Buried in the Middle but Guilty: Intronic Mutations in the TCIRG1 Gene Cause Human Autosomal Recessive Osteopetrosis


Human osteopetrosis is a genetic bone disease characterized by increased bone density owing to failure in bone resorption by osteoclasts. For a long time, two main forms have been distinguished: an autosomal recessive form, also called malignant infantile, because of its early onset and frequent lethal outcome in the absence of a therapy; and an autosomal dominant form, also termed benign, because of its later presentation and milder course. Since 2000, the molecular basis of both forms has largely been unraveled, revealing a great genetic heterogeneity.[1] Subsequently, careful clinical characterization and longer follow-up have identified patients who do not fit within either class, documenting a wider variability of phenotypes, some of which escaped molecular characterization, because a responsible mutation could not be identified. In particular, it has become clear that, besides the paradigmatic recessive malignant and dominant benign forms, an intermediate group exists, in which the defect can be inherited as either a recessive or a dominant trait. These intermediate cases often represent a diagnostic challenge but also constitute the opportunity to learn important lessons on the bone biology. On this regard, we have recently reported on a young osteopetrotic patient in which an incomplete splicing defect in the TCIRG1 gene allowed for the production of the limited amount of wild-type transcript sufficient to dampen the severity of the disease to an almost completely normal lifestyle.[2] However, in that article, we pointed out that a definitive conclusion regarding the prognosis of the pathology was not possible because of the young age of the patient and the extraordinary nature of the mutation.

Exome sequencing is a powerful, high-throughput technique that in few years has greatly improved the discovery of the genetic defect underlying Mendelian disorders.[3] This approach is fundamentally based on the observation that the vast majority of mutations causing inherited diseases are located in coding regions of the genome and, vice versa, a large fraction of rare variants altering a protein structure are predicted to impact on its function. However, current sets of probes for exome capture target not only coding regions but also 5′ and 3′ untranslated regions (5’UTR and 3′UTR, respectively) and stretches of intronic regions, including exon-flanking regions and short introns contained between targeted exons.

Here, we describe the tortuous and, to some extent, serendipitous identification of the molecular defect in the middle of intron 15 of the TCIRG1 gene in two siblings affected by intermediate recessive osteopetrosis and in three additional patients in which a single mutated allele in the same gene had previously been found.