Association of the IRF6 rs2235371 and rs861019 Polymorphisms with Non-Syndromic Cleft Lip with or without Cleft Palate in the Yakut Population

Nadezhda I. Pavlova, Aleksandra T. Diakonova, Vladislav A. Alekseev, Lyubov S. Mironova, Vladimir V. Dodokhov, Khariton A. Kurtanov, Innokenty D. Ushnitsky

International Journal of Biomedicine. 2021;11(4):570-575.
DOI: 10.21103/Article11(4)_OA28
Originally published December 10, 2021


Background: Non-syndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common birth defects. NSCL/P can be broadly divided into cleft lip only (CLO), cleft palate only (CPO), and cleft lip with cleft palate (CLP) based on clinical presentation. The aim of this study was to investigate the relationship between the IRF6 gene polymorphisms and non-syndromic cleft lip with or without cleft palate (NSCL/P) in the Yakut population.
Methods and Results: In 23 OFC patients and 58 unrelated control subjects from the Yakut population, we tested two SNPs (rs2235371 and rs861019) with a minor allele frequency of more than 5% in the candidate gene IRF6. We found that the SNP marker rs861019 showed significant differences in allele frequencies (OR=2.07, 95%CI: 1.01–4.23, P=0.04) between the NSCL/P patients and the comparison group. Analysis of allele frequencies for rs861019 SNP in subgroups showed that there was a difference in the frequency between CLP and control (OR=5, 95% CI: 1.61-15.53, P=0.11); however, this result was not significant.
Genotype analysis showed significant differences in patients from the CLP subgroup in comparison with controls for homozygous (AA compared with GG) (OR=9.00, 95% CI: 1.03–78.58, P=0.03), heterozygous (GA compared with GG) (OR=5.50, 95% CI: 1.05-28.75, P=0.04,), recessive (GG compared with GA + AA) (OR=6.67, 95% CI: 1.61-27.58; RR=4.78, 95% CI: 1.42–16.10, P=0.008,) and co-dominant (GG compared with GA, compared with AA) (P=0.02)  inheritance models.
Diplotype analysis showed that the NSCL/P group was more likely to have the [CC]-[GG] diplotype than the comparison group. This diplotype carries the risk GG genotype (rs861019) (30.4%) and does not carry the risk T allele(rs2235371). In the CLP subgroup, two diplotypes ([CT]-[GG] and [CC]-[GG]) were found more often than in the comparison group. Both diplotypes carry the risk GG genotype(rs861019; 33.3%). In the CPO subgroup, the [CT]-[GG] diplotype was more common. In the CLO subgroup, only two diplotypes ([CC]-[GA] and [CC]-[GG]) were found, both of which were more common than in the comparison group (75% and 25%).. It is likely that these results for the CLO and CPO subgroups were influenced by the small size of both samples. Unlike the NSCL/P and CLP groups, in these samples, diplotypes with the homozygous genotype GG (rs861019) without the homozygous genotype TT (rs2235371) were more common. Diplotypes with a homozygous genotype of the TT risk allele were not found in the studied groups except for the comparison group, where the [TT]-[AA] diplotype was represented by a low frequency (0.17%).
Conclusion: The present study provides strong statistical support (for the first time to our knowledge) that genetic variants of the IRF6 rs861019 SNP are associated with NSCL/P in Yakuts.

orofacial cleft • IRF6 gene • Yakuts • haplotype • diplotype • rs2235371 • rs861019
  1. Jugessur A, Rahimov F, Lie RT, Wilcox AJ, Gjessing HK, Nilsen RM, Nguyen TT, Murray JC. Genetic variants in IRF6 and the risk of facial clefts: single-marker and haplotype-based analyses in a population-based case-control study of facial clefts in Norway. Genet Epidemiol. 2008 Jul;32(5):413-24. doi: 10.1002/gepi.20314. 
  2. Wehby GL, Cassell CH. The impact of orofacial clefts on quality of life and healthcare use and costs. Oral Dis. 2010 Jan;16(1):3-10. doi: 10.1111/j.1601-0825.2009.01588.x. 
  3. Mossey PA, Modell B. Epidemiology of oral clefts 2012: an international perspective. Front Oral Biol. 2012;16:1-18. doi: 10.1159/000337464. 
  4. Gorlin RJ, Cohen MM, Hennekam RCM. Syndromes of the Head and Neck. New York: Oxford University Press; 2001.
  5. Mossey PA, Castilla EE. Global Registry and Database on Craniofacial Anomalies: Report of a WHO Registry Meeting on Craniofacial Anomalies. Geneva, Switzerland: World Health Organization; 2001.
  6. Allam E, Windsor L, Stone C. Cleft lip and palate: etiology, epidemiology, preventive and intervention strategies. Anat Physiol. 2014;4: 940–2161. doi:10.4172/2161-0940.1000150
  7. Ahmed MK, Bui AH, Taioli E. Epidemiology of Cleft Lip and Palate. Designing Strategies for Cleft Lip and Palate Care. In TechOpen. 2017;22. doi: 10.5772/67165
  8. Forrester MB, Merz RD. Descriptive epidemiology of oral clefts in a multiethnic population, Hawaii, 1986-2000. Cleft Palate Craniofac J. 2004 Nov;41(6):622-8. doi: 10.1597/03-089.1.
  9. Abdurahmonov AZ. [Congenital cleft lip and palate in children from Tajikistan in 2009–2019]. Aspirantskiy Vestnik Povolzhiya. 2020;20(1-2):75-79. doi: 10.17816/2072-2354.2020.20.1.75-79. [Article in Russian].
  10. Ushnitsky ID, Mironova LS, Gogolev II, Davydova MM. Clinical and genetic aspects of congenital lip and palate clefts in children of Yakutia. Yakut Medical Journal. 2018; 1(61).  doi: 10.25789/YMJ.2018.61.06
  11. Dixon MJ, Marazita ML, Beaty TH, Murray JC. Cleft lip and palate: understanding genetic and environmental influences. Nat Rev Genet. 2011 Mar;12(3):167-78. doi: 10.1038/nrg2933. 
  12. Jagomägi T, Nikopensius T, Krjutskov K, Tammekivi V, Viltrop T, Saag M, Metspalu A. MTHFR and MSX1 contribute to the risk of nonsyndromic cleft lip/palate. Eur J Oral Sci. 2010 Jun;118(3):213-20. doi: 10.1111/j.1600-0722.2010.00729.x. 
  13. Zucchero TM, Cooper ME, Maher BS, Daack-Hirsch S, Nepomuceno B, Ribeiro L, et al. Interferon regulatory factor 6 (IRF6) gene variants and the risk of isolated cleft lip or palate. N Engl J Med. 2004 Aug 19;351(8):769-80. doi: 10.1056/NEJMoa032909. 
  14. Ingraham CR, Kinoshita A, Kondo S, Yang B, Sajan S, Trout KJ, Malik MI, Dunnwald M, Goudy SL, Lovett M, Murray JC, Schutte BC. Abnormal skin, limb and craniofacial morphogenesis in mice deficient for interferon regulatory factor 6 (Irf6). Nat Genet. 2006 Nov;38(11):1335-40. doi: 10.1038/ng1903. 
  15. Richardson RJ, Dixon J, Malhotra S, Hardman MJ, Knowles L, Boot-Handford RP, Shore P, Whitmarsh A, Dixon MJ. Irf6 is a key determinant of the keratinocyte proliferation-differentiation switch. Nat Genet. 2006 Nov;38(11):1329-34. doi: 10.1038/ng1894.
  16. Wang M, Pan Y, Zhang Z, Wang L. Three polymorphisms in IRF6 and 8q24 are associated with nonsyndromic cleft lip with or without cleft palate: evidence from 20 studies. Am J Med Genet A. 2012 Dec;158A(12):3080-6. doi: 10.1002/ajmg.a.35634. 
  17. de Souza LT, Kowalski TW, Ferrari J, Monlléo IL, Ribeiro EM, de Souza J, Fett-Conte AC, de Araujo TK, Gil-da-Silva-Lopes VL, Ribeiro-Dos-Santos ÂK, dos Santos SE, Félix TM. Study of IRF6 and 8q24 region in non-syndromic oral clefts in the Brazilian population. Oral Dis. 2016 Apr;22(3):241-5. doi: 10.1111/odi.12432. 
  18. Rafighdoost H, Hashemi M, Danesh H, Bizhani F, Bahari G, Taheri M. Association of single nucleotide polymorphisms in AXIN2, BMP4, and IRF6 with Non-Syndromic Cleft Lip with or without Cleft Palate in a sample of the southeast Iranian population. J Appl Oral Sci. 2017 Nov-Dec;25(6):650-656. doi: 10.1590/1678-7757-2017-0191. 
  19. Pegelow M, Peyrard-Janvid M, Zucchelli M, Fransson I, Larson O, Kere J, Larsson C, Karsten A. Familial non-syndromic cleft lip and palate--analysis of the IRF6 gene and clinical phenotypes. Eur J Orthod. 2008 Apr;30(2):169-75. doi: 10.1093/ejo/cjm097.
  20. Pavlova NI, Kurtanov KhA, Diakonova AT, Mironova LS, Solovyeva NA, Borisova YP, et al. Genetic Predictors for the Development of Congenital Orofacial Clefts. International Journal of Biomedicine. 2020;10(1):50-53. doi: 10.21103/Article10(1)_OA7

Download Article
Received October 26, 2021.
Accepted November 15, 2021.
©2021 International Medical Research and Development Corporation.