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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:SLC1A1-SMARCA2 (FusionGDB2 ID:81808)

Fusion Gene Summary for SLC1A1-SMARCA2

check button Fusion gene summary
Fusion gene informationFusion gene name: SLC1A1-SMARCA2
Fusion gene ID: 81808
HgeneTgene
Gene symbol

SLC1A1

SMARCA2

Gene ID

6505

6595

Gene namesolute carrier family 1 member 1SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
SynonymsDCBXA|EAAC1|EAAT3|SCZD18BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a
Cytomap

9p24.2

9p24.3

Type of geneprotein-codingprotein-coding
Descriptionexcitatory amino acid transporter 3excitatory amino acid carrier 1neuronal and epithelial glutamate transportersodium-dependent glutamate/aspartate transporter 3solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xprobable global transcription activator SNF2L2ATP-dependent helicase SMARCA2BAF190BBRG1-associated factor 190BSNF2-alphaSNF2/SWI2-like protein 2SWI/SNF-related matrix-associated actin-dependent regulator of chromatin a2brahma homologglobal transcr
Modification date2020031320200315
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000262352, ENST00000490167, 
ENST00000357248, ENST00000349721, 
ENST00000382203, ENST00000382194, 
ENST00000491574, ENST00000324954, 
ENST00000302401, ENST00000382186, 
ENST00000382185, 
Fusion gene scores* DoF score1 X 1 X 1=115 X 14 X 8=1680
# samples 116
** MAII scorelog2(1/1*10)=3.32192809488736log2(16/1680*10)=-3.39231742277876
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SLC1A1 [Title/Abstract] AND SMARCA2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSLC1A1(4490770)-SMARCA2(2096657), # samples:3
Anticipated loss of major functional domain due to fusion event.SLC1A1-SMARCA2 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
SLC1A1-SMARCA2 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
SLC1A1-SMARCA2 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
SLC1A1-SMARCA2 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
* 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
HgeneSLC1A1

GO:0015813

L-glutamate transmembrane transport

21123949|26690923

HgeneSLC1A1

GO:0042883

cysteine transport

21123949

HgeneSLC1A1

GO:0051938

L-glutamate import

7521911

HgeneSLC1A1

GO:0070779

D-aspartate import across plasma membrane

7521911

HgeneSLC1A1

GO:0098712

L-glutamate import across plasma membrane

26690923

TgeneSMARCA2

GO:0008285

negative regulation of cell proliferation

14660596

TgeneSMARCA2

GO:0045892

negative regulation of transcription, DNA-templated

12065415

TgeneSMARCA2

GO:0045893

positive regulation of transcription, DNA-templated

17984088

TgeneSMARCA2

GO:0045944

positive regulation of transcription by RNA polymerase II

15774904


check buttonFusion gene breakpoints across SLC1A1 (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 SMARCA2 (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
ChimerDB4LUSCTCGA-NC-A5HJ-01ASLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
ChimerDB4LUSCTCGA-NC-A5HJSLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
ChimerDB4LUSCTCGA-NC-A5HJ-01ASLC1A1chr9

4490770

-SMARCA2chr9

2096657

+


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Fusion Gene ORF analysis for SLC1A1-SMARCA2

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
Frame-shiftENST00000262352ENST00000357248SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
Frame-shiftENST00000262352ENST00000349721SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
Frame-shiftENST00000262352ENST00000382203SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
Frame-shiftENST00000262352ENST00000382194SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
5CDS-intronENST00000262352ENST00000491574SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
5CDS-intronENST00000262352ENST00000324954SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
5CDS-intronENST00000262352ENST00000302401SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
5CDS-intronENST00000262352ENST00000382186SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
5CDS-intronENST00000262352ENST00000382185SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
intron-3CDSENST00000490167ENST00000357248SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
intron-3CDSENST00000490167ENST00000349721SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
intron-3CDSENST00000490167ENST00000382203SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
intron-3CDSENST00000490167ENST00000382194SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
intron-intronENST00000490167ENST00000491574SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
intron-intronENST00000490167ENST00000324954SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
intron-intronENST00000490167ENST00000302401SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
intron-intronENST00000490167ENST00000382186SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+
intron-intronENST00000490167ENST00000382185SLC1A1chr9

4490770

+SMARCA2chr9

2096657

+

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 SLC1A1-SMARCA2


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)
SLC1A1chr94490770+SMARCA2chr92096656+2.56E-091
SLC1A1chr94490770+SMARCA2chr92096656+2.56E-091
SLC1A1chr94490770+SMARCA2chr92096656+2.56E-091
SLC1A1chr94490770+SMARCA2chr92096656+2.56E-091

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 SLC1A1-SMARCA2


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
..
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: 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 SLC1A1-SMARCA2


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 SLC1A1-SMARCA2


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 SLC1A1-SMARCA2


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 SLC1A1-SMARCA2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSLC1A1C1857253Dicarboxylicaminoaciduria3CLINGEN;CTD_human;ORPHANET;UNIPROT
HgeneSLC1A1C0005586Bipolar Disorder1PSYGENET
HgeneSLC1A1C0006111Brain Diseases1CTD_human
HgeneSLC1A1C0009241Cognition Disorders1CTD_human
HgeneSLC1A1C0011570Mental Depression1PSYGENET
HgeneSLC1A1C0011581Depressive disorder1PSYGENET
HgeneSLC1A1C0014175Endometriosis1CTD_human
HgeneSLC1A1C0014544Epilepsy1CTD_human
HgeneSLC1A1C0014556Epilepsy, Temporal Lobe1CTD_human
HgeneSLC1A1C0014558Uncinate Epilepsy1CTD_human
HgeneSLC1A1C0022333Jacksonian Seizure1CTD_human
HgeneSLC1A1C0027746Nerve Degeneration1CTD_human
HgeneSLC1A1C0035304Retinal Degeneration1CTD_human
HgeneSLC1A1C0036572Seizures1CTD_human
HgeneSLC1A1C0085584Encephalopathies1CTD_human
HgeneSLC1A1C0086237Epilepsy, Cryptogenic1CTD_human
HgeneSLC1A1C0149958Complex partial seizures1CTD_human
HgeneSLC1A1C0152136Low Tension Glaucoma1CTD_human
HgeneSLC1A1C0234533Generalized seizures1CTD_human
HgeneSLC1A1C0234535Clonic Seizures1CTD_human
HgeneSLC1A1C0236018Aura1CTD_human
HgeneSLC1A1C0269102Endometrioma1CTD_human
HgeneSLC1A1C0270824Visual seizure1CTD_human
HgeneSLC1A1C0270844Tonic Seizures1CTD_human
HgeneSLC1A1C0270846Epileptic drop attack1CTD_human
HgeneSLC1A1C0333641Atrophic1CTD_human
HgeneSLC1A1C0393672Epilepsy, Benign Psychomotor, Childhood1CTD_human
HgeneSLC1A1C0393682Epilepsy, Lateral Temporal1CTD_human
HgeneSLC1A1C0393729Immersion Related Epilepsy1ORPHANET
HgeneSLC1A1C0422850Seizures, Somatosensory1CTD_human
HgeneSLC1A1C0422852Seizures, Auditory1CTD_human
HgeneSLC1A1C0422853Olfactory seizure1CTD_human
HgeneSLC1A1C0422854Gustatory seizure1CTD_human
HgeneSLC1A1C0422855Vertiginous seizure1CTD_human
HgeneSLC1A1C0431380Cortical Dysplasia1CTD_human
HgeneSLC1A1C0494475Tonic - clonic seizures1CTD_human
HgeneSLC1A1C0751056Non-epileptic convulsion1CTD_human
HgeneSLC1A1C0751110Single Seizure1CTD_human
HgeneSLC1A1C0751111Awakening Epilepsy1CTD_human
HgeneSLC1A1C0751123Atonic Absence Seizures1CTD_human
HgeneSLC1A1C0751494Convulsive Seizures1CTD_human
HgeneSLC1A1C0751495Seizures, Focal1CTD_human
HgeneSLC1A1C0751496Seizures, Sensory1CTD_human
HgeneSLC1A1C1510586Autism Spectrum Disorders1CTD_human
HgeneSLC1A1C1955869Malformations of Cortical Development1CTD_human
HgeneSLC1A1C3495874Nonepileptic Seizures1CTD_human
HgeneSLC1A1C4048158Convulsions1CTD_human
HgeneSLC1A1C4316903Absence Seizures1CTD_human
HgeneSLC1A1C4317109Epileptic Seizures1CTD_human
HgeneSLC1A1C4317123Myoclonic Seizures1CTD_human
HgeneSLC1A1C4505436Generalized Absence Seizures1CTD_human
HgeneSLC1A1C4551550EPILEPSY, HOT WATER, 11ORPHANET
TgeneSMARCA2C0036341Schizophrenia4PSYGENET
TgeneSMARCA2C1303073Nicolaides Baraitser syndrome4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneSMARCA2C0010606Adenoid Cystic Carcinoma1CTD_human
TgeneSMARCA2C0265338Coffin-Siris syndrome1CTD_human;GENOMICS_ENGLAND
TgeneSMARCA2C0345967Malignant mesothelioma1CTD_human
TgeneSMARCA2C3281201MENTAL RETARDATION, AUTOSOMAL DOMINANT 121GENOMICS_ENGLAND