Data_Sheet_2_Case report: Altered pre-mRNA splicing caused by intronic variant c.1499 + 1G > A in the SLC4A4 gene.ZIP

Proximal renal tubular acidosis (pRTA) with ocular abnormalities is an autosomal recessive disease caused by variants in the Solute Carrier Family 4 Member 4 (SLC4A4) gene. Patients present with metabolic acidosis and low plasma bicarbonate concentration (3∼17 mmol/L). In addition, they are often accompanied by ocular abnormalities, intellectual disability, and growth retardation. The patient underwent whole exome sequencing (WES) and bioinformatics analysis of variant pathogenicity in this study. Then, a minigene assay was conducted to analyze the splicing site variant further. Compound heterozygous variants in the SLC4A4 gene (NM_003759.3), c.145C > T (p.Arg49*) and c.1499 + 1G > A, were detected by WES. The minigene assay showed an mRNA splicing aberration caused by the c.1499 + 1G > A variant. Compared with the wild type, the mutant type caused 4-base insertion between exons 10 and 11 of SLC4A4 after expression in HEK293 cells. In conclusion, the c.1499 + 1G > A variant in the SLC4A4 gene may be one of the genetic causes in the patient. Moreover, our study provides the foundation for future gene therapy of such pathogenic variants.

伴眼部异常的近端肾小管酸中毒（pRTA）是一类由溶质载体家族4成员4（SLC4A4）基因变异引发的常染色体隐性遗传病。患者表现为代谢性酸中毒及血浆碳酸氢盐浓度降低（3~17 mmol/L），此外常伴随眼部异常、智力障碍与生长发育迟缓。本研究对该患者实施了全外显子组测序（WES）以及变异致病性的生物信息学分析，随后通过迷你基因实验进一步分析该剪接位点变异。全外显子组测序检测到SLC4A4基因（NM_003759.3）存在复合杂合变异：c.145C>T（p.Arg49*）与c.1499+1G>A。迷你基因实验结果显示，c.1499+1G>A变异可导致mRNA剪接异常；与野生型相比，该突变在HEK293细胞中表达后，会在SLC4A4基因第10与第11号外显子之间插入4个碱基。综上，SLC4A4基因的c.1499+1G>A变异可能是该患者的致病遗传因素之一。此外，本研究为此类致病性变异的后续基因治疗研究奠定了基础。