Gitelman Syndrome via the SLC12A3 Gene

Gitelman syndrome (OMIM# 263800) is an inherited salt-losing tubulopathy characterized by hypokalemic metabolic alkalosis with hypomagnesemia and hypocalciuria (Simon et al. Nat Genet 12(1):24-30, 1996; Vargas-Poussou et al. J Am Soc Nephrol 22(4):693-703, 2011; Glaudemans et al. Eur J Hum Genet 20(3):263-70, 2012). It is the most common renal tubular disorder in Whites with a prevalence of 1 in 40,000. Gitelman syndrome has been mostly diagnosed during adulthood while some affected children have been observed from the age of 6. Common clinical features include transient periods of muscle weakness and tetany that may be accompanied by abdominal pains, vomiting and fever. Completely asymptomatic patients may only have chondrocalcinosis in adulthood.

Gitelman syndrome is an autosomal recessive disorder mostly caused by loss-of-function mutations in the solute carrier family 12, member 3 (SLC12A3) gene (Simon et al., 1996; Vargas-Poussou et al., 2011; Glaudemans et al., 2012). SLC12A3 has 26 coding exons that encode the thiazide-sensitive NaCl cotransporter (NCC), which is the target for thiazide-type diuretics (a first-line pharmacological treatment of hypertension). Genetic defects of SLC12A3 occur throughout the whole gene and include missense (59%), nonsense (5%), splicing site mutations (13%), small deletion/insertions (17%) and large deletions/duplications (6%) (Human Gene Mutation Database; Vargas-Poussou et al., 2011). Nearly half of patients who only had a single mutation detected by direct sequencing have been found to have a large deletion or duplication at the second allele via exon-level copy number testing (Vargas-Poussou et al., 2011). Notably, two recurrent deep intronic splicing mutations c.1670-191C>T and c.2548+253C>T have been reported with an indication of mutational hot spots rather than a founder effect (Nozu et al. Pediatr Res 66(5):590-593, 2009; Lo et al. Clin J Am Soc Nephrol 6(3):630-639, 2011). A minority of the Gitelman syndrome phenotype are caused by mutations in the CLCNKB gene, which is a major causative gene for Bartter syndrome (Simon et al. Nat Genet 17(2):171-178, 1997; Vargas-Poussou et al., 2011).

In a large cohort of 448 patients in whom Gitelman syndrome was suspected, direct sequencing identified homozygous and compound heterozygous SLC12A3 mutations in 70% of patients; only one mutated allele was identified in 18% of patients (Vargas-Poussou et al. J Am Soc Nephrol 22(4):693-703, 2011). In another study of 163 patients with a clinical suspicion of Gitelman syndrome, direct sequencing identified homozygous (39/163) and compound heterozygous (99/163) SLC12A3 mutations in 138 (~ 85%) of patients; only one mutated allele was identified in the remaining 25 patients (Glaudemans et al. Eur J Hum Genet 20(3):263-270, 2012).

This test provides full coverage of all coding exons of the SLC12A3 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

This test also includes targeted testing of two deep intronic splicing mutations c.1670-191C>T and c.2548+253C>T (Nozu et al., 2009; Lo et al., 2011).