RGD Reference Report - A GABRB3 promoter haplotype associated with childhood absence epilepsy impairs transcriptional activity. - Rat Genome Database

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A GABRB3 promoter haplotype associated with childhood absence epilepsy impairs transcriptional activity.

Authors: Urak, L  Feucht, M  Fathi, N  Hornik, K  Fuchs, K 
Citation: Urak L, etal., Hum Mol Genet. 2006 Aug 15;15(16):2533-41. Epub 2006 Jul 11.
RGD ID: 1601269
Pubmed: PMID:16835263   (View Abstract at PubMed)
DOI: DOI:10.1093/hmg/ddl174   (Journal Full-text)

Childhood absence epilepsy (CAE) is considered to exhibit a complex non-Mendelian pattern of inheritance. So far, only few CAE susceptibility genes have been identified. In a previous study of our group, an association between the GABA(A) receptor beta3 subunit (GABRB3) gene and CAE was shown. To further investigate this association, we screened 45 CAE patients of the first study for mutations in the 10 exons, the exon-intron boundaries and the regulatory sequences of GABRB3. Although we found no functionally relevant mutation, we did identify 13 single nucleotide polymorphisms (SNPs) in the GABRB3 gene region from the exon 1a promoter to the beginning of intron 3. Using these SNPs we defined four haplotypes for the respective GABRB3 gene region. A transmission disequilibrium test in the same 45 CAE patients and their parents indicated a significant association of this region and CAE (P=0.007075). Reporter gene assays in NT2 cells using exon 1a promoter constructs indicated that the disease-associated haplotype 2 promoter causes a significantly lower transcriptional activity than the haplotype 1 promoter that is over-represented in the controls. In silico analysis suggested that an exchange from T (haplotype 1) to C (haplotype 2) within this promoter impairs binding of the neuron-specific transcriptional activator N-Oct-3. Electrophoretic mobility shift assays demonstrated that the respective polymorphism reduces the nuclear protein binding affinity, thus explaining the results of the reporter gene assays. Reduced expression of the GABRB3 gene could therefore be one potential cause for the development of CAE, pathogenetically relevant in our patient group.

RGD Manual Disease Annotations    Click to see Annotation Detail View
TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
childhood absence epilepsy  IAGP 1601269DNA:SNPsRGD 
childhood absence epilepsy  ISOGABRB3 (Homo sapiens)1601269; 1601269DNA:SNPsRGD 

Objects Annotated

Genes (Rattus norvegicus)
Gabrb3  (gamma-aminobutyric acid type A receptor subunit beta 3)

Genes (Mus musculus)
Gabrb3  (GABRB3, gamma-aminobutyric acid type A receptor subunit beta 3)

Genes (Homo sapiens)
GABRB3  (gamma-aminobutyric acid type A receptor subunit beta3)


Additional Information