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A common haplotype at the 5′ end of the RET proto‐oncogene, overrepresented in Hirschsprung patients, is associated with reduced gene expression
Author(s) -
Griseri Paola,
Bachetti Tiziana,
Puppo Francesca,
Lantieri Francesca,
Ravazzolo Roberto,
Devoto Marcella,
Ceccherini Isabella
Publication year - 2005
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.20135
Subject(s) - biology , haplotype , genetics , single nucleotide polymorphism , allele , exon , gene , linkage disequilibrium , pathogenesis , genotype , immunology
Abstract Hirschsprung disease (HSCR) is a complex genetic defect of intestinal innervation mainly ascribed to loss of function mutations of the RET gene. Although RET coding mutations account for only 15% of HSCR sporadic cases, several linkage and association studies still indicate RET as a major HSCR gene, suggesting the existence of noncoding RET variants or common polymorphisms which can act in HSCR pathogenesis. We previously described a predisposing RET haplotype (A‐C‐A) composed of alleles at three SNPs (−1 bp and −5 bp from the RET transcription start site, NT_033985.6:g.975824G>A and NT_033985.6:g.975820C>A, respectively, and silent polymorphism c.135G>A), which was present in 62% of chromosomes from HSCR patients but only in 22% of control chromosomes. Here we address the question of how this 5′ ACA haplotype may functionally act as a predisposing factor in HSCR pathogenesis by performing functional analysis of the same three SNPs. We demonstrate that neither the two promoter variants nor the exon 2 SNP interfere with reporter gene transcription or RET mRNA splicing, respectively. However, real‐time RT‐PCR, performed in RNA obtained from lymphoblasts of selected individuals, has shown that homozygosity for the whole ACA haplotype is associated with reduced RET gene expression. We propose that a yet unidentified variant in linkage disequilibrium with the ACA haplotype, rather than the single characterizing SNPs, acts as a HSCR susceptibility allele by affecting the normal amount of RET receptor on the cell surface. Hum Mutat 25:189–195, 2005. © 2005 Wiley‐Liss, Inc.