Polymorphisms in the 3' UTR in the neurocalcin delta gene affect mRNA stability, and confer susceptibility to diabetic nephropathy

Hum Genet. 2007 Nov;122(3-4):397-407. doi: 10.1007/s00439-007-0414-3. Epub 2007 Aug 2.


Using a large-scale genotyping analysis of gene-based single nucleotide polymorphisms (SNPs) in Japanese type 2 diabetic patients, we have identified a gene encoding neurocalcin delta (NCALD) as a candidate for a susceptibility gene to diabetic nephropathy; the landmark SNP was found in the 3' UTR of NCALD (rs1131863: exon 4 +1340 A vs. G, P = 0.00004, odds ratio = 1.59, 95% CI 1.27-1.98). We also discovered two other SNPs in exon 4 of this gene (+999 T/A, +1307 A/G) that showed absolute linkage disequilibrium to the landmark SNP. Subsequent in vitro functional analysis revealed that synthetic mRNA corresponding to the disease susceptible haplotype (exon 4 +1340 G, +1307 G, +999 A) was degraded faster than mRNA corresponding to the major haplotype (exon 4 +1340 A, +1307 A, +999 T), and allelic mRNA expression of the disease susceptibility allele was significantly lower than that of the major allele in normal kidney tissues. In an experiment using a short interfering RNA targeting NCALD, we found that silencing of the NCALD led to a considerable enhancement of cell migration, accompanied by a significant reduction in E-cadherin expression, and by an elevation of alpha smooth muscle actin expression in cultured renal proximal tubular epithelial cells. We also identified the association of the landmark SNP with the progression of diabetic nephropathy in a 8-year prospective study (A vs. G, P = 0.03, odds ratio = 1.91, 95% CI 1.07-3.42). These results suggest that the NCALD gene is a likely candidate for conferring susceptibility to diabetic nephropathy.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions
  • Alleles
  • Base Sequence
  • Case-Control Studies
  • Cells, Cultured
  • Cohort Studies
  • DNA Primers / genetics
  • DNA-Binding Proteins / genetics
  • Diabetes Mellitus, Type 2 / genetics
  • Diabetes Mellitus, Type 2 / metabolism
  • Diabetic Neuropathies / genetics*
  • Gene Expression Profiling
  • Genetic Predisposition to Disease
  • Humans
  • In Vitro Techniques
  • Linkage Disequilibrium
  • Neurocalcin / genetics*
  • Polymorphism, Single Nucleotide*
  • Prospective Studies
  • RNA Interference
  • RNA Stability / genetics*
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism*
  • Transcription Factors / genetics


  • 3' Untranslated Regions
  • DNA Primers
  • DNA-Binding Proteins
  • GRHL2 protein, human
  • NCALD protein, human
  • Neurocalcin
  • RNA, Messenger
  • Transcription Factors