We have isolated a 1,192-base-long cDNA which encodes the entire structure of a precursor form of human H-protein. The tentatively calculated number of copies for this cDNA appeared to be about four times as many as that of the antithrombin III gene specified by a single locus in the human haploid genome. Southern analysis using H-protein cDNA probe demonstrates a deletion of the 5.0-kb SacI fragment in the genome of a patient with an atypical nonketotic hyperglycinemia in whom there was an inactive H-protein. This SacI fragment was also deleted from the genome of one of seven patients with nonketotic hyperglycinemia resulting from the lesion of glycine decarboxylase. The remaining six patients had common aberrations identified with the 5.2-kb EcoRI and 5.5-kb SacI fragments. Although implication of these defective fragments in pathogenesis is unclear at present, it is suggested that rearrangements occur in multiple genomic loci of patients with nonketotic hyperglycinemia and that this H-protein cDNA can be used for carrier screening.