Nephrolithiasis and Nephrocalcinosis Panel

Nephrolithiasis is a clinical condition in which urinary supersaturation leads to stone formation in the urinary system (the lumen of the collecting system, ureter, and bladder) (Braun et al. 2016; Halbritter et al. 2015; Gee et al. 2016). Patients with kidney stones may have no symptoms or may present with flank pain, gross or microscopic hematuria, obstruction of one or both kidneys, and urinary infections. It affects 10%-15% of adults in their lifetime.

Nephrocalcinosis is a clinical-pathological entity referring to the diffuse, radiologically demonstrable deposition of calcium salts within the kidney parenchyma (Piccoli et al. 2016; Hsi et al. 2015).

The formation of kidney stones is a multifactorial process involving an interaction of environmental, dietary, and genetic factors. Therefore, it is a group of highly genetically heterogeneous diseases. To date, at least 30 genes have been linked to a monogenic form of nephrolithiasis or nephrocalcinosis in autosomal-dominant, autosomal-recessive, or X-linked inheritance as listed below (Braun et al. 2016; Halbritter et al. 2015; Gee et al. 2016). The spectrum of pathogenic variants throughout these genes includes all types of changes.

Autosomal dominant: ADCY10 (hypercalciuria, calcium oxalate nephrolithiasis), NHERF1/SLC9A3R1 (nephrolithiasis due to impaired renal phosphate reabsorption), CASR (hypocalcemia), HNF4A (MODY, Fanconi syndrome and nephrocalcinosis)

Autosomal dominant or recessive: SLC3A1 (cystinuria, type A), SLC7A9 (cystinuria, type B), SLC22A12 (renal hypouricemia, type 1), SLC2A9 (renal hypouricemia, type 2), SLC34A1 (hypophosphataemic nephrolithiasis/osteoporosis; hypercalcemia), VDR (vitamin D resistant rickets or osteoporosis), SLC4A1 (distal renal tubular acidosis)

Autosomal recessive: ATP6V0A4 (distal renal tubular acidosis), ATP6V1B1 (distal renal tubular acidosis with deafness), CA2 (distal renal tubular acidosis with osteopetrosis), CLDN16 (renal hypomagnesemia 3), CLDN19 (renal hypomagnesemia 5 with ocular abnormalities), AGXT (primary hyperoxaluria, type 1), GRHPR (primary hyperoxaluria, type 2), HOGA1 (primary hyperoxaluria, type 3), CYP24A1 (infantile hypercalcaemia), SLC34A3 (hypophosphatemic rickets with hypercalciuria), APRT (adenine phosphoribosyltransferase deficiency), FAM20A (Enamel-Renal syndrome, amelogenesis imperfecta and nephrocalcinosis), SLC12A1 (Bartter syndrome, type 2), KCNJ1 (Bartter syndrome, type 2), XDH (xanthinuria), SLC26A1 (calcium oxalate nephrolithiasis)

X-Linked recessive: CLCN5 (Dent disease 1), OCRL (Lowe syndrome/Dent disease 2), HPRT1 (Lesch-Nyhan syndrome)

See individual gene test descriptions for more information on molecular biology of gene products.

In an international cohort comprising 272 genetically unresolved individuals (106 children and 166 adults) from 268 families with nephrolithiasis (n=256) or isolated nephrocalcinosis (n=16), Halbritter et al. detected likely (or suspected) causative variants in 14 of 30 analyzed genes, leading to a molecular diagnosis in 14.9% (40 of 268) of all cases (Halbritter et al. 2015). The mutation detection rates of these 14 individual genes can be found at the Halbritter et al. report.

In another international pediatric cohort comprising 143 individuals under 18 years of age, with nephrolithiasis (n=123) or isolated nephrocalcinosis (n=20), Braun et al. detected likely (or suspected) causative variants in 14 of the same set of 30 known nephrolithiasis/nephrocalcinosis genes, leading to a molecular diagnosis in 16.8% (24 of 143) of affected individuals (Braun et al. 2016). The mutation detection rates of these 14 individual genes can be found at the Braun et al. report.

Our current panel includes 29 of the 30 genes described above. The CLCNKB gene (Bartter syndrome, type 3) is excluded due to next generation sequencing technology’s limitations with highly similar sequences. No plausible pathogenic variants were found in CLCNKB in either the Halbritter et al. or Braun et al. study. Therefore, the overall mutation detection rate thorough our current panel is expected to be nearly the same as that of the two studies mentioned above for nephrolithiasis or nephrocalcinosis patients.

Our current panel also includes the very recently identified nephrolithiasis causative gene SLC26A1 (Gee et al. 2016). In 348 individuals with nephrolithiasis or isolated nephrocalcinosis who are negative for the 30 genes mentioned above, recessive SLC26A1 causative variants were found in 2 patients (0.57%).

Large deletions and/or duplications appear to be relatively common in Human Gene Mutation Database (HGMD) for these genes: AGXT, OCRL, CLCN5, SLC3A1, SLC7A9 and HPRT1.

Large deletions and/or duplications have been documented in HGMD in these genes but are relatively uncommon: ATP6V0A4, CASR, KCNJ1, CLDN16, CLDN19, HNF4A, CYP24A1, FAM20A, SLC2A9, VDR, XDH and SLC26A1.

No large deletions or duplications have been reported in the other 10 genes of the current panel.

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel provides 100% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).