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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: 16441

FusionGeneSummary for HMGA2_GABRA3

check button Fusion gene summary
Fusion gene informationFusion gene name: HMGA2_GABRA3
Fusion gene ID: 16441
HgeneTgene
Gene symbol

HMGA2

GABRA3

Gene ID

8091

2556

Gene namehigh mobility group AT-hook 2gamma-aminobutyric acid type A receptor alpha3 subunit
SynonymsBABL|HMGI-C|HMGIC|LIPO|STQTL9-
Cytomap

12q14.3

Xq28

Type of geneprotein-codingprotein-coding
Descriptionhigh mobility group protein HMGI-CHMGA2/KRT121P fusionhigh-mobility group (nonhistone chromosomal) protein isoform I-Cgamma-aminobutyric acid receptor subunit alpha-3GABA(A) receptor subunit alpha-3GABA(A) receptor, alpha 3gamma-aminobutyric acid (GABA) A receptor, alpha 3gamma-animobutyric acid (GABA) A receptor, alpha 3
Modification date2018052320180523
UniProtAcc

P52926

P34903

Ensembl transtripts involved in fusion geneENST00000403681, ENST00000541363, 
ENST00000393577, ENST00000393578, 
ENST00000425208, ENST00000536545, 
ENST00000354636, 
ENST00000370314, 
ENST00000535043, ENST00000497894, 
Fusion gene scores* DoF score23 X 14 X 7=22546 X 5 X 5=150
# samples 306
** MAII scorelog2(30/2254*10)=-2.90945310967634
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/150*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HMGA2 [Title/Abstract] AND GABRA3 [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
HgeneHMGA2

GO:0000122

negative regulation of transcription by RNA polymerase II

14627817

HgeneHMGA2

GO:0002062

chondrocyte differentiation

21484705

HgeneHMGA2

GO:0006284

base-excision repair

19465398

HgeneHMGA2

GO:0007095

mitotic G2 DNA damage checkpoint

16061642

HgeneHMGA2

GO:0010564

regulation of cell cycle process

14645522

HgeneHMGA2

GO:0010628

positive regulation of gene expression

18832382

HgeneHMGA2

GO:0031052

chromosome breakage

19549901

HgeneHMGA2

GO:0031507

heterochromatin assembly

16901784

HgeneHMGA2

GO:0035978

histone H2A-S139 phosphorylation

16061642

HgeneHMGA2

GO:0035986

senescence-associated heterochromatin focus assembly

16901784

HgeneHMGA2

GO:0035988

chondrocyte proliferation

21484705

HgeneHMGA2

GO:0042769

DNA damage response, detection of DNA damage

19465398

HgeneHMGA2

GO:0043065

positive regulation of apoptotic process

16061642

HgeneHMGA2

GO:0043066

negative regulation of apoptotic process

19465398

HgeneHMGA2

GO:0043392

negative regulation of DNA binding

14645522

HgeneHMGA2

GO:0043922

negative regulation by host of viral transcription

17005673

HgeneHMGA2

GO:0045869

negative regulation of single stranded viral RNA replication via double stranded DNA intermediate

17005673

HgeneHMGA2

GO:0045892

negative regulation of transcription, DNA-templated

18832382

HgeneHMGA2

GO:0045893

positive regulation of transcription, DNA-templated

15225648|15755872|17005673|17324944|17426251

HgeneHMGA2

GO:0045944

positive regulation of transcription by RNA polymerase II

14645522|18832382

HgeneHMGA2

GO:0071158

positive regulation of cell cycle arrest

16061642

HgeneHMGA2

GO:0090402

oncogene-induced cell senescence

16901784

HgeneHMGA2

GO:2000648

positive regulation of stem cell proliferation

21484705

HgeneHMGA2

GO:2000679

positive regulation of transcription regulatory region DNA binding

18832382

HgeneHMGA2

GO:2000685

positive regulation of cellular response to X-ray

16061642

HgeneHMGA2

GO:2001022

positive regulation of response to DNA damage stimulus

16061642|19465398

HgeneHMGA2

GO:2001033

negative regulation of double-strand break repair via nonhomologous end joining

19549901

HgeneHMGA2

GO:2001038

regulation of cellular response to drug

16061642


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
TCGARVSKCMTCGA-GN-A26D-06AHMGA2chr12

66232349

+GABRA3chrX

151393317

-
* 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
Frame-shitENST00000403681ENST00000370314HMGA2chr12

66232349

+GABRA3chrX

151393317

-
Frame-shitENST00000403681ENST00000535043HMGA2chr12

66232349

+GABRA3chrX

151393317

-
5CDS-intronENST00000403681ENST00000497894HMGA2chr12

66232349

+GABRA3chrX

151393317

-
Frame-shitENST00000541363ENST00000370314HMGA2chr12

66232349

+GABRA3chrX

151393317

-
Frame-shitENST00000541363ENST00000535043HMGA2chr12

66232349

+GABRA3chrX

151393317

-
5CDS-intronENST00000541363ENST00000497894HMGA2chr12

66232349

+GABRA3chrX

151393317

-
Frame-shitENST00000393577ENST00000370314HMGA2chr12

66232349

+GABRA3chrX

151393317

-
Frame-shitENST00000393577ENST00000535043HMGA2chr12

66232349

+GABRA3chrX

151393317

-
5CDS-intronENST00000393577ENST00000497894HMGA2chr12

66232349

+GABRA3chrX

151393317

-
Frame-shitENST00000393578ENST00000370314HMGA2chr12

66232349

+GABRA3chrX

151393317

-
Frame-shitENST00000393578ENST00000535043HMGA2chr12

66232349

+GABRA3chrX

151393317

-
5CDS-intronENST00000393578ENST00000497894HMGA2chr12

66232349

+GABRA3chrX

151393317

-
Frame-shitENST00000425208ENST00000370314HMGA2chr12

66232349

+GABRA3chrX

151393317

-
Frame-shitENST00000425208ENST00000535043HMGA2chr12

66232349

+GABRA3chrX

151393317

-
5CDS-intronENST00000425208ENST00000497894HMGA2chr12

66232349

+GABRA3chrX

151393317

-
Frame-shitENST00000536545ENST00000370314HMGA2chr12

66232349

+GABRA3chrX

151393317

-
Frame-shitENST00000536545ENST00000535043HMGA2chr12

66232349

+GABRA3chrX

151393317

-
5CDS-intronENST00000536545ENST00000497894HMGA2chr12

66232349

+GABRA3chrX

151393317

-
Frame-shitENST00000354636ENST00000370314HMGA2chr12

66232349

+GABRA3chrX

151393317

-
Frame-shitENST00000354636ENST00000535043HMGA2chr12

66232349

+GABRA3chrX

151393317

-
5CDS-intronENST00000354636ENST00000497894HMGA2chr12

66232349

+GABRA3chrX

151393317

-

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FusionProtFeatures for HMGA2_GABRA3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
HMGA2

P52926

GABRA3

P34903

Functions as a transcriptional regulator. Functions incell cycle regulation through CCNA2. Plays an important role inchromosome condensation during the meiotic G2/M transition ofspermatocytes. Plays a role in postnatal myogenesis, is involvedin satellite cell activation (By similarity).{ECO:0000250|UniProtKB:P52927, ECO:0000269|PubMed:14645522}. GABA, the major inhibitory neurotransmitter in thevertebrate brain, mediates neuronal inhibition by binding to theGABA/benzodiazepine receptor and opening an integral chloridechannel.

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 HMGA2_GABRA3


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 HMGA2_GABRA3


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
HMGA2RELA, NFKB1, PIAS3, RB1, PRMT6, NPM1, SMAD1, SMAD5, SMAD9, PRKCA, HDGF, PTBP1, APEX1, SYNCRIP, XRCC6, PSIP1, PA2G4, PCBP2, E4F1, OBSL1, HIST1H3A, CREB1, NFATC1, PCGF1, POU5F1, DLSTGABRA3UBQLN1, UGT2B7, SDCBP2, EGFR, GABRA5, ABCA7, SEC11C, TMEM131, GLRB, TUSC3, AMIGO1, TMEM59L, TTC17, EDA, POMT1, SPCS1, WLS, ALG9, SLC47A1, HLA-C, GPAA1


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 HMGA2_GABRA3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneGABRA3P34903DB00425ZolpidemGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved
TgeneGABRA3P34903DB00546AdinazolamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved
TgeneGABRA3P34903DB00842OxazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved
TgeneGABRA3P34903DB00849MethylphenobarbitalGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved
TgeneGABRA3P34903DB00898EthanolGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved
TgeneGABRA3P34903DB01198ZopicloneGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved
TgeneGABRA3P34903DB01354HeptabarbitalGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved
TgeneGABRA3P34903DB01355HexobarbitalGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved
TgeneGABRA3P34903DB01594CinolazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved
TgeneGABRA3P34903DB01595NitrazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved
TgeneGABRA3P34903DB09166EtizolamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved
TgeneGABRA3P34903DB13872LormetazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved
TgeneGABRA3P34903DB00306TalbutalGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit
TgeneGABRA3P34903DB00371MeprobamateGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit
TgeneGABRA3P34903DB00683MidazolamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit
TgeneGABRA3P34903DB01215EstazolamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit
TgeneGABRA3P34903DB01351AmobarbitalGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit
TgeneGABRA3P34903DB01352AprobarbitalGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit
TgeneGABRA3P34903DB01353ButethalGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit
TgeneGABRA3P34903DB01544FlunitrazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit
TgeneGABRA3P34903DB01559ClotiazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit
TgeneGABRA3P34903DB01567FludiazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit
TgeneGABRA3P34903DB01588PrazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit
TgeneGABRA3P34903DB01589QuazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit
TgeneGABRA3P34903DB00690FlurazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit|investigational
TgeneGABRA3P34903DB01558BromazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit|investigational
TgeneGABRA3P34903DB00829DiazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit|investigational|vet_approved
TgeneGABRA3P34903DB00801HalazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|illicit|withdrawn
TgeneGABRA3P34903DB00231TemazepamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|investigational
TgeneGABRA3P34903DB00402EszopicloneGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|investigational
TgeneGABRA3P34903DB00897TriazolamGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|investigational
TgeneGABRA3P34903DB00312PentobarbitalGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|investigational|vet_approved
TgeneGABRA3P34903DB00418SecobarbitalGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|vet_approved
TgeneGABRA3P34903DB00599ThiopentalGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|vet_approved
TgeneGABRA3P34903DB00794PrimidoneGamma-aminobutyric acid receptor subunit alpha-3small moleculeapproved|vet_approved

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RelatedDiseases for HMGA2_GABRA3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHMGA2C0005612Birth Weight1CTD_human
TgeneGABRA3C0005586Bipolar Disorder5PSYGENET
TgeneGABRA3C0004352Autistic Disorder1CTD_human
TgeneGABRA3C0011570Mental Depression1PSYGENET
TgeneGABRA3C0011581Depressive disorder1PSYGENET