Cryptic exon activation in SLC12A3 in Gitelman syndrome

Abstract

Gitelman syndrome (GS) is an autosomal recessive renal tubulopathy characterized by hypokalemic metabolic alkalosis with hypocalciuria and hypomagnesemia. GS clinical symptoms range from mild weakness to muscular cramps, paralysis or even sudden death as a result of cardiac arrhythmia. GS is caused by loss-of-function mutations in the solute carrier family 12 member 3 (SLC12A3) gene, but molecular mechanisms underlying such a wide range of symptoms are poorly understood. Here we report cryptic exon activation in SLC12A3 intron 12 in a clinically asymptomatic GS, resulting from an intronic mutation c.1669+297 T>G that created a new acceptor splice site. The cryptic exon was sandwiched between the L3 transposon upstream and a mammalian interspersed repeat downstream, possibly contributing to inclusion of the cryptic exon in mature transcripts. The mutation was identified by targeted next-generation sequencing of candidate genes in GS patients with missing pathogenic SLC12A3 alleles. Taken together, this work illustrates the power of next-generation sequencing to identify causal mutations in intronic regions in asymptomatic individuals at risk of developing potentially fatal disease complications, improving clinical management of these cases.

Hydrochlorothiazide Test as a Tool in the Diagnosis of Gitelman Syndrome in Chinese Patients

“…Previous studies have shown inconsistent results of correlations between phenotype and genotype in GS patients ( 8 , 26 , 27 ). Since HCT test can effectively evaluate NCC function regardless of the specific mutation in SLC12A3 gene, it may be helpful to connect the genotype with the salt-losing phenotype and narrow the screening population ( 4 , 5 ). In addition, in patients with GS-like manifestations, a negative HCT test result may justify the use of whole exome sequencing rather than traditional GS and BS gene testing to help identify novel mutation and disease effectively ( 28 ).…”

“…However, given its high cost and technical requirements, it is difficult to advocate genetic testing in community-level hospitals, especially in resource-limited areas. Moreover, exon sequencing may fail to detect mutations in introns or gene regulatory areas, thus limiting its sensitivity ( 4 , 5 ). Therefore, the clinical diagnostic strategy of GS is still the cornerstone of the patient care.…”

Gitelman syndrome with a novel frameshift variant in SLC12A3 gene accompanied by chronic kidney disease and type 2 diabetes mellitus

“…Furthermore, our next-generation sequencing panel-based analysis excluded any causal variants in both CLCNKB and HNF1B. Variant c.2927C > T has been reported as a causative mutation for Gitelman syndrome [5,6]. The Japanese database, jMorp (Japanese Multi Omics Reference Panel) indicates an occurrence rate of 0.042%.…”

“…Variant c.137del is novel variant and meets the criteria of very strong pathogenicity (PSV1), in addition to moderate (PM2) and supporting (PP4) evidence of pathogenicity, according to the American College of Medical Genetics and Genomics/the Association for Molecular Pathology (ACMG/AMP) standards guidelines, thereby leading to pathogenic based on the scoring rules [4]. Variant c.2927C > T has been previously reported as the cause of Gitelman syndrome [5,6]. Based on these results, we diagnosed this patient with Gitelman syndrome.…”

A pediatric case of hypomagnesemia 1 (HOMG1) caused by novel compound heterozygous mutations in TRPM6

“…The father’s blood sample was not taken because we could not contact the divorced father. Inherited hypomagnesemia-responsible genes including TRPM6, CLCNKB, BSND, SLC12A3, CASR, KCNJ10, CLDN16, CLDN19, FXYD2, EGF, KCNA1, CNNM2 , and HNF1B were screened by next-generation sequencing analysis with targeting sequencing 5,6 . Finally, Sanger sequencing confirmed compound heterozygous mutations (NM_017662.5 (TRPM6_v001): c.1483C>T [p.Gln495*] and NM_017662.5 (TRPM6_v001): c.2715del [p.Trp905*]) in TRPM6 (Fig.…”