Digenic Heterozygous Mutations in SLC34A3 and SLC34A1 Cause Dominant Hypophosphatemic Rickets with Hypercalciuria

Abstract

Context: Hypophosphatemia and metabolic bone disease are associated with hereditary hypophosphatemic rickets with hypercalciuria (HHRH) due to biallelic mutations of SLC34A3 encoding the NPT2C sodium-phosphate cotransporter and nephrolithiasis/osteoporosis, hypophosphatemic 1 (NPHLOP1) due to monoallelic mutations in SLC34A1 encoding the NPT2A sodium-phosphate cotransporter.

Objective: To identify a genetic cause of apparent dominant transmission of HHRH.

Design and setting: Retrospective and prospective analysis of clinical and molecular characteristics of patients studied in 2 academic medical centers.

Methods: We recruited 4 affected and 3 unaffected members of a 4-generation family in which the proband presented with apparent HHRH. We performed clinical examinations, biochemical and radiological analyses, and molecular studies of genomic DNA.

Results: The proband and her affected sister and mother carried pathogenic heterozygous mutations in 2 related genes, SLC34A1 (exon 13, c.1535G>A; p.R512H) and SLC34A3 (exon 13, c.1561dupC; L521Pfs*72). The proband and her affected sister inherited both gene mutations from their mother, while their clinically less affected brother, father, and paternal grandmother carried only the SLC34A3 mutation. Renal phosphate-wasting exhibited both a gene dosage-effect and an age-dependent attenuation of severity.

Conclusions: We describe a kindred with autosomal dominant hypophosphatemic rickets in which whole exome analysis identified digenic heterozygous mutations in SLC34A1 and SLC34A3. Subjects with both mutations were more severely affected than subjects carrying only one mutation. These findings highlight the challenges of assigning causality to plausible genetic variants in the next generation sequencing era.

Keywords: SLC34A; SLC34A1; digenic; hypercalciuria; hypophosphatemia; rickets.

Figure 1.

Four-generation family pedigree. The phenotype and genotype is indicated for each individual, SLC34A3 exon 13, c.1561dupC; p.L521Pfs*72, SLC34A1 exon 13, c.1535 G>A; p.R512H. WT denotes wild-type allele; NT, not tested. Subject II-1 was still-born (SB) at 38 weeks while subject II-2 died at 3 years of uncertain cause; neither subject was tested. The arrow indicates the proband, circles denote females and squares denote males.

Figure 2.

Sequencing electropherograms. Sequence electropherograms demonstrating a missense mutation in SLC34A1 (exon 13, c.1535G>A; p.R512H) and a frameshift mutation in SLC34A3 (exon 13, Leu521Profs*72). Homozygous wild-type sequences are shown above, and heterozygous mutations are shown below, and indicated with arrows.

Figure 3.

Haplotype imputation by using polymorphism markers flanking the SLC34A3 mutation. Note that rs28434439 (in bold) is the closest informative SNP to the site of the SLC34A3 mutation and it was used to design the subcloning assay. Based on the results shown in Supplemental Fig. 1 (24), both parents of the proband carried the SLC34A3 (c.1561dupC) mutation on the same haplotype (blue). However, the father and mother carried distinct wild-type alleles, shown in red and black, respectively, that allow us to assign parental origin of the mutant allele to their children.