Mutation timing, accumulation and selection in the male germline shape inheritance risk for developmental disorders

Transmissible de novo disease risk in children is mainly shaped by universal germline processes, with early mosaic variants being uncommon but significant outliers.

Summary and findings

This study investigated the relationship between de novo mutations (DNMs) in the paternal germline and the risk of developmental disorders in children. Whole-genome sequencing of 168 parent-child trios and duplex sequencing of paternal sperm were utilized. Findings indicated that most fathers did not carry a significantly altered burden of transmissible germline risk.

Abstract

De novo mutations (DNMs) arising in the parental germline are a major cause of severe developmental disorders. While most DNMs originate in the paternal germline, it remains unclear whether fathers of affected children carry a systematically altered burden of transmissible germline risk, or whether disease largely reflects stochastic outcomes of shared population-wide mutational processes. Here, we combined whole-genome sequencing of 168 parent–child trios with ultra-accurate duplex sequencing of paternal sperm to directly relate transmitted DNMs to the broader mutational and selective landscape of the male germline. In 127 fathers, sperm mutation burden and mutational spectra were indistinguishable from population reference cohorts. Positive selection metrics were likewise concordant, with a global dN/dS of 1.56 (95% CI 1.45–1.67) compared to 1.44 (95% CI 1.17–1.77) in controls and 28 of 32 significantly selected genes overlapping with prior findings. Six fathers harboured a pathogenic early mosaic variant detectable in sperm at allele fractions that ranged from 0.7% to 14.8%. Although these variants generated substantial individual-level risk outliers, they accounted for only ∼11% of the aggregated exome pathogenic burden across the cohort. The remaining burden was distributed across low-VAF mutations, including positively selected driver variants and other rare mutations accumulating with paternal age. Together, these results show that transmissible de novo disease risk is governed primarily by universal germline mutational and selective processes, while early developmental mosaicism produces uncommon but clinically meaningful deviations. This integrated view clarifies how mutation timing, age-associated accumulation and germline selection jointly shape inheritance risk.

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