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Background  Very recently, a sub-analysis of genome-wide association scans revealed that the non-coding single nucleotide polymorphism (SNP) rs12212067 in the  FOXO3A  gene is associated with a milder course of Crohn's disease (CD) ( Cell  2013;155:57–69). The aim of our study was to evaluate the clinical value of the SNP rs12212067 in predicting the severity of CD by correlating CD patient genotype status with the most relevant complications of CD such as stenoses, fistulas, and CD-related surgery.    Methodology/Principal Findings  We genotyped 550 CD patients for rs12212067 ( FOXO3A ) and the three common CD-associated  NOD2  mutations rs2066844, rs2066847, and rs2066847 and performed genotype-phenotype analyses.    Results  No significant phenotypic differences were found between the wild-type genotype TT of the  FOXO3A  SNP rs12212067 and the minor genotypes TG and GG independently from  NOD2  variants. The allele frequency of the minor G allele was 12.7%. Age at diagnosis, disease duration, body mass index, surgery rate, stenoses, fistula, need for immunosuppressive therapy, and disease course were not significantly different. In contrast, the NOD2 mutant p.Leu1007fsX1008 (rs2066847) was highly associated with penetrating CD (p = 0.01), the development of fistulas (p = 0.01) and stenoses (p = 0.01), and ileal disease localization (p = 0.03). Importantly, the  NOD2  SNP rs2066847 was a strong separator between an aggressive and a mild course of CD (p = 2.99×10 −5 ), while the  FOXO3A  SNP rs12212067 did not separate between mild and aggressive CD behavior in our cohort (p = 0.35). 96.2% of the homozygous NOD2 p.Leu1007fsX1008 carriers had an aggressive disease behavior compared to 69.3% of the patients with the  NOD2  wild-type genotype (p = 0.007).    Conclusion/Significance  In clinical practice, the NOD2 variant p.Leu1007fsX1008 (rs2066847), in particular in homozygous form, is a much stronger marker for a severe clinical phenotype than the  FOXO3A  rs12212067 SNP for a mild disease course on an individual patient level despite its important impact on the inflammatory response of monocytes.

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The NOD2 p.Leu1007fsX1008 Mutation (rs2066847) Is a Stronger Predictor of the Clinical Course of Crohn's Disease than the FOXO3A Intron Variant rs12212067