Skeletal dysplasias are disorders which involve bone deformities and short stature. The genetic causes for some of these disorders are unknown. We describe for the first time a missense variant of a gene, GNPNAT1 which results in severe short stature in four patients due to extreme shortening of the proximal segments of the limbs. GNPNAT1 is one of the enzymes required for synthesis of uridine diphosphate N-acetylglucosamine, which participates in protein glycosylation. The variant affects the catalytic domain of the enzyme and likely impairs chondrocyte differentiation. Our findings implicate skeletal dysplasia due to GNPNAT1 variant as a novel disorder of glycosylation. (https://jmg.bmj.com/content/early/2020/06/26/jmedgenet-2020-106929 )