Whole genome sequencing identifies missense mutation in MTBP in Shar-Pei affected with Autoinflammatory Disease (SPAID)

Table 3 Case–control test results for candidate variants for SPAID

CFA	Polymorphism	MAF total	Wild type allele	Minor allele	MAF controls	MAF cases	Allele odds ratio	Chi-Square Genotype (Probability)	Chi-Square Allele (Probability)	Chi-Square Trend (Probability)
1	CD79A:g.112413114insGTGATG	0.149	C	del	0.137	0.152	1.128	2.287 (P = 0.319)	0.136 (P = 0.712)	0.156 (P = 0.693)
6	C16orf96:g.36821482G > T	0.149	G	C	0.169	0.142	1.230	2.445 (P = 0.295)	0.442 (P = 0.507)	0.438 (P = 0.508)
6	ENSCAFG00000024344:g.40648375C > T	0.334	C	C	0.387	0.305	0.695	4.450 (P = 0.108)	2.311 (P = 0.128)	2.470 (P = 0.116)
6	RPAP2:g.56637047delACAA	0.301	TACAA	ins	0.307	0.299	1.036	0.436 (P = 0.804)	0.020 (P = 0.887)	0.020 (P = 0.887)
6	TGFBR3:g.57204844A > G	0.455	A	G	0.436	0.465	0.886	6.180 (P = 0.050)	0.276 (P = 0.599)	0.267 (P = 0.605)
13	MTBP:g.19383758G > A	0.247	G	G	0.395	0.157	3.517	25.671 (P = 2.664E-06)	23.550 (P = 1.217E-06)	23.551 (P = 1.217E-06)
15	HCFC2:g.42583230A > C	0.408	A	C	0.395	0.422	0.896	0.193 (P = 0.908)	0.222 (P = 0.637)	0.192 (P = 0.661)
22	CLN5:g.30574626C > T	0.214	C	T	0.266	0.177	1.692	3.787 (P = 0.151)	3.732 (P = 0.053)	3.633 (P = 0.057)
37	OSGEPL1:g.502225delCTTGTGCAA	0.485	CCTTGTGCAA	del	0.500	0.466	0.872	1.341 (P = 0.511)	0.364 (P = 0.546)	0.388 (P = 0.533)

SPAID-associated variants with predicted high or moderate effects (SNPEff) were genotyped for 102 SPAID-affected and 62 SPAID-unaffected Shar-Pei

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