Table 1.

Nominally significant (P <0.05) rare variants detected from our analysis for the 13 genes described in Prokopenko et al. P-values for the 13 genes from our gene-based analysis on both familial and unrelated datasets are also shown.

	Single-variant analysis					Gene-based analysis
						Familial		Unrelated
Prokopenko nearest genes	Dataset	Variant	P-value	p.change	Effect	P-value (MAF ≤1 %)	P- value (CADD ≥20)	P-value (MAF ≤1 %)	P- value (CADD ≥20)
FNBP1L	-	-	-	-	-	0.11 (23)	0.72 (18)	0.31 (11)	0.31 (8)
SEL1L	-	-	-	-	-	0.47 (40)	0.33 (31)	0.9 (18)	1 (14)
ID2 (LINC00298)	-	-	-	-	-	0.81 (10)	0.73 (8)	0.14 (2)	0.14 (2)
C15orf41	-	-	-	-	-	0.62 (25)	0.35 (15)	0.62 (9)	0.36 (7)
PRKCH	-	-	-	-	-	0.09 (41)	0.08 (30)	0.53 (17)	0.54 (14)
C2CD3	unrelated	11:74118187:C:T	0.047	-	intron_variant	0.99 (149)	0.54 (95)	0.48 (77)	0.16 (50)
KIF2A	-	-	-	-	-	0.25 (15)	0.29 (11)	0.25 (10)	0.26 (6)
APC	-	-	-	-	-	0.25 (184)	0.9 (121)	0.68 (89)	1 (57)
LHX9	-	-	-	-	-	0.24 (20)	0.24 (18)	0.55 (10)	0.54 (10)
NALCN	familial	13:101095770:G:A	0.024	-	intron_variant	0.33 (65)	0.66 (55)	0.7 (24)	0.81 (20)
CTNNA2	-	-	-	-	-	0.05 (39)	0.08 (33)	0.27 (8)	0.23 (7)
SYTL3	-	-	-	-	-	0.5 (77)	0.73 (44)	0.11 (39)	0.42 (25)
CLSTN2	-	-	-	-	-	0.83 (75)	0.7 (58)	0.44 (38)	0.26 (27)

• Numbers within the brackets are the total variants included in the gene-based analysis