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A Variant in the IRF6 Promoter Associated with the Risk for Orofacial Clefting.

M-J Li1, P Kumari2, Y-S Lin1

  • 1State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China.

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A new genetic variant, rs12403599, is strongly linked to nonsyndromic cleft lip and palate (NSCL/P), particularly microform cleft lip. This finding refines understanding of the genetic basis for NSCL/P in Han Chinese populations.

Keywords:
deep sequencinggenetic association studiesgenetic susceptibilitylogistic modelorofacialpromoter region

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Area of Science:

  • Genetics
  • Developmental Biology
  • Oral and Maxillofacial Surgery

Background:

  • The single-nucleotide polymorphism (SNP) rs2235371 (IRF6 V274I) has been associated with nonsyndromic cleft lip with or without cleft palate (NSCL/P).
  • However, rs2235371 appears to lack a direct functional effect, suggesting it tags a more significant etiological variant.

Purpose of the Study:

  • To identify the functional genetic variant(s) responsible for NSCL/P risk associated with the rs2235371-tagged haplotype.
  • To investigate the association of identified variants with specific NSCL/P phenotypes, including microform cleft lip (MCL).

Main Methods:

  • Targeted sequencing of the IRF6 gene interval in Han Chinese individuals with NSCL/P.
  • Replication in larger case-control cohorts.
  • Reporter assays in GMSM-K cells and analysis of IRF6 expression in patient lip tissues.

Main Results:

  • The SNP rs12403599 in the IRF6 promoter was identified as strongly associated with all NSCL/P phenotypes, especially nonsyndromic cleft lip (NSCLO) and MCL.
  • Conditional logistic analysis revealed that the association of rs2235371 was lost when rs12403599 was accounted for.
  • The G allele of rs12403599 significantly increases risk for MCL, showing higher promoter activity and increased IRF6 expression in affected individuals.

Conclusions:

  • rs12403599 is a more accurate tag for the risk haplotype of NSCL/P in Han Chinese than rs2235371.
  • The G allele of rs12403599 enhances IRF6 promoter activity, suggesting a mechanism for its role in NSCL/P pathogenesis.
  • Further investigation into the functional impact of rs12403599 and its association in diverse populations is warranted.