#5302 REVISITING THE PATHOGENIC ROLE OF THE SLC8A1 GENE IN A FAMILY WITH A NOVEL TERMINAL GROSS DELETION IN THE UMOD GENE
Authors: Gonçalves Francisco , Gonçalves Pedro Lisboa , Quental Rita , Fernandes Susana , Quental Sofia , Tavares Isabel , Oliveira João Paulo 
Published: June 2023

Background and Aims

Autosomal dominant tubulointerstitial kidney disease (ADTKD) - the third most common genetic disorder in adults with CKD - comprises a heterogeneous group of rare, hereditary kidney diseases characterized by family history of progressive chronic kidney disease (CKD) with bland urine sediment, absence of significant proteinuria and normal or small-sized kidneys. Biopsy findings are nonspecific and the gold standard for definitive diagnosis is identification of a pathogenic variant in the genes UMOD, MUC1, HNF1β, REN or SEC61A1.

Method

Case report.

Results

The proband was a 27-year-old white male referred for CKD, KDIGO stage 3a. His medical history was relevant for nocturnal enuresis until age 10; arterial hypertension diagnosed at age 19; and asymptomatic hyperuricemia, disproportional to the level of renal function impairment. Urinalysis was negative for protein, red blood cells or leucocytes and magnetic resonance imaging showed normal sized kidneys with bilateral cysts in the medulla and the corticomedullary junction. The family pedigree (Figure 1) illustrates that hyperuricemic nephropathy and CKD segregated in this family with an autosomal dominant pattern of inheritance. A custom NGS-based gene panel allowed to identify in the proband (IV-2) and his affected brother (IV-1): (i) a previously unreported large deletion in the UMOD gene, encompassing the entire exon 11, classified as “likely pathogenic”; ii) an ultra-rare nonsense SLC8A1 allele — c.16C&gt;T p.(Arg6*), classified as “variant of uncertain clinical significance (VUS)”; (iii) an ultra-rare missense variant in the gene encoding polycystin-1 (PKD1) — c.9170T&gt;C p.(Val3057Ala), classified as VUS. Since the latter was inherited from their healthy mother (III-1) it was considered a benign variation, similar to the more common p.Val3057Met variant affecting the same codon. Other affected family member (III-5) was heterozygous for the UMOD exon 11 deletion, which was excluded in two healthy relatives (III-1, III-4), establishing the primary diagnosis of ADTKD-UMOD. It is noteworthy that the only two gross UMOD deletions associated with ADTKD affected evolutionarily conserved residues in exon 4 [1]. The presence of the SLC8A1 p.(Arg6*) allele in patients IV-1 and IV-2, who had early clinical presentations, together with its absence in patient III-5, who had a significantly later clinical onset than her older brother (III-2), suggests that it exerted a pathogenic or disease modifier role in this family, in accordance with the predicted protein truncating effect. Indeed, genome-wide linkage analysis in 5 multiplex families with ADTKD identified involvement of chromosome 2p22.1-p21; SLC8A1 was the most likely gene but no pathogenic variants could be identified; copy number variants might have been missed [2]. Unfortunately, in our family study, we could not identify any subject segregating only the SLC8A1 p.(Arg6*) allele, which would have been indispensable to demonstrate its pathogenicity.

Conclusion

Herein, we report a family with hyperuricemic nephropathy where genetic testing identified a novel, likely pathogenic UMOD variant. The mechanisms underlying the pathogenicity of exon 11 deletion require further study. Additionally, the co-segregation of an ultra-rare nonsense SLC8A1 variant in some individuals was associated with earlier onset and faster progression of CKD, suggesting once again a role for SLC8A1 in the pathogenesis of ADTKD.