Table 1.

Phenotypic Effects of Rare Nonsynonymous Variants in African Populations.

Genotype A	Genotype B	Mean Difference (Genotype A − Genotype B)	Standard Error	Significance (Exact P Value)
AVI/AVI	At least one AVI subhaplotype	0.90	1.77	0.614
N = 25	N = 3
Mean PTC score = 3.350	Mean PTC score = 2.447
AAI/AVI	At least one AAI or AVI subhaplotype			0.000 (P < 0.001) ***
N = 28	N = 7	3.33	0.82	Mann–Whitney (P = 0.005) **
Mean PTC score = 6.788	Mean PTC score = 3.459
AAI/AAI	At least one AAI subhaplotype	1.97	1.31	0.162
N = 7	N = 9
Mean PTC score = 7.607	Mean PTC score = 5.640
AAV/AVI	At least one AVI subhaplotype	N/A	N/A	N/A
N = 1	N = 0
AAV/AAV	At least one AAV subhaplotype	N/A	N/A	N/A
N = 4	N = 0
PAV/AVI	At least one AVI or PAV subhaplotype	0.22	0.49	0.659
N = 134	N = 18
Mean PTC score = 8.572	Mean PTC score = 8.356
PAV/AAI	At least one PAV or AAI subhaplotype	0.17	0.46	0.517
N = 62	N = 31
Mean PTC score = 8.430	Mean PTC score = 8.260
PAV/AAV	At least one PAV subhaplotype	N/A	N/A	N/A
N = 9	N = 0
PAV/PAV	At least one PAV subhaplotype	0.580	0.41	0.207
N = 106	N = 19
Mean PTC Score = 9.580	Mean PTC score = 9.000

Note.—In the GLM ANOVA adjusting for age and sex in 463 African individuals, raw PTC response was entered as the dependent variable; fixed variables consisted of two comparative groups: 1) individuals homozygous for two common haplotypes within a given genotypic class and 2) individuals who were either homozygous or heterozygous for a subhaplotype containing rare nonsynonymous variants within the same genotypic class. In this model, age and sex were included as covariates. A Bonferroni correction for multiple comparisons was applied, and only significant results are shown as underlined. Significant P values, P < 0.01 and P < 0.001, for the ANOVA and Mann–Whitney tests are indicated by ** and ***, respectively. N/A means the ANOVA could not be applied to the data.