De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay.

Susan M Hiatt,Gregory S Barsh,Ingrid M Wentzensen,Cyril Mignot,Jeremy W Prokop,Jan Prchal,Rebecca Willaert,Yves Lacassie,Lauren Brick,Ryne C Ramaker,Nicholas Stong,Mariya Kozenko,Andrew A Hardigan,Boris Keren,Matthew B Neu,Patricia G Wheeler,Caroline Nava,Parisa Hemati,Gregory M Cooper,James W Wheless,Sharon F Suchy,Anna Hurst ,Zdeněk Sedláček ,Zӧe Powis ,Miroslava Hančárová ,Alejandro Iglesias ,Anya Revah‐Politi ,R Myers ,Darina Prchalová ,Dwight K.c Yim ,Marlène Rio ,Markéta Havlovičová ,Viktor Stránecký

doi:10.1371/journal.pgen.1007671

Abstract

Mutations that alter signaling of RAS/MAPK-family proteins give rise to a group of Mendelian diseases known as RASopathies. However, among RASopathies, the matrix of genotype-phenotype relationships is still incomplete, in part because there are many RAS-related proteins and in part because the phenotypic consequences may be variable and/or pleiotropic. Here, we describe a cohort of ten cases, drawn from six clinical sites and over 16,000 sequenced probands, with de novo protein-altering variation in RALA, a RAS-like small GTPase. All probands present with speech and motor delays, and most have intellectual disability, low weight, short stature, and facial dysmorphism. The observed rate of de novo RALA variants in affected probands is significantly higher (p = 4.93 x 10−11) than expected from the estimated random mutation rate. Further, all de novo variants described here affect residues within the GTP/GDP-binding region of RALA; in fact, six alleles arose at only two codons, Val25 and Lys128. The affected residues are highly conserved across both RAL- and RAS-family genes, are devoid of variation in large human population datasets, and several are homologous to positions at which disease-associated variants have been observed in other GTPase genes. We directly assayed GTP hydrolysis and RALA effector-protein binding of the observed variants, and found that all but one tested variant significantly reduced both activities compared to wild-type. The one exception, S157A, reduced GTP hydrolysis but significantly increased RALA-effector binding, an observation similar to that seen for oncogenic RAS variants. These results show the power of data sharing for the interpretation and analysis of rare variation, expand the spectrum of molecular causes of developmental disability to include RALA, and provide additional insight into the pathogenesis of human disease caused by mutations in small GTPases.

Highlights

Developmental delay and intellectual disability (DD/ID) affect about 1–2% of individuals worldwide [1]
Using DNA sequencing, and by sharing information among many doctors and researchers, we have identified a set of individuals with developmental problems who all have changes to the same gene, RALA
Functional experiments show that the genetic changes found in these individuals alter two key functions of RALA

Summary

Introduction

Developmental delay and intellectual disability (DD/ID) affect about 1–2% of individuals worldwide [1]. Many highly penetrant genetic variants underlying DD/ID have been identified, but a large fraction of disease risk remains unexplained [2, 3]. While some DD/ID-cases may result from environmental factors and small-effect common variants [4], it is likely that many probands harbor pathogenic, highly penetrant variation in as-yet-unknown diseaseassociated genes. The RASopathies are a group of genetic conditions often associated with developmental disorders [5], having in common mutational disruption of genes in the RAS/MAPK pathway that alter patterns of signal transduction. RASopathies are individually rare and pleiotropic but are collectively one of the most common causes of developmental disorders.

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