Splicing defects in the ataxia-telangiectasia gene, ATM: Underlying mutations and consequences

Mutations resulting in defective splicing constitute a significant proporti on (30/62 [48%]) of a new series of mutations in the ATM gene in patients w ith ataxia-telangiectasia (AT) that were detected by the protein-truncation assay followed by sequence analysis of genomic DNA. Fewer than half of the splicing mutations involved the canonical AG splice-acceptor site or GT sp lice-donor site. A higher percentage of mutations occurred at less stringen tly conserved sites, including silent mutations of the last nucleotide of e xons, mutations in nucleotides other than the conserved AG and GT in the co nsensus splice sites, and creation of splice-acceptor or splice-donor sites in either introns or exons. These splicing mutations led to a variety of c onsequences, including exon skipping and, to a lesser degree, intron retent ion, activation of cryptic splice sites, or creation of new splice sites. I n addition, 5 of 12 nonsense mutations and 1 missense mutation were associa ted with deletion in the cDNA of the exons in which the mutations occurred. No ATM protein was detected by western blotting in any AT cell line in whi ch splicing mutations were identified. Several cases of exon skipping in bo th normal controls and patients for whom no underlying defect could be foun d in genomic DNA were also observed, suggesting caution in the interpretati on of exon deletions observed in ATM cDNA when there is no accompanying ide ntification of genomic mutations.