Table 1 New rare single variants achieving significance

From: Large-scale exome analyses reveal new rare variant contributions in amyotrophic lateral sclerosis

 

Discovery

Replication

Meta-analysis

Variant

Gene

Consequence

Case MAC (MAF)

Control MAC (MAF)

OR (95% CI)

P

Case MAC (MAF)

Control MAC (MAF)

OR (95% CI)

P

P

9:133154147:C:A

GBGT1

c.455 G>T/p.R152L

14 (5.34 × 10−4)

3 (2.15 × 10−5)

26.9 (9.19–104)

1.68 × 10−10

1 (1.05 × 10−4)

0 (0.00)

44.7 (2.38–6,522)

1.34 × 10−2

1.99 × 10−11

7:44206388:A:G

YKT6

c.191 A>G/p.Y64C

48 (1.83 × 10−3)

91 (6.52 × 10−4)

2.84 (1.97–4.05)

9.08 × 10−8

15 (1.57 × 10−3)

164 (6.26 × 10−4)

2.54 (1.37–4.37)

4.15 × 10−3

1.50 × 10−9

1:223762207:A:G

CAPN2

c.1588 A>G/p.I530V

12 (4.57 × 10−4)

3 (2.15 × 10−5)

25.3 (8.30–100)

3.66 × 10−9

1 (1.05 × 10−4)

3 (1.15 × 10−5)

5.11 (0.434–38.4)

1.69 × 10−1

1.18 × 10−8

3:184057041:A:G

HTR3C

c.556 A>G/p.T186A

39 (1.48 × 10−3)

70 (5.05 × 10−4)

3.41 (2.27–5.04)

1.87 × 10−8

6 (6.28 × 10−4)

97 (3.71 × 10−4)

2.18 (0.868–4.57)

9.15 × 10−2

1.71 × 10−8

12:122547457:T:A

KNTC1

c.859 T>A/p.W287R

9 (3.43 × 10−4)

2 (1.43 × 10−5)

27.7 (7.80–145)

1.07 × 10−7

1 (1.05 × 10−4)

2 (7.64 × 10−6)

12.2 (1.05–106)

4.67 × 10−2

2.96 × 10−8

  1. Listed are new variants that reached significance in the exome-wide discovery analysis (P < 1.83 × 10−7). Test statistics are shown for the discovery phase (ncases = 13,138; ncontrols = 69,775), replication phase (ncases = 4,781; ncontrols = 130,928) and the combined meta-analysis (Stouffer’s Z score method, weighted by effective sample size). Association statistics were estimated using Firth’s logistic regression with profile penalized likelihood CIs. P values are two-tailed and presented uncorrected for multiple testing.
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