Trio-WES and functional validation reveals a novel splice site variant of SLC26A3 in a case with congenital chloride diarrhea and a systematic review of SLC26A3 mutations in China.

Congenital chloride diarrhea (CCD) is an autosomal recessive disease, characterized by watery diarrhea, hypochloremia and metabolic alkalosis. It is associated with defects in solute carrier family 26 member 3 (SLC26A3) which acts as Na⁺-independent Cl^-/HCO₃^- exchanger. Early diagnosis allows planning of perinatal care and timely treatment to improve the prognosis of CCD. However, only few cases were diagnosed in the fetus period, while most of CCD cases were diagnosed after birth without timely diagnosis and treatment. This study was conducted to verify the disease-causing gene by prenatal genetic and functional tests for assisting prenatal diagnosis of a fetus with suspected CCD and reviewed the mutation spectrum of Chinese CCD patients for the first time. Here, we reported a suspected CCD fetus with signs of polyhydramnios and intestinal dilatation by prenatal ultrasound. Subsequent prenatal Trio-whole-exome sequencing identified a novel homozygous mutation (c.383-5A > G) of SLC26A3, which was classified as uncertain significance (VUS). Mini-Gene Splicing Assay confirmed the effect of VUS variant on abnormal splicing of SLC26A3, increasing pathogenicity evidence, and determining the prenatal diagnosis and subsequent treatment of CCD. Literature review of 18 CCD cases showed that t c.270_271insAA (p.G91Kfs*3) was the most frequent mutation in China. In conclusion, our study found the novel c.383-5A > G mutation of SLC26A3 as the pathogenic cause in the proband, which expanded the mutation spectrum of SLC26A3. There also highlights the importance of integrative genetic and functional tests that provide a reference for prenatal diagnosis of suspected CCD to access postnatal management in a timely manner.