Table 2.

Most significant variants detected in our discovery set

Gene	Position	MA	cDNA change	Aa change	Rs	MAF cases-controls (%)	MAF ExAC (%)	SIFT	Polyphen	Mutation assessor	aa/Aa/AA cases	aa/Aa/AA controls	p-value	Corr. p-value	OR (95% CI)
ABCA7	19:1043103	A	c.G643A	p.G215S	rs72973581	4.66–7.24a	4.31b	Tolerated	Benign	Low	0/31/301	1/96/579	0.02	0.8	0.61 (0.38–0.95)
											0/55/584c	1/164/1012c	0.0006c	0.024	0.57c (0.41–0.80)
ABCA7	19:1050996	A	c.G2629A	p.A877Td	rs74176364	0.3–1.18	1.69	Deleterious	Benign	Low	0/2/330	0/16/660	0.07	2.8	0.25 (0.02–1.07)
EPHA1	7:143095153	A	c.G1475A	p.R492Qe	rs11768549	2.56–1.47	1.21	Tolerated	Benign		0/17/315	1/18/657	0.07	2.8	1.86 (0.89–3.84)
ABCA7	19:1059056	A	c.G5435A	p.R1812Hd	rs114782266	1.5–0.81	1.05	Tolerated	Benign	Neutral	0/10/322	0/11/665	0.16	6.4	1.87 (0.70–4.92)
ABCA7	19:1057343	A	c.G4795A	p.V1599Md	rs117187003	0.6–0.22	0.3	Deleterious	Possibly damaging	Medium	0/4/328	0/3/673	0.22	8.8	2.73 (0.45–18.7)
CD2AP	6:47573971	A	c.G1488A	p.M496I	rs143297472	0.3–0.07	NA	Tolerated	Benign		0/2/330	0/1/675	0.25	10	4.08 (0.21–241.3)
ABCA7	19:1047537	C	c.A2153C	p.N718T	rs3752239	1.65–2.44	7.02	Deleterious	Benign	Low	0/11/321	0/33/641	0.32	12.8	0.66 (0.29–1.37)

Position is in hg19/GRCh37.

Key: cDNA, complementary DNA; CI, confidence interval; Corr, corrected p-value, p-value after Bonferroni correction (p-value∗ 40 [number of variants considered in the single-variant association test]); ExAC, Exome Aggregation Consortium; ​MA, minor allele; MAF, minor allele frequency; ExAC, Exome Aggregation Consortium; OR, odds ratio.

^aMAF cases-controls reported a Belgian cohort = 4.66%–6.27% (Cuyvers et al., 2015).

^bMAF in ExAC (European non-Finnish) = 6.14% and MAF in EVS (European American) = 6.24%.

^cCombined results discovery and follow-up data set.

^dVariants reported associated also with autism spectrum disorders (ASD) (He et al., 2014).

^eVariant reported associated to a more rapid disease progression.