A novel SMARCA2 missense variant in the proband was found due to low‐level paternal germline mosaicism as the first disease‐causing variant in the QLQ domain associated with solely neurological and developmental phenotypes of NCBRS, which provides new insights into the structure–function relationship of this subunit in the SWI/SNF complexes. This evidence concerns the gene SMARCA2 and intellectual disability-sparse hair-brachydactyly syndrome.