRIA1P42261DB00898EthanolSmall moleculeApproved
TgeneGRIA1P42261DB00898EthanolSmall moleculeApproved
TgeneGRIA1P42261DB00898EthanolSmall moleculeApproved
TgeneGRIA1P42261DB01189DesfluraneAntagonistSmall moleculeApproved
TgeneGRIA1P42261DB01189DesfluraneAntagonistSmall moleculeApproved
TgeneGRIA1P42261DB01189DesfluraneAntagonistSmall moleculeApproved
TgeneGRIA1P42261DB08883PerampanelAntagonistSmall moleculeApproved
TgeneGRIA1P42261DB08883PerampanelAntagonistSmall moleculeApproved
TgeneGRIA1P42261DB08883PerampanelAntagonistSmall moleculeApproved
TgeneGRIA1P42261DB13146Fluciclovine (18F)InhibitorSmall moleculeApproved
TgeneGRIA1P42261DB13146Fluciclovine (18F)InhibitorSmall moleculeApproved
TgeneGRIA1P42261DB13146Fluciclovine (18F)InhibitorSmall moleculeApproved
TgeneGRIA1P42261DB00237ButabarbitalAntagonistSmall moleculeApproved|Illicit
TgeneGRIA1P42261DB00237ButabarbitalAntagonistSmall moleculeApproved|Illicit
TgeneGRIA1P42261DB00237ButabarbitalAntagonistSmall moleculeApproved|Illicit
TgeneGRIA1P42261DB00555LamotrigineInhibitorSmall moleculeApproved|Investigational
TgeneGRIA1P42261DB00555LamotrigineInhibitorSmall moleculeApproved|Investigational
TgeneGRIA1P42261DB00555LamotrigineInhibitorSmall moleculeApproved|Investigational
TgeneGRIA1P42261DB01028MethoxyfluraneAntagonistSmall moleculeApproved|Investigational|Vet_approved
TgeneGRIA1P42261DB01028MethoxyfluraneAntagonistSmall moleculeApproved|Investigational|Vet_approved
TgeneGRIA1P42261DB01028MethoxyfluraneAntagonistSmall moleculeApproved|Investigational|Vet_approved
TgeneGRIA1P42261DB00142Glutamic acidSmall moleculeApproved|Nutraceutical
TgeneGRIA1P42261DB00142Glutamic acidSmall moleculeApproved|Nutraceutical
TgeneGRIA1P42261DB00142Glutamic acidSmall moleculeApproved|Nutraceutical
TgeneGRIA1P42261DB00753IsofluraneAntagonistSmall moleculeApproved|Vet_approved
TgeneGRIA1P42261DB00753IsofluraneAntagonistSmall moleculeApproved|Vet_approved
TgeneGRIA1P42261DB00753IsofluraneAntagonistSmall moleculeApproved|Vet_approved
TgeneGRIA1P42261DB01236SevofluraneAntagonistSmall moleculeApproved|Vet_approved
TgeneGRIA1P42261DB01236SevofluraneAntagonistSmall moleculeApproved|Vet_approved
TgeneGRIA1P42261DB01236SevofluraneAntagonistSmall moleculeApproved|Vet_approved

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Related Diseases for SQSTM1-GRIA1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSQSTM1C4085252PAGET DISEASE OF BONE 39GENOMICS_ENGLAND;UNIPROT
HgeneSQSTM1C0002736Amyotrophic Lateral Sclerosis5CTD_human;ORPHANET
HgeneSQSTM1C4225326FRONTOTEMPORAL DEMENTIA AND/OR AMYOTROPHIC LATERAL SCLEROSIS 34CTD_human;UNIPROT
HgeneSQSTM1C0029463Osteosarcoma2GENOMICS_ENGLAND
HgeneSQSTM1C0221054Welander Distal Myopathy1ORPHANET
HgeneSQSTM1C0242383Age related macular degeneration1CTD_human
HgeneSQSTM1C0393554Amyotrophic Lateral Sclerosis With Dementia1CTD_human
HgeneSQSTM1C0543859Amyotrophic Lateral Sclerosis, Guam Form1CTD_human
HgeneSQSTM1C1853926NONAKA MYOPATHY1CTD_human;GENOMICS_ENGLAND
HgeneSQSTM1C2931290Welander distal myopathy, Swedish type1ORPHANET
HgeneSQSTM1C3888102Frontotemporal Dementia With Motor Neuron Disease1ORPHANET
HgeneSQSTM1C4011788Behavioral variant of frontotemporal dementia1ORPHANET
TgeneGRIA1C0009171Cocaine Abuse5CTD_human
TgeneGRIA1C0011570Mental Depression5PSYGENET
TgeneGRIA1C0011581Depressive disorder5PSYGENET
TgeneGRIA1C0236736Cocaine-Related Disorders5CTD_human
TgeneGRIA1C0600427Cocaine Dependence5CTD_human
TgeneGRIA1C0005586Bipolar Disorder4PSYGENET
TgeneGRIA1C0036341Schizophrenia2PSYGENET
TgeneGRIA1C0038587Substance Withdrawal Syndrome2CTD_human
TgeneGRIA1C0086189Drug Withdrawal Symptoms2CTD_human
TgeneGRIA1C0087169Withdrawal Symptoms2CTD_human
TgeneGRIA1C0751217Hyperkinesia, Generalized2CTD_human
TgeneGRIA1C3887506Hyperkinesia2CTD_human
TgeneGRIA1C0004352Autistic Disorder1CTD_human
TgeneGRIA1C0016722Frigidity1CTD_human
TgeneGRIA1C0020594Hypoactive Sexual Desire Disorder1CTD_human
TgeneGRIA1C0020649Hypotension1CTD_human
TgeneGRIA1C0023186Learning Disorders1CTD_human
TgeneGRIA1C0026552Morphine Dependence1CTD_human
TgeneGRIA1C0029261Orgasmic Disorder1CTD_human
TgeneGRIA1C0033953Psychosexual Disorders1CTD_human
TgeneGRIA1C0036337Schizoaffective Disorder1PSYGENET
TgeneGRIA1C0036902Sexual Arousal Disorder1CTD_human
TgeneGRIA1C0600272Morphine Abuse1CTD_human
TgeneGRIA1C0751262Adult Learning Disorders1CTD_human
TgeneGRIA1C0751263Learning Disturbance1CTD_human
TgeneGRIA1C0751265Learning Disabilities1CTD_human
TgeneGRIA1C1330966Developmental Academic Disorder1CTD_human
TgeneGRIA1C3714756Intellectual Disability1GENOMICS_ENGLAND