Analysis of novel missense ATR mutations reveals new splicing defects underlying Seckel syndrome

Ataxia Telangiectasia and Rad3 related (ATR) is one of the main regulators of the DNA damage response. It coordinates cell cycle checkpoint activation, replication fork stability, restart and origin firing to maintain genome integrity. Mutations of the ATR gene have been reported in Seckel patients, who suffer from a rare genetic disease characterized by severe microcephaly and growth retardation. Here, we report the case of a Seckel patient with compound heterozygous mutations in ATR. One allele has an intronic mutation affecting splicing of neighboring exons, the other an exonic missense mutation, producing the variant p.Lys1665Asn, of unknown pathogenicity. We have modeled this novel missense mutation, as well as a previously described missense mutation p.Met1159Ile, and assessed their effect on ATR function. Interestingly, our data indicate that both missense mutations have no direct effect on protein function, but rather result in defective ATR splicing. These results emphasize the importance of splicing mutations in Seckel Syndrome. Modelling of novel missense mutations within the ATR cDNA did not result in loss of protein function. Rather, these mutations in their genomic context impacted upon normal splicing, resulting in exon skipping and Seckle Syndrome. For example, ATR (c.4995G>T) results in skipping of exon 28 and subsequent abrogation of ATR function.