Effect of SPTLC1 on type 2 diabetes mellitus

Table 2 The rare variant gene-level association between SPTLC1 and type 2 diabetes mellitus

Mask	Methods	Sample size	Combined allele frequency (%)	Passing variants	Singleton variants	SD	Odds ratio	P value
LofTee	Predicted loss of function	43125	0.03942	14	11	0.52284	2.1014	0.13368
16/16	Predicted deleterious by 16 methods	43125	0.04638	15	11	0.47401	1.8749	0.16848
11/11	Predicted deleterious by 11 methods	43125	0.09507	29	20	0.33683	2.0718	0.025839
5/5	Predicted deleterious by 5 methods	43125	0.15072	31	21	0.2571	1.3852	0.20087
5/5 + LofTee LC	Predicted deleterious by 5 methods, plus LofTee low confidence	43125	0.16464	33	21	0.24528	1.3551	0.21151
5/5 + 1/5, 1%	Predicted deleterious by 5 methods, plus variants with MAF < 1% that are predicted to be deleterious by 1 of 5 methods	43125	0.85565	95	59	0.10614	1.0444	0.68172
5/5 + 0/5, 1%	Predicted deleterious by 5 methods, plus variants with MAF < 1% that are not predicted to be deleterious by any of 5 methods	43125	0.92058	102	63	0.10226	1.0154	0.88112
Total		43125					2.4968	0.0164

LC: Low confidence; LofTee: Loss-of-function transcript effect estimator; MAF: Minor allele frequency.