<p>Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder that is characterized by three major symptoms such as social communication deficits, stereotypic and repetitive behaviours. Gamma amino butyric acid (GABA) is the chief inhibitory neurotransmitter and alteration in GABA signalling is a potential cause for ASD symptoms. In this study, we aimed to investigate the role of genetic variant rs2201169 of Gamma amino butyric acid receptor alpha 3 subunit gene (<i>GABRA3</i>, located on the X chromosome) in the etiology of ASD in an affected population of West Bengal, India. 349 Indo-Caucasoid ASD probands, their parents, and 230 healthy controls were recruited for this study. Genotyping was done by PCR–RFLP method and the gene expression study was done by RT-PCR. The rs2201169G allele showed significant risk among female probands (cases) in our population. The G allele and the GG genotype showed significant association with one or more phenotypic traits such as ‘Nonverbal communication’, and ‘Fear or nervousness’ for female probands. Gene expression levels were studied in a subset of the population, where the gene expression levels of GABRA3 showed significant down-regulation in cases compared to control subjects. Down regulation was also found in the female probands carrying the G allele (“AG/GG” genotypes) compared to the controls. This study for the first time showed the association of rs2201169 with ASD in the Indo-Caucasoid population of West Bengal, India.</p> Graphical Abstract <p></p>