A novel PAX9 compound heterozygous variant in a Chinese family with non-syndromic oligodontia and genotype-phenotype analysis of PAX9 variants

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A novel PAX9 compound heterozygous variant in a Chinese family with non-syndromic oligodontia and genotype-phenotype analysis of PAX9 variants
Ren, Jiabao; Zhao, Ya; Yuan, Yunyun; Zhang, Jing; Ding, Yulin; Li, Meikang; An, Yilin; Chen, Wenjing; Zhang, Li; Liu, Boyu; Zheng, Shushen; Shen, Wenjing, 2023, "A novel PAX9 compound heterozygous variant in a Chinese family with non-syndromic oligodontia and genotype-phenotype analysis of PAX9 variants", https://doi.org/10.48331/scielodata.OMMQEH, SciELO Data, V1
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Description
It has been reported that >91.9% of non-syndromic tooth agenesis cases are caused by seven pathogenic genes. Objective: Here, we report novel heterozygous PAX9 variants in a Chinese family with non-syndromic oligodontia and summarize the reported genotype-phenotype relationship of PAX9 variants. Methodology: We recruited 28 patients with non-syndromic oligodontia who were admitted to the Hospital of Stomatology Hebei Medical University (China) between 2018 and 2021. Peripheral blood was collected from the probands and their core family members for whole-exome sequencing (WES) and variants were verified by Sanger sequencing. Bioinformatics tools were used to predict the pathogenicity of the variants. SWISS-MODEL homology modeling was used to analyze the three-dimensional structural changes of variant proteins. We also analyzed the genotype-phenotype relationships of PAX9 variants. Results: We identified novel compound heterozygous PAX9 variants (reference sequence NM_001372076.1) in a Chinese family with non-syndromic oligodontia: a new missense variant c.1010C>A (p.T337K) in exon 4 and a new frameshift variant c.330_331insGT (p.D113Afs*9) in exon 2, which was identified as the pathogenic variant in this family. This expanded the known variant spectrum of PAX9, and we then summarized the phenotypes of non-syndromic oligodontia with PAX9 variants. Conclusion: We found that PAX9 variants commonly lead to loss of the second molars. (2023-1-25)
Subject Medicine, Health and Life Sciences
Keyword Anodontia, PAX9 Transcription Factor, Exome Sequencing, Genetic Association Studies
Related Publication Ren J, Zhao Y, Yuan Y, Zhang J, Ding Y, Li M, et al. Novel PAX9 compound heterozygous variants in a Chinese family with non-syndromic oligodontia and genotype-phenotype analysis of PAX9 variants. J Appl Oral Sci. 2023;31:e20220403. doi: 10.1590/1678-7757-2022-0403 doi: 10.1590/1678-7757-2022-0403
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DATASET_README.txt
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Identification of a compound heterozygous PAX9 variant in a Chinese family with non-syndromic oligodontia. (a) The pedigree of the Chinese family. The black arrow indicates the proband. (b) DNA sequencing chromatograms of the family and TA cloning sequencing of the proband showing a new frameshift variant c.330_331insGT (p.D113Afs*9) in exon 2 and a new missense variant c.1010C>A (p.T337K) in exon 4 (reference sequence NM_001372076.1).
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Dental characteristics of a Chinese family with non-syndromic oligodontia. a-d: (a) Facial characteristics of the proband; (b-c) Intraoral images; (d) Panoramic radiographs and schematic diagram of missing teeth; (e) Facial characteristics of the proband’s mother; (f-g) Intraoral images; (h) Panoramic radiographs and schematic of missing teeth. Black squares indicate missing teeth; Max, maxillary; Mand, mandibular.
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Conservation and bioinformatics analysis and structural modeling of PAX9. (a) Schematic diagram of the wild-type PAX9 protein and the localization of the novel compound heterozygous PAX9 variant identified in this study. (b) Conservation analysis of PAX9 amino acid sequences in six species. (c) WebLogo analysis of PAX9 amino acid sequences in six species. (d) Structural modeling of the wild-type PAX9 protein (the amino acids encoded by the 113Afs are shown in red). (e) Structural modeling of the PAX9 p.D113Afs*9 variant (the changed amino acids are shown in orange).
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Phenotype composition of the 160 patients reviewed.
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Permanent tooth loss rate of the upper and lower jaws of NSO patients with PAX9 variants (n = 132)
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Sanger sequencing result of the proband's father of PAX9 exon2(NM_001372076.1).
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Sanger sequencing result of the proband's father of PAX9 exon4(NM_001372076.1).
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Sanger sequencing result of the proband's little sister of PAX9 exon2(NM_001372076.1).
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Sanger sequencing result of the proband's little sister of PAX9 exon4(NM_001372076.1).
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