Single nucleotide polymorphisms in odontogenesis-related genes associated with tooth-size discrepancy

Genes	SNPs	Type of Alteration	Base Change	Global MAF*	Genotyping success rate
RUNX2	rs59983488	Upstream Variant	G > T	0.15	88.7%
RUNX2	Rs1200425	Intron Variant	G > A	0.44	87.0%
SMAD6	rs3934908	Intron Variant	C > T	0.41	91.9%
SMAD6	Rs211261	Intron Variant	C > T	0.19	90.3%
BMP2	rs1005464	Intron Variant	G > A	0.19	91.9%
BMP2	rs235768	Missense Variant	T > A	0.32	90.3%
BMP4	Rs17563	Missense Variant	A > G	0.42	88.7%

1 A, adenine; C, cytosine; G, guanine; MAF, Minor Allele Frequency; T, thymine.

Data are available in https://www.ncbi.nlm.nih.gov/snp.

Table II.

Allelic and Genotypic distribution between anterior TSD groups and comparison by Fisher Test.

					Control vs. Maxillary tooth-size anterior excess				Control vs. Mandibular tooth-size anterior excess
Gene	SNP	Comparison Type	Alleles or Genotypes	Control (%)	Maxillary (%)	p-value	OR	95% CI	Mandibular (%)	p-value	Odds Ratio	95% Confidence Interval
RUNX2	rs59983488	Allelic	G	60 (96.8)	14 (87.5)			Ref.	23 (71.9)		Ref.
			T	2 (3.2)	2 (12.5)	0.184	4.28	0.61–28.44	9 (28.1)	<0.001**	' 11.74	2.61–55.80
		Genotypic	GG	29 (93.5)	6 (75.0)			Ref.	8 (50)			Ref.
			GT	2 (6.5)	2 (25.0)	0.180	4.83	0.62–33.70	7 (43.8)	0.002**	12.69	2.47–64.83
			TT	0 (0.0)	0 (0.0)	>0.999	-	-	1 (6.3)	0.236	-	-
	rs1200425	Allelic	G	37 (63.8)	13 (81.3)			Ref.	21 (61.8)			Ref.
			A	21 (36.2)	3 (18.7)	0.237	0.40	0.11–1.56	13 (38.2)	>0.999	1.09	0.47–2.64
		Genotypic	GG	14 (48.3)	6 (75.0)			Ref.	6 (35.3)			Ref.
			GA	9 (31.0)	1 (12.5)	0.371	0.25	0.02–2.47	9 (52.9)	0.320	2.33	0.61–7.90
			AA	6 (20.7)	1 (12.5)	0.633	0.38	0.02–2.87	2 (11.8)	0.268	4.66	0.44–71.52
SMAD6	rs3934908	Allelic	C	33 (53.2)	7 (43.7)			Ref.	19 (52.8)			Ref.
			T	29 (46.8)	9 (56.3)	0.580	1.46	0.47–4.12	17 (47.2)	>0.999	1.01	0.45–2.25
		Genotypic	CC	9 (29.0)	2 (25.0)			Ref.	4 (22.2)			Ref.
			CT	15 (48.4)	3 (37.5)	>0.999	0.90	0.15–5.84	11 (61.1)	0.728	1.65	0.38–5.76
			TT	7 (22.6)	3 (37.5)	0.635	1.92	0.31–12.80	3 (16.7)	0.134	0.25	0.06–1.12
	rs211261	Allelic	C	29 (55.8)	10 (62.5)			Ref.	19 (55.9)			Ref.
			T	23 (44.2)	6 (37.5)	0.774	0.75	0.22–2.42	15 (44.1)	>0.999	0.99	0.39–2.41
		Genotypic	CC	10 (32.3)	2 (25.0)			Ref.	3 (17.6)			Ref.
			CT	19 (61.3)	6 (75.0)	>0.999	1.57	0.27–8.71	13 (76.5)	0.322	2.28	0.53–8.75
			TT	2 (6.5)	0 (0.0)	>0.999	-	-	1 (5.9)	>0.999	1.66	0.08–18.07
BMP2	rs1005464	Allelic	G	52	13			Ref.	29			Ref.
			A	10	3	0.723	1.20	0.31–4.59	5	>0.999	0.89	0.31–2.82
		Genotypic	GG	23 (74.2)	6 (75.0)			Ref.	12 (70.6)			Ref.
			GA	6 (19.4)	1 (12.5)	>0.999	0.63	0.04–4.54	5 (29.4)	0.721	1.59	0.41–5.53

1 *p < 0.05. **p < 0.007.

Table II.

Allelic and Genotypic distribution between anterior TSD groups and comparison by Fisher Test.

Gene	SNP	Comparison Type	Alleles or Genotypes	Control (%)	Control vs. Maxillary tooth-size anterior excess				Control vs. Mandibular tooth-size anterior excess
Gene	SNP	Comparison Type	Alleles or Genotypes	Control (%)	Maxillary (%)	p-value	OR	95% CI	Mandibular (%)	p-value	Odds Ratio	95% Confidence Interval
			AA	2 (6.5)	1 (12.5)	0.536	1.91	0.11–18.28	0 (0.0)	>0.999	-	-
	rs235768	Allelic	T	47 (75.8)	11 (68.7)			Ref.	26 (72.2)			Ref.
			A	15 (24.2)	5 (31.3)	0.539	1.42	0.46–4.88	10 (27.8)	0.810	1.20	0.44–2.92
		Genotypic	TT	16 (51.6)	4 (50.0)			Ref.	9 (50.0)			Ref.
			TA	15 (48.4)	3 (37.5)	>0.999	0.80	0.17–3.41	8 (44.4)	>0.999	0.94	0.30–2.84
			AA	0 (0.0)	1 (12.5)	0.23	-	-	1 (5.6)	0.384	-	-
BMP4	rs17563	Allelic	A	39 (62.9)	9 (64.3)			Ref.	21 (61.8)			Ref.
			G	23 (37.1)	5 (35.7)	>0.999	0.94	0.31–3.11	13 (38.2)	>0.999	1.05	0.46–2.47
		Genotypic	AA	13 (41.9)	2 (28.6)			Ref.	7(41.2)			Ref.
			AG	13 (41.9)	5 (71.4)	0.413	2.50	0.37–13.97	7(41.2)	>0.999	1.00	0.25–3.96
			GG	5 (16.1)	0 (0.0)	>0.999	-	-	3 (17.6)	>0.999	1.11	0.23–5.39

1 *p < 0.05. **p < 0.007.

Table III.

Allelic and Genotypic distribution between overall TSD groups and comparison by Fisher Test.

					Control vs. Maxillary tooth-size overall excess				Control vs. Mandibular tooth-size overall excess
Gene	SNP	Model	Alleles or Genotypes	Control (%)	Maxillary (%)	p-value	Odds ratio	95% Confidence Interval	Mandibular (%)	p-value	Odds Ratio	95% Confidence Interval
RUNX2	rs59983488	Allelic	G	56 (93.3)	8 (80.0)			Ref.	33 (82.5)			Ref.
			T	4 (6.7)	2 (20.0)	0.201	3.50	0.57–17.98	7 (17.5)	0.110	2.97	0.83–9.51
		Genotypic	GG	26 (86.7)	3 (60.0)			Ref.	14 (70.0)			Ref.
			GT	4 (13.3)	2 (40.0)	0.195	4.33	0.58–25.79	5 (25.0)	0.281	2.32	0.53–8.40
			TT	0 (0.0)	0 (0.0)	>0.999	-	-	1 (5.0)	0.365	-	-
	rs1200425	Allelic	G	35 (60.3)	8 (80.0)			Ref.	28 (70.0)			Ref.
			A	23 (39.7)	2 (20.0)	0.303	0.38	0.07–1.88	12 (30.0)	0.393	0.65	0.28–1.49
		Genotypic	GG	14 (48.3)	3 (60.0)			Ref.	9 (45.0)			Ref.
			GA	7 (24.1)	2 (40.0)	>0.999	1.33	0.19 - 7.73	10 (50.0)	0.337	2.22	0.64–7.51
			AA	8 (27.6)	0 (0.0)	0.527	-	-	1 (5.0)	0.210	0.19	0.01–1.58
SMAD6	rs33408	Allelic	C	38 (59.4)	0 (0.0)			Ref.	21 (52.5)			Ref.
			T	26 (40.6)	10 (100)	<0.001**	∞	3.75 - ∞	19 (47.5)	0.544	1.32	0.57–2.85
		Genotypic	CC	10 (31.3)	0 (0.0)			Ref.	5 (25.0)			Ref.
			CT	18 (56.3)	0 (0.0)	>0.999	-	-	11 (55.0)	>0.999	1.22	0.34–4.33
			TT	4 (12.4)	5 (100)	0.010*	∞	1.96-∞	4 (20.0)	0.657	2.00	0.39–10.88
	rs211261	Allelic	C	38 (61.3)	6 (60.0)			Ref.	24 (60.0)			Ref.
			T	24 (38.7)	4 (40.0)	>0.999	1.05	0.31–3.72	16 (40.0)	>0.999	1.05	0.47–2.28
		Genotypic	CC	9 (29.0)	1 (20.0)			Ref.	5 (25.0)			Ref.
			CT	20 (64.5)	4 (80.0)	>0.999	1.80	0.22–24.21	14 (70.0)	>0.999	1.26	0.36–4.31
			TT	2 (6.5)	0 (0.0)	>0.999	-	-	1 (5.0)	>0.999	0.90	0.05–9.37
BMP2	rs1005464	Allelic	G	50 (80.6)	8 (80.0)			Ref.	36 (90.0)			Ref.
			A	12 (19.4)	2 (20.0)	>0.999	1.04	0.20–5.72	4 (10.0)	0.269	0.46	0.15–1.44
		Genotypic	GG	22 (71.0)	3 (60.0)			Ref.	16 (80.0)			Ref.
			GA	6 (19.3)	2 (40.0)	0.573	2.44	0.35–13.91	4 (20.0)	>0.999	0.91	0.25–3.29

1 Notes: *p < 0.05. **p < 0.007.

Table III.

Allelic and Genotypic distribution between overall TSD groups and comparison by Fisher Test.

					Control vs. Maxillary tooth-size overall excess				Control vs. Mandibular tooth-size overall excess
Gene	SNP	Model	Alleles or Genotypes	Control (%)	Maxillary (%)	p-value	Odds ratio	95% Confidence Interval	Mandibular (%)	p-value	Odds Ratio	95% Confidence Interval
			AA	3 (9.7)	0 (0.0)	>0.999	-	-	0 (0.0)	0.268	-	-
	rs235768	Allelic	T	48 (75.0)	8 (80.0)			Ref.	28 (70.0)			Ref.
			A	16 (25.0)	2 (20.0)	>0.999	0.75	0.14–3.84	12 (30.0)	0.651	1.28	0.55–3.18
		Genotypic	TT	17 (53.1)	3 (60.0)			Ref.	9 (45.0)			Ref.
			TA	14 (43.8)	2 (40.0)	>0.999	0.80	0.13–4.44	10 (50.0)	0.771	1.34	0.40–3.89
			AA	1 (3.1)	0 (0.0)	>0.999	-	-	1 (5.0)	>0.999	1.88	0.09–37.71
BMP4	rs17563	Allelic	A	34 (55.7)	6 (60.0)			Ref.	29 (72.5)			Ref.
			G	26 (43.3)	4 (40.0)	>0.999			11 (27.5)	0.139	0.49	0.21–1.13
		Genotypic	AA	10 (33.3)	2 (40.0)			Ref.	10 (50.0)			Ref.
			AG	14 (46.7)	2 (40.0)	>0.999	0.71	0.10–5.21	9 (45.0)	0.547	0.64	0.19–1.99
			GG	6 (20.0)	1 (20.0)	>0.999	0.83	0.05–8.47	1 (5.0)	0.183	0.16	0.01–1.64

1 Notes: *p < 0.05. **p < 0.007.

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DOI: https://doi.org/10.2478/aoj-2023-0008 | Journal eISSN: 2207-7480 | Journal ISSN: 2207-7472

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Language: English

Page range: 86 - 95

Submitted on: Aug 1, 2022

Accepted on: Jan 1, 2023

Published on: Feb 27, 2023

Published by: Australian Society of Orthodontists Inc.

In partnership with: Paradigm Publishing Services

Publication frequency: 1 issue per year

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© 2023 Caio Luiz Bitencourt Reis, Guido Artemio Marañón-Vásquez, Mirian Aiko Nakane Matsumoto, Flares Baratto-Filho, Maria Bernadete Sasso Stuani, Peter Proff, Christian Kirschneck, Erika Calvano Küchler, published by Australian Society of Orthodontists Inc.
This work is licensed under the Creative Commons Attribution 4.0 License.

Volume 39 (2023): Issue 1 (January 2023)

Single nucleotide polymorphisms in odontogenesis-related genes associated with tooth-size discrepancy

Figures & Tables

Table I.

Figure 1.

Table II.

Table II.

Table III.

Table III.

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