Sequence variants affect the genome-wide rate of germline microsatellite mutations

Microsatellites are polymorphic tracts of short tandem repeats (STRs) with one to six base-pair (bp) motifs and are some of the most polymorphic markers in the genome. Using 6,084 Icelandic parent-offspring trios we estimate 63.7 (95% CI: 61.9–65.4) microsatellite de novo mutations (mDNMs) per offspring per generation. Paternal mDNMs occur at longer repeats, while maternal mDNMs affect more bp. mDNMs increase by 0.97 (95% CI: 0.90–1.04) and 0.31 (95% CI: 0.25–0.37) per year of father‘s and mother‘s age at conception, respectively. We found two independent coding variants associated with an increased number of mDNMs transmitted to offspring; A missense variant (allele frequency (AF) = 1.9%) in MSH2, a mismatch repair gene, increases transmitted mDNMs from both parents (effect: 13.1 paternal and 7.8 maternal mDNMs). A synonymous variant (AF = 20.3%) in NEIL2, a DNA damage repair gene, increases paternally transmitted mDNMs (effect: 4.4 mDNMs). Thus, the microsatellite mutation rate in humans is in part under genetic control.