Werner mesomelic syndrome (WMS), an autosomal dominant disorder characterized by hypoplastic tibiae, triphalangeal thumbs and polydactyly, is caused by a specific point mutation at the position 404 in zone of polarizing activity regulatory sequence (ZRS). Here we identified two additional families with WMS. All three patients in three generations of Family 1 were found to harbor the same heterozygous 406A>G mutation in ZRS. The fourth patient from Family 2 was a sporadic case with the known 404 point mutation. The novel 406A>G mutation expands mutational spectrum in ZRS causing WMS, provides evidence for a functionally important nucleotide position 406 of ZRS in humans and has implications for genetic counseling.