Table 1 Meta-analysis identifies MAGEC3 as a high-confidence Autism spectrum disorder (ASD) gene

From: Rare X-linked variants carry predominantly male risk in autism, Tourette syndrome, and ADHD

Gene

ID gene

P value

Bonferroni P value (Chr-X-wide)

BH FDR (Chr-X-wide)

Bonferroni P value (exome-wide)

BH FDR (exome-wide)

Brain expression level

MAGEC3

No

2.10E-07

1.70E-04

1.70E-04

4.05E-03

4.05E-03

Low

MAGEC1

No

1.11E-04

0.090

0.032

1.00

0.77

Low

SLITRK4

No

4.58E-04

0.37

0.074

1.00

1.00

High

ANOS1

No

1.32E-03

1.00

0.18

1.00

1.00

High

  1. We combined samples from the SSC and SPARK datasets and then leveraged a modified transmission disequilibrium test (TDT) to identify risk genes in ASD. To account for the systematic undercalling of rare variants, we estimated the null transmission probabilities for each gene in a window of 3MB based on data from control samples. Using this test, we identified MAGEC3 as a high-confidence ASD gene (exome-wide Bonferroni corrected P value & Benjamini–Hochberg FDR < 0.05). We also identified three genes (MAGEC1, SLITRK4, and ANOS1) with suggestive levels of association. ID gene, whether a gene is a known intellectual disability (ID) gene according to ref. 91. P value, raw p value from the modified TDT; Bonferroni P value (Chr-X-wide), TDT P value adjusted by Bonferroni correction for the 808 genes present within Chr X non-pseudoautosomal regions; BH FDR (Chr-X-wide), Benjamini–Hochberg FDR derived from the TDT P value by correcting for the 808 genes present within the Chr X non-pseudoautosomal regions; Bonferroni P value (exome-wide), TDT P value adjusted by Bonferroni correction for the 19,251 genes present exome-wide; BH FDR (Chr-X-wide), Benjamini–Hochberg FDR derived from the TDT P value by correcting for the 19,251 genes present exome-wide; Expression level: high, gene is among the top 50% of genes expressed in ASD-associated brain regions44,98; low, gene is among the bottom 50% of genes expressed in ASD-associated brain regions. See also Fig. 4 and Supplementary Data 1.
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