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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:ATG7-SLC6A1 (FusionGDB2 ID:HG10533TG6529)

Fusion Gene Summary for ATG7-SLC6A1

check button Fusion gene summary
Fusion gene informationFusion gene name: ATG7-SLC6A1
Fusion gene ID: hg10533tg6529
HgeneTgene
Gene symbol

ATG7

SLC6A1

Gene ID

10533

6529

Gene nameautophagy related 7solute carrier family 6 member 1
SynonymsAPG7-LIKE|APG7L|GSA7GABATHG|GABATR|GAT1|MAE
Cytomap('ATG7')('SLC6A1')

3p25.3

3p25.3

Type of geneprotein-codingprotein-coding
Descriptionubiquitin-like modifier-activating enzyme ATG7APG7 autophagy 7-likeATG12-activating enzyme E1 ATG7hAGP7ubiquitin-activating enzyme E1-like proteinsodium- and chloride-dependent GABA transporter 1GABA transporter 1solute carrier family 6 (neurotransmitter transporter), member 1solute carrier family 6 (neurotransmitter transporter, GABA), member 1
Modification date2020032920200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000354449, ENST00000354956, 
ENST00000446450, ENST00000469654, 
Fusion gene scores* DoF score15 X 16 X 9=21602 X 1 X 2=4
# samples 202
** MAII scorelog2(20/2160*10)=-3.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/4*10)=2.32192809488736
Context

PubMed: ATG7 [Title/Abstract] AND SLC6A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATG7(11314116)-SLC6A1(11057358), # 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
HgeneATG7

GO:0006497

protein lipidation

12890687

HgeneATG7

GO:0009267

cellular response to starvation

20543840

HgeneATG7

GO:0031401

positive regulation of protein modification process

12890687

HgeneATG7

GO:0071455

cellular response to hyperoxia

20543840



check button Fusion gene information
* 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
ChimerDB4UCECTCGA-BK-A0CC-01AATG7chr3

11314116

+SLC6A1chr3

11057358

+


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Fusion Gene ORF analysis for ATG7-SLC6A1

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-3UTRENST00000354449ENST00000462473ATG7chr3

11314116

+SLC6A1chr3

11057358

+
5UTR-3UTRENST00000354956ENST00000462473ATG7chr3

11314116

+SLC6A1chr3

11057358

+
5UTR-3UTRENST00000446450ENST00000462473ATG7chr3

11314116

+SLC6A1chr3

11057358

+
5UTR-5UTRENST00000354449ENST00000287766ATG7chr3

11314116

+SLC6A1chr3

11057358

+
5UTR-5UTRENST00000354956ENST00000287766ATG7chr3

11314116

+SLC6A1chr3

11057358

+
5UTR-5UTRENST00000446450ENST00000287766ATG7chr3

11314116

+SLC6A1chr3

11057358

+
5UTR-intronENST00000354449ENST00000536032ATG7chr3

11314116

+SLC6A1chr3

11057358

+
5UTR-intronENST00000354956ENST00000536032ATG7chr3

11314116

+SLC6A1chr3

11057358

+
5UTR-intronENST00000446450ENST00000536032ATG7chr3

11314116

+SLC6A1chr3

11057358

+
intron-3UTRENST00000469654ENST00000462473ATG7chr3

11314116

+SLC6A1chr3

11057358

+
intron-5UTRENST00000469654ENST00000287766ATG7chr3

11314116

+SLC6A1chr3

11057358

+
intron-intronENST00000469654ENST00000536032ATG7chr3

11314116

+SLC6A1chr3

11057358

+

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 ATG7-SLC6A1


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)
ATG7chr311314116+SLC6A1chr311057357+4.95E-050.9999505
ATG7chr311314116+SLC6A1chr311057357+4.95E-050.9999505


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.
genomic feature of top 1%

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Fusion Protein Features for ATG7-SLC6A1


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:11314116/:11057358)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (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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Fusion Gene Sequence for ATG7-SLC6A1


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 ATG7-SLC6A1


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 ATG7-SLC6A1


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 ATG7-SLC6A1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneATG7C0002871Anemia1CTD_human
HgeneATG7C0023380Lethargy1CTD_human
HgeneATG7C0024312Lymphopenia1CTD_human
HgeneATG7C0027540Necrosis1CTD_human
HgeneATG7C0919267ovarian neoplasm1CTD_human
HgeneATG7C1140680Malignant neoplasm of ovary1CTD_human
HgeneATG7C1262477Weight decreased1CTD_human
HgeneATG7C2239176Liver carcinoma1CTD_human
TgeneC0011570Mental Depression2PSYGENET
TgeneC0011581Depressive disorder2PSYGENET
TgeneC1535926Neurodevelopmental Disorders2CTD_human
TgeneC0001973Alcoholic Intoxication, Chronic1PSYGENET
TgeneC0002736Amyotrophic Lateral Sclerosis1CTD_human
TgeneC0014544Epilepsy1CTD_human
TgeneC0022333Jacksonian Seizure1CTD_human
TgeneC0036341Schizophrenia1CTD_human
TgeneC0036572Seizures1CTD_human
TgeneC0038587Substance Withdrawal Syndrome1CTD_human
TgeneC0086189Drug Withdrawal Symptoms1CTD_human
TgeneC0086237Epilepsy, Cryptogenic1CTD_human
TgeneC0087169Withdrawal Symptoms1CTD_human
TgeneC0149958Complex partial seizures1CTD_human
TgeneC0234533Generalized seizures1CTD_human
TgeneC0234535Clonic Seizures1CTD_human
TgeneC0236018Aura1CTD_human
TgeneC0270824Visual seizure1CTD_human
TgeneC0270844Tonic Seizures1CTD_human
TgeneC0270846Epileptic drop attack1CTD_human
TgeneC0393554Amyotrophic Lateral Sclerosis With Dementia1CTD_human
TgeneC0393702Myoclonic Astatic Epilepsy1ORPHANET
TgeneC0422850Seizures, Somatosensory1CTD_human
TgeneC0422852Seizures, Auditory1CTD_human
TgeneC0422853Olfactory seizure1CTD_human
TgeneC0422854Gustatory seizure1CTD_human
TgeneC0422855Vertiginous seizure1CTD_human
TgeneC0494475Tonic - clonic seizures1CTD_human
TgeneC0543859Amyotrophic Lateral Sclerosis, Guam Form1CTD_human
TgeneC0751056Non-epileptic convulsion1CTD_human
TgeneC0751110Single Seizure1CTD_human
TgeneC0751111Awakening Epilepsy1CTD_human
TgeneC0751123Atonic Absence Seizures1CTD_human
TgeneC0751494Convulsive Seizures1CTD_human
TgeneC0751495Seizures, Focal1CTD_human
TgeneC0751496Seizures, Sensory1CTD_human
TgeneC3495874Nonepileptic Seizures1CTD_human
TgeneC4048158Convulsions1CTD_human
TgeneC4085238MYOCLONIC-ATONIC EPILEPSY1CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC4316903Absence Seizures1CTD_human
TgeneC4317109Epileptic Seizures1CTD_human
TgeneC4317123Myoclonic Seizures1CTD_human
TgeneC4505436Generalized Absence Seizures1CTD_human
TgeneC4727877Epilepsy with myoclonic-atonic seizures1GENOMICS_ENGLAND