Structure of the GM2A gene:: Identification of an exon 2 nonsense mutation and a naturally occurring transcript with an in-frame deletion of exon 2

Deficiency of the GM2 activator protein, encoded by GM2A, results in the rare AB-variant form of GM2 gangliosidosis. Four mutations have been identified, but the human gene structure has been only partially characterized. We report a new patient from a Laotian deme whose cells are deficient in both GM2-activator mRNA and protein. However, reverse transcription (RT)-PCR detected some normal-sized cDNA and a smaller cDNA species, which was not seen in the RT-PCR products from normal controls. Sequencing revealed that, although the patient's normal-sized cDNA contained a single nonsense mutation in exon 2, his smaller cDNA was the result of an in-frame deletion of exon 2. Long PCR was used to amplify introns 1 and 2 from patient and normal genomic DNA, and no differences in size, in 5' and 3' end sequences, or in restriction-mapping patterns were observed. From these data we developed a set of four PCR primers that can be used to identify GM2A mutations. We use this procedure to demonstrate that the patient is likely homozygous for the nonsense mutation. Other reports have associated nonsense mutations with dramatically reduced levels of mRNA and with an increased level of skipping of the exon containing the mutation, thus reestablishing an open reading frame. However, a recent article has concluded that, in some cases, the latter observation is caused by an artifact of RT-PCR. In support of this conclusion, we demonstrate that, if the competing, normal-sized cDNA is removed from the initial RT-PCR products, from both patient and normal cells, by an exon 2-specific restriction digest; a second round of PCR produces similar amounts of exon 2-deleted cDNA.