Quantifying the contribution of recessive coding variation to developmental disorders.
Martin HC., Jones WD., McIntyre R., Sanchez-Andrade G., Sanderson M., Stephenson JD., Jones CP., Handsaker J., Gallone G., Bruntraeger M., McRae JF., Prigmore E., Short P., Niemi M., Kaplanis J., Radford EJ., Akawi N., Balasubramanian M., Dean J., Horton R., Hulbert A., Johnson DS., Johnson K., Kumar D., Lynch SA., Mehta SG., Morton J., Parker MJ., Splitt M., Turnpenny PD., Vasudevan PC., Wright M., Bassett A., Gerety SS., Wright CF., FitzPatrick DR., Firth HV., Hurles ME., Barrett JC., Deciphering Developmental Disorders Study None.
We estimated the genome-wide contribution of recessive coding variation in 6040 families from the Deciphering Developmental Disorders study. The proportion of cases attributable to recessive coding variants was 3.6% in patients of European ancestry, compared with 50% explained by de novo coding mutations. It was higher (31%) in patients with Pakistani ancestry, owing to elevated autozygosity. Half of this recessive burden is attributable to known genes. We identified two genes not previously associated with recessive developmental disorders, KDM5B and EIF3F, and functionally validated them with mouse and cellular models. Our results suggest that recessive coding variants account for a small fraction of currently undiagnosed nonconsanguineous individuals, and that the role of noncoding variants, incomplete penetrance, and polygenic mechanisms need further exploration.