Tooth agenesis is one of the most common craniofacial disorders in humans. More than 350 genes have been associated with teeth development. In this study, we enrolled 60 child patients (age 13 to 17) with various types of tooth agenesis. Whole gene sequences of PAX9, MSX1, AXIN2, EDA, EDAR and WNT10a genes were sequenced by next generation sequencing on the Illumina MiSeq platform. We found previously undescribed heterozygous nonsense mutation g.8177G>T (c.610G>T) in MSX1 gene in one child. Mutation was verified by Sanger sequencing. Sequencing analysis was performed in other family members of the affected child. All family members carrying g.8177G>T mutation suffered from oligodontia (missing more than 6 teeth excluding third molars). Mutation g.8177G>T leads to a stop codon (p.E204X) and premature termination of Msx1 protein translation. Based on previous in vitro experiments on mutation disrupting function of Msx1 homeodomain, we assume that the heterozygous g.8177G>T nonsense mutation affects the amount and function of Msx1 protein and leads to tooth agenesis.

Biomolecular Modelling Laboratory The Francis Crick Institute London United Kingdom

Clinic of Stomatology Faculty of Medicine Masaryk University and St Anne's University Hospital Brno Czech Republic

Institute of Dentistry and Oral Sciences Faculty of Medicine and Dentistry Palacký University Olomouc Czech Republic

Laboratory of Neurobiology and Molecular Psychiatry Department of Biochemistry Faculty of Science Masaryk University Brno Czech Republic

Laboratory of Neurobiology and Pathological Physiology Institute of Animal Physiology and Genetics The Academy of Sciences of the Czech Republic Brno Czech Republic

Laboratory of Neurochemistry Bosch Institute and Discipline of Anatomy and Histology School of Medical Sciences Sydney Medical School The University of Sydney Sydney New South Wales Australia

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Weston JA, Yoshida H, Robinson V, Nishikawa S, Fraser ST, Nishikawa S. Neural crest and the origin of ectomesenchyme: neural fold heterogeneity suggests an alternative hypothesis. Dev Dyn. 2004;229(1): 118–130. 10.1002/dvdy.10478 PubMed DOI

Jussila M, Thesleff I. Signaling networks regulating tooth organogenesis and regeneration, and the specification of dental mesenchymal and epithelial cell lineages. Cold Spring Harb Perspect Biol. 2012;4(4): a008425 10.1101/cshperspect.a008425 PubMed DOI PMC

Tucker AS, Sharpe PT. Molecular genetics of tooth morphogenesis and patterning: the right shape in the right place. J Dent Res. 1999;78(4): 826–834. 10.1177/00220345990780040201 PubMed DOI

Tucker A, Sharpe P. The cutting-edge of mammalian development; how the embryo makes teeth. Nat Rev Genet. 2004;5(7): 499–508. 10.1038/nrg1380 PubMed DOI

Huang Z, Hu X, Lin C, Chen S, Huang F, Zhang Y. Genome-wide analysis of gene expression in human embryonic tooth germ. J Mol Histol. 2014;45(6): 609–617. 10.1007/s10735-014-9580-5 PubMed DOI

Prasad MK, Geoffroy V, Vicaire S, Jost B, Dumas M, Le Gras S, et al. A targeted next-generation sequencing assay for the molecular diagnosis of genetic disorders with orodental involvement. J Med Genet. 2016;53(2): 98–110. 10.1136/jmedgenet-2015-103302 PubMed DOI PMC

Park ST, Kim J. Trends in Next-Generation Sequencing and a New Era for Whole Genome Sequencing. Int Neurourol J. 2016;20(Suppl 2): S76–83. 10.5213/inj.1632742.371 PubMed DOI PMC

Šerý O, Krejčí P, Bonczek O, Míšek I. Usage of modern DNA methods in the research of molecular causes of hypodontia. Ortodoncie. 2013;22(3): 173–178.

Polder BJ, Van’t Hof MA, Van der Linden FP, Kuijpers-Jagtman AM. A meta-analysis of the prevalence of dental agenesis of permanent teeth. Community Dent Oral Epidemiol. 2004;32(3): 217–226. 10.1111/j.1600-0528.2004.00158.x PubMed DOI

Rakhshan V. Congenitally missing teeth (hypodontia): A review of the literature concerning the etiology, prevalence, risk factors, patterns and treatment. Dent Res J. 2015;12(1): 1–13. PubMed PMC

Haque S, Alam MK. Common dental anomalies in cleft lip and palate patients. Malays J Med Sci. 2015;22(2): 55–60. PubMed PMC

Fekonja A. Hypodontia in orthodontically treated children. Eur J Orthod. 2005;27(5): 457–460. 10.1093/ejo/cji027 PubMed DOI

Ghaderi F, Hekmat S, Ghaderi R, Fardaei M. MSX1 mutation in witkop syndrome; a case report. Iran J Med Sci. 2013;38(2 Suppl): 191–194. PubMed PMC

Salas-Alanis JC, Wozniak E, Mein CA, Duran Mckinster CC, Ocampo-Candiani J, Kelsell DP, et al. Mutations in EDA and EDAR Genes in a Large Mexican Hispanic Cohort with Hypohidrotic Ectodermal Dysplasia. Ann Dermatol. 2015;27(4): 474–477. 10.5021/ad.2015.27.4.474 PubMed DOI PMC

Kim JW, Simmer JP, Lin BP, Hu JC. Novel MSX1 frameshift causes autosomal-dominant oligodontia. J Dent Res. 2006;85(3): 267–271. 10.1177/154405910608500312 PubMed DOI PMC

Šerý O, Bonczek O, Hloušková A, Černochová P, Vaněk J, Míšek I, et al. A screen of a large Czech cohort of oligodontia patients implicates a novel mutation in the PAX9 gene. Eur J Oral Sci. 2015;123(2): 65–71. 10.1111/eos.12170 PubMed DOI

Shahid M, Balto HA, Al-Hammad N, Joshi S, Khalil HS, Somily AM, et al. Mutations in MSX1, PAX9 and MMP20 genes in Saudi Arabian patients with tooth agenesis. Eur J Med Genet. 2016;59(8): 377–385. 10.1016/j.ejmg.2016.06.004 PubMed DOI

Lidral AC, Reising BC. The role of MSX1 in human tooth agenesis. J Dent Res. 2002;81(4): 274–278. 10.1177/154405910208100410 PubMed DOI PMC

van den Boogaard MJ, Dorland M, Beemer FA, van Amstel HK. MSX1 mutation is associated with orofacial clefting and tooth agenesis in humans. Nat Genet. 2000;24(4): 342–343. 10.1038/74155 PubMed DOI

Kimura M, Machida J, Yamaguchi S, Shibata A, Tatematsu T, Miyachi H, et al. Novel nonsense mutation in MSX1 in familial nonsyndromic oligodontia: subcellular localization and role of homeodomain/MH4. Eur J Oral Sci. 2014;122(1): 15–20. 10.1111/eos.12105 PubMed DOI

Kamamoto M, Machida J, Yamaguchi S, Kimura M, Ono T, Jezewski PA, et al. Clinical and functional data implicate the Arg(151)Ser variant of MSX1 in familial hypodontia. Eur J Hum Genet. 2011;19(8): 844–850. 10.1038/ejhg.2011.47 PubMed DOI PMC

Mu YD, Xu Z, Contreras CI, McDaniel JS, Donly KJ, Chen S. Mutational analysis of AXIN2, MSX1, and PAX9 in two Mexican oligodontia families. Genet Mol Res. 2013;12(4): 4446–4458. 10.4238/2013.October.10.10 PubMed DOI PMC

Yamaguchi S, Machida J, Kamamoto M. Characterization of novel MSX1 mutations identified in Japanese patients with nonsyndromic tooth agenesis. PLoS One. 2014;9(8): e102944 10.1371/journal.pone.0102944 PubMed DOI PMC

Bergendal B, Klar J, Stecksén-Blicks C, Norderyd J, Dahl N. Isolated oligodontia associated with mutations in EDARADD, AXIN2, MSX1, and PAX9 genes. Am J Med Genet A. 2011;155A(7): 1616–1622. 10.1002/ajmg.a.34045 PubMed DOI

De Muynck S, Schollen E, Matthijs G, Verdonck A, Devriendt K, Carels C. A novel MSX1 mutation in hypodontia. Am J Med Genet A. 2004;128A(4): 401–403. 10.1002/ajmg.a.30181 PubMed DOI

Liang J, Zhu L, Meng L, Chen D, Bian Z. Novel nonsense mutation in MSX1 causes tooth agenesis with cleft lip in a Chinese family. Eur J Oral Sci. 2012;120(4): 278–282. 10.1111/j.1600-0722.2012.00965.x PubMed DOI

Abid MF, Simpson MA, Petridis C, Cobourne MT, Sharpe PT. Non-syndromic severe hypodontia caused by a novel frameshift insertion mutation in the homeobox of the MSX1 gene. Arch Oral Biol. 2017;75: 8–13. 10.1016/j.archoralbio.2016.11.018 PubMed DOI

Mostowska A, Biedziak B, Trzeciak WH. A novel c.581C>T transition localized in a highly conserved homeobox sequence of MSX1: is it responsible for oligodontia? J Appl Genet. 2006;47(2): 159–164. 10.1007/BF03194616 PubMed DOI

Vastardis H, Karimbux N, Guthua SW, Seidman JG, Seidman CE. A human MSX1 homeodomain missense mutation causes selective tooth agenesis. Nat Genet. 1996;13(4): 417–421. 10.1038/ng0896-417 PubMed DOI

Jumlongras D, Bei M, Stimson JM, Wang WF, DePalma SR, Seidman CE, et al. A Nonsense Mutation in MSX1 Causes Witkop Syndrome. Am J Hum Genet. 2001;69(1): 67–74. 10.1086/321271 PubMed DOI PMC

Chishti MS, Muhammad D, Haider M, Ahmad W. A novel missense mutation in MSX1 underlies autosomal recessive oligodontia with associated dental anomalies in Pakistani families. J Hum Genet. 2006;51(10): 872–878. 10.1007/s10038-006-0037-x PubMed DOI

Xuan K, Jin F, Liu YL, Yuan LT, Wen LY, Yang FS, et al. Identification of a novel missense mutation of MSX1 gene in Chinese family with autosomal-dominant oligodontia. Oral Biology. 2008;53(8): 773–779. 10.1016/j.archoralbio.2008.02.012 PubMed DOI

Arte S, Parmanen S, Pirinen S, Alaluusua S, Nieminen P. Candidate gene analysis of tooth agenesis identifies novel mutations in six genes and suggests significant role for WNT and EDA signaling and allele combinations. PLoS One. 2013;8(8): e73705 10.1371/journal.pone.0073705 PubMed DOI PMC

Mostowska A, Biedziak B, Jagodzinski PP. Novel MSX1 mutation in a family with autosomal-dominant hypodontia of second premolars and third molars. Arch Oral Biol. 2012;57(6): 790–795. 10.1016/j.archoralbio.2012.01.003 PubMed DOI

AlFawaz S, Plagnol V, Wong FS, Kelsell DP. A novel frameshift MSX1 mutation in a Saudi family with autosomal dominant premolar and third molar agenesis. Arch Oral Biol. 2015;60(7): 982–988. 10.1016/j.archoralbio.2015.02.023 PubMed DOI

Wong SW, Liu HC, Han D, Chang HG, Zhao HS, Wang YX, et al. A novel non-stop mutation in MSX1 causing autosomal dominant non-syndromic oligodontia. Mutagenesis. 2014;29(5): 319–323. 10.1093/mutage/geu019 PubMed DOI

Satokata I, Maas R. Msx1 deficient mice exhibit cleft palate and abnormalities of craniofacial and tooth development. Nat Genet. 1994;6(4): 348–356. 10.1038/ng0494-348 PubMed DOI

Chen Y, Bei M, Woo I, Satokata I, Maas R. Msx1 controls inductive signaling in mammalian tooth morphogenesis. Development. 1996;122(10): 3035–3044. PubMed

Roche: Sequencing Solutions Technical Note: How To Evaluate NimbleGen SeqCap EZ Target Enrichment Data, Roche Diagnostics: Mannheim. 2017. http://netdocs.roche.com/DDM/Effective/07187009001_RNG_SeqCap-EZ_TchNote_Eval-data_v2.1.pdf

Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics. 2009;25(14): 1754–1760. 10.1093/bioinformatics/btp324 PubMed DOI PMC

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15): 2114–2120. 10.1093/bioinformatics/btu170 PubMed DOI PMC

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics. 2009;25(16): 2078–2079. 10.1093/bioinformatics/btp352 PubMed DOI PMC

Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27(21): 2987–2993. 10.1093/bioinformatics/btr509 PubMed DOI PMC

R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria: 2015. https://www.R-project.org/

Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative Genomics Viewer. Nat Biotechnol. 2011;29(1): 24–26. 10.1038/nbt.1754 PubMed DOI PMC

Thorvaldsdóttir H, Robinson James T., Mesirov Jill P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2): 178–192. 10.1093/bib/bbs017 PubMed DOI PMC

Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993;234(3): 779–815. 10.1006/jmbi.1993.1626 PubMed DOI

Humphrey W, Dalke A, Schulten K. VMD: Visual molecular dynamics. J Mol Graphics. 1996;14(1): 33–38. PubMed

Bonczek O, Balcar VJ, Šerý O. PAX9 gene mutations and tooth agenesis: A review. Clin Genet. 2017;92(5): 467–476. 10.1111/cge.12986 PubMed DOI

Nieminen P, Arte S, Tanner D, Paulin L, Alaluusua S, Thesleff I, et al. Identification of a nonsense mutation in the PAX9 gene in molar oligodontia. Eur J Hum Genet. 2001;9(10): 743–674. 10.1038/sj.ejhg.5200715 PubMed DOI

Zhang H, Hu G, Wang H, Sciavolino P, Iler N, Shen MM, et al. Heterodimerization of Msx and Dlx Homeoproteins Results in Functional Antagonism. Mol Cell Biol. 1997;17(5): 2920–2932. PubMed PMC

Hu G, Vastardis H, Bendall AJ, Wang Z, Logan M, Zhang H, et al. Haploinsufficiency of MSX1: a mechanism for selective tooth agenesis. Mol Cell Biol. 1998;18(10): 6044–6051. PubMed PMC

Isaac VE, Sciavolino P, Abate C. Multiple amino acids determine the DNA binding specificity of the Msx-1 homeodomain. Biochemistry. 1995;34(21): 7127–7134. PubMed

Ogawa T, Kapadia H, Wang B, D’Souza RN. Studies on Pax9-Msx1 protein interactions. Arch Oral Biol. 2005;50(2): 141–145. 10.1016/j.archoralbio.2004.09.011 PubMed DOI

Gene-Environment Interactions in Major Mental Disorders in the Czech Republic