Gene Page: GABRA3

Summary ?
GeneID2556
SymbolGABRA3
Synonyms-
Descriptiongamma-aminobutyric acid type A receptor alpha3 subunit
ReferenceMIM:305660|HGNC:HGNC:4077|Ensembl:ENSG00000011677|HPRD:02375|Vega:OTTHUMG00000024183
Gene typeprotein-coding
Map locationXq28
Fetal beta-0.586
eGeneMyers' cis & trans
SupportLIGAND GATED ION SIGNALING
Potential synaptic genes

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 4 

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs6733654chr21963270GABRA325560.07trans
rs891877chr22043348GABRA325560.14trans
rs6544404chr241502544GABRA325560.08trans
rs1155107chr326843376GABRA325560.05trans
rs1395163chr331028951GABRA325560.08trans
rs17029291chr332402138GABRA325563.403E-11trans
rs1553189chr3112939422GABRA325560.06trans
rs624496chr3120506736GABRA325560.15trans
rs16858348chr3173958675GABRA325560.11trans
rs750544chr551749054GABRA325560.05trans
rs17146240chr5119522933GABRA325560.05trans
rs17146261chr5119534252GABRA325560.05trans
rs2807510chr673090536GABRA325560.13trans
rs4617108chr749423831GABRA325560.04trans
rs4607971chr1019407890GABRA325560.06trans
rs11000486chr1074762547GABRA325560.08trans
rs12253630chr1074768923GABRA325560.04trans
rs7078127chr1074847633GABRA325560.03trans
rs3829166chr1074879373GABRA325560.1trans
rs12569493chr1074886042GABRA325560.01trans
rs7072086chr1074886597GABRA325560.1trans
rs16930362chr1074890320GABRA325567.313E-4trans
rs7083730chr1074890448GABRA325560.13trans
rs2271904chr1074894374GABRA325560.03trans
rs7092445chr1074921991GABRA325560.01trans
rs12256576chr1074934313GABRA325560.03trans
rs1867565chr1074977780GABRA325560.05trans
rs11000557chr1074987393GABRA325560.03trans
rs16915029chr1075001994GABRA325560trans
rs14488chr1075007274GABRA325560.03trans
rs16930466chr1075007587GABRA325560.01trans
rs11000579chr1075027961GABRA325560.05trans
rs11000594chr1075064566GABRA325560.2trans
rs11000607chr1075089777GABRA325560.01trans
rs6480700chr1075101689GABRA325560.02trans
rs16930573chr1075167645GABRA325560.1trans
rs12571454chr1075208954GABRA325560trans
rs909288chr10124257417GABRA325560.17trans
rs17136959chr1178373036GABRA325560.12trans
rs4944213chr1178395188GABRA325560.12trans
rs17133022chr1198980829GABRA325560.03trans
rs17034050chr12103914944GABRA325560.16trans
rs2254834chr1443596184GABRA325560.17trans
rs1954396chr1443601835GABRA325560.01trans
rs8055506chr1613661723GABRA325560.2trans
rs16962446chr1613694936GABRA325560.2trans
rs16958358chr1755502410GABRA325560.02trans
rs6040268chr2010956100GABRA325560.08trans
rs6040269chr2010956136GABRA325560.08trans
rs11906936chr2010957136GABRA325560.04trans
rs1327232chr2010958909GABRA325560.09trans
rs6098023chr2053113740GABRA325560.03trans
rs6015314chr2057167224GABRA325560.14trans
rs12157904chr2237982011GABRA325563.039E-4trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
SLC32A10.760.90
HS6ST20.680.80
RCN10.670.64
DLX50.660.40
TMEM1230.630.42
GAD10.630.85
CDC25B0.630.60
TBL1X0.630.45
DLX10.630.39
MOBKL2B0.630.44
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
METRNL-0.32-0.42
DAB1-0.270.00
SCUBE1-0.27-0.22
NEUROD6-0.27-0.06
RNF182-0.27-0.28
AF347015.2-0.26-0.12
KLHL1-0.260.07
SLA-0.260.06
AF347015.18-0.26-0.12
TMEM108-0.26-0.04

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0004890GABA-A receptor activityIEAGABA (GO term level: 7)-
GO:0008503benzodiazepine receptor activityTASGABA, Neurotransmitter (GO term level: 6)8391122 
GO:0005254chloride channel activityIEA-
GO:0005216ion channel activityIEA-
GO:0005230extracellular ligand-gated ion channel activityIEA-
GO:0031404chloride ion bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007214gamma-aminobutyric acid signaling pathwayTASGABA, Neurotransmitter (GO term level: 8)8391122 
GO:0006821chloride transportIEA-
GO:0006811ion transportIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0045211postsynaptic membraneIEASynap, Neurotransmitter (GO term level: 5)-
GO:0045202synapseIEAneuron, Synap, Neurotransmitter, Glial (GO term level: 2)-
GO:0005856cytoskeletonIDA18029348 
GO:0005737cytoplasmIDA18029348 
GO:0005886plasma membraneIEA-
GO:0005887integral to plasma membraneTAS8391122 
GO:0030054cell junctionIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION 272195All SZGR 2.0 genes in this pathway
BIOCARTA GABA PATHWAY 1010All SZGR 2.0 genes in this pathway
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES 186155All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM 279221All SZGR 2.0 genes in this pathway
REACTOME NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 137110All SZGR 2.0 genes in this pathway
REACTOME TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 413270All SZGR 2.0 genes in this pathway
REACTOME GABA A RECEPTOR ACTIVATION 1212All SZGR 2.0 genes in this pathway
REACTOME GABA RECEPTOR ACTIVATION 5240All SZGR 2.0 genes in this pathway
REACTOME ION CHANNEL TRANSPORT 5542All SZGR 2.0 genes in this pathway
REACTOME LIGAND GATED ION CHANNEL TRANSPORT 2121All SZGR 2.0 genes in this pathway
FIRESTEIN CTNNB1 PATHWAY 3323All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305895All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE 721492All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR DN 8859All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA PRONEURAL 177132All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway