Whole exome sequencing frequently detects a monogenic cause in early onset nephrolithiasis and nephrocalcinosis

Kidney Int. 2018 Jan;93(1):204-213. doi: 10.1016/j.kint.2017.06.025. Epub 2017 Oct 12.

Abstract

The incidence of nephrolithiasis continues to rise. Previously, we showed that a monogenic cause could be detected in 11.4% of individuals with adult-onset nephrolithiasis or nephrocalcinosis and in 16.7-20.8% of individuals with onset before 18 years of age, using gene panel sequencing of 30 genes known to cause nephrolithiasis/nephrocalcinosis. To overcome the limitations of panel sequencing, we utilized whole exome sequencing in 51 families, who presented before age 25 years with at least one renal stone or with a renal ultrasound finding of nephrocalcinosis to identify the underlying molecular genetic cause of disease. In 15 of 51 families, we detected a monogenic causative mutation by whole exome sequencing. A mutation in seven recessive genes (AGXT, ATP6V1B1, CLDN16, CLDN19, GRHPR, SLC3A1, SLC12A1), in one dominant gene (SLC9A3R1), and in one gene (SLC34A1) with both recessive and dominant inheritance was detected. Seven of the 19 different mutations were not previously described as disease-causing. In one family, a causative mutation in one of 117 genes that may represent phenocopies of nephrolithiasis-causing genes was detected. In nine of 15 families, the genetic diagnosis may have specific implications for stone management and prevention. Several factors that correlated with the higher detection rate in our cohort were younger age at onset of nephrolithiasis/nephrocalcinosis, presence of multiple affected members in a family, and presence of consanguinity. Thus, we established whole exome sequencing as an efficient approach toward a molecular genetic diagnosis in individuals with nephrolithiasis/nephrocalcinosis who manifest before age 25 years.

Keywords: monogenic cause; nephrocalcinosis; nephrolithiasis; whole exome sequencing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Age of Onset
  • Child
  • Child, Preschool
  • Disease Progression
  • Female
  • Genetic Association Studies
  • Genetic Markers
  • Genetic Predisposition to Disease
  • Heredity
  • Humans
  • Infant
  • Male
  • Mutation*
  • Nephrocalcinosis / diagnostic imaging
  • Nephrocalcinosis / epidemiology
  • Nephrocalcinosis / genetics*
  • Nephrolithiasis / diagnostic imaging
  • Nephrolithiasis / epidemiology
  • Nephrolithiasis / genetics*
  • Pedigree
  • Phenotype
  • Predictive Value of Tests
  • Prognosis
  • Risk Factors
  • Tomography, X-Ray Computed
  • Ultrasonography
  • Whole Exome Sequencing*
  • Young Adult

Substances

  • Genetic Markers