Quantifying the contribution of recessive coding variation to developmental disorders

Abstract

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.

Fig. 1

Clinical features of DDD probands analysed here. Proportion of probands in different groups with clinical features indicated, extracted from HPO terms. Asterisks indicate nominally significant differences between indicated groups (Fisher’s exact test).

Fig. 2

Contribution of recessive coding variants to genetic architecture in this study. (A) Number of observed and expected biallelic genotypes per individual across all genes. Nominally significant p-values from a Poisson test of enrichment are shown. (B) Left: number of probands grouped by diagnostic category. The inherited dominant and X-linked diagnoses (narrow pink bar) include only those in known genes, whereas the proportion of probands with de novo and recessive coding diagnoses was inferred as described in (10), including those in as-yet-undiscovered genes. Right: the proportion of probands in various patient subsets inferred to have diagnostic variants in the indicated classes.

Fig. 3

Functional consequences of the pathogenic EIF3F recessive missense variant. A) The Phe232Val variant impairs translation. Plot shows median fluorescence intensity (MFI) in iPSC lines heterozygous or homozygous for or without the Phe232Val variant (correcting for replicate effects), measured using a Click-iT protein synthesis assay (10). MFI correlates with methionine analogue incorporation in nascent proteins. The p-value indicates a non-zero effect of genotype from a linear regression of MFI on genotype and replicate. Red lines: means. B) The Phe232Val variant impairs iPSC proliferation in the homozygous but not heterozygous form. Results from a cell trace violet (CTV) proliferation assay, in which CTV concentration reduces on each division. The population of cells that have been through zero, one or multiple divisions is labelled.

Fig. 4

KDM5B is a recessive DD gene in which heterozygous LoFs are incompletely penetrant. A) Summary of damaging variants found in KDM5B. B) Positions of likely damaging variants found in this and previous studies in KDM5B (ENST00000367264.2; introns not to scale), omitting two large deletions. Colors correspond to those shown in (A). There are no differences in the spatial distribution of LoFs by inheritance mode, nor in their likelihood of escaping nonsense-mediated decay by alternative splicing in GTex (https://gtexportal.org/home/). C-E) Behavioral defects of homozygous Kdm5b-null versus wild-type mice (n=14-16). C) Knockout mice displayed increased anxiety, spending significantly less time in the light compartment of the Light-Dark box. D) Reduced sociability, in the three-chamber sociability test. Knockout mice spent less time investigating a novel mouse. E) 24h memory impairment. While wild-type mice preferentially investigated an unfamiliar mouse over a familiar one, homozygous knockout mice showed no discrimination.