We screened 10 children with sporadic severe isolated GH deficiency (IGHD) for GH-1 gene splice site mutations using ectopic transcript analysis. None had a history of birth trauma, congenital defects, thyroid disorders, or PRL deficiency. The mean age of these patients at diagnosis was 3.5 yr; the mean height at diagnosis was -4.0 SD score. GH-1 gene deletion was excluded in all cases. Ribonucleic acid (RNA) from lymphocytes was reverse transcribed and amplified by nested polymerase chain reaction, using two primer pairs with annealing sites within exons 2 and 5 of the GH-1 gene. The main polymerase chain reaction fragment obtained was 460 basepairs and proved to be the amplification of the GH-1 transcript. We also found three shorter fragments which were alternatively spliced GH-1 transcripts, including a variant devoid of the first 45 basepairs of exon 3, a second lacking the whole exon 3, and a third one, not previously described, lacking both exon 3 and exon 4. We found the same pattern of alternative splicing in RNA from GH-producing pituitary tumor tissue, which served as a positive control. In 1 of 10 patients, a pathologically shortened main fragment lacking exon 3 was detected. As proved by sequencing genomic DNA, this was the result of a heterozygous splice site mutation, with transversion from G to C of the first base of the donor splice site of intron III generating a new DdeI recognition site. The other allele had no mutation. DdeI digestion enabled us to rule out the defect in the parents' DNA. Thus, the mutation was de novo. As the patient with the mutation displayed the most severe and earliest growth retardation in the study group and had virtually no GH in serum, it must be assumed that the heterozygous genetic defect resulted in a dominant negative effect. The reason for this is still unclear. Recently, within a family that exhibited the autosomal dominant phenotype of IGHD (IGHD-II), a heterozygous point mutation was located 5 bases down-stream from that we describe here. A similar effect on splicing was observed. In conclusion, analysis of ectopic GH-1 transcripts enabled us to detect 1) a new alternatively spliced GH-1 messenger RNA variant lacking exons 3 and 4, and 2) 1 of 10 sporadic cases of severe idiopathic IGHD due to a heterozygous de novo splice site mutation in the GH-1 gene that changes G to C in the first base of intron III.(ABSTRACT TRUNCATED AT 400 WORDS)