Table 2.
Genes with excess DNV burden in DD versus ASD patients
| Gene | DD DNV (dnLGD/dnMIS) | ASD DNV (dnLGD/dnMIS) | P | q | OR (95% CI) | Significant variant |
|---|---|---|---|---|---|---|
| ARID1B | 119 (106/13) | 22 (12/10) | 2.51e–6 | 5.02e–3 | 2.7 (1.7–4.5) | DNV&dnLGD |
| DDX3X | 115 (50/65) | 5 (1/4) | 5.41e–15 | 1.08e–10 | 11.6 (4.8–36.3) | DNV&dnLGD&dnMIS |
| KMT2A | 90 (64/26) | 9 (6/3) | 2.25e–8 | 1.50e–4 | 5 (2.5–11.3) | DNV&dnLGD |
| DYRK1A | 80 (64/16) | 4 (4/0) | 3.11e–10 | 3.11e–6 | 10 (3.8–37.8) | DNV&dnLGD |
| MED13L | 72 (42/30) | 10 (5/5) | 1.71e–5 | 2.14e–2 | 3.6 (1.9–7.9) | DNV |
| SATB2 | 68 (32/36) | 5 (0/5) | 1.31e–7 | 4.37e–4 | 6.8 (2.8–21.7) | DNV&dnLGD |
| STXBP1 | 67 (28/39) | 8 (3/5) | 7.10e–6 | 1.18e–2 | 4.2 (1–10.1) | DNV |
| CTNNB1 | 62 (60/2) | 5 (4/1) | 7.84e–7 | 1.74e–3 | 6.2 (2.5–19.8) | DNV&dnLGD |
| TCF4 | 51 (31/20) | 4 (3/1) | 9.21e–6 | 1.42e–2 | 6.4 (2.4–24.4) | DNV |
| KMT2D | 47 (30/17) | 3 (0/3) | 6.63e–6 | 1.18e–2 | 7.9 (2.5–39.5) | DNV&dnLGD |
| KCNQ2 | 45 (0/45) | 1 (0/1) | 3.01e–7 | 8.61e–4 | 22.6 (3.9–907.9) | DNV&dnMIS |
| CACNA1A | 43 (3/40) | 1 (0/1) | 5.05e–7 | 1.26e–3 | 21.6 (3.7–868.6) | DNV&dnMIS |
| EFTUD2 | 43 (31/12) | 3 (1/2) | 2.67e–5 | 3.14e–2 | 7.2 (2.3–36.2) | DNV |
| WDR45 | 35 (24/11) | 1 (1/0) | 1.06e–5 | 1.51e–2 | 17.6 (3–710.9) | DNV |
| CASK | 34 (24/10) | 1 (1/0) | 1.71e–5 | 2.14e–2 | 17.1 (2.9–691.2) | DNV |
| GATAD2B | 42 (39/3) | 0 (0/0) | 5.52e–8 | 2.21e–4 | Inf (5.5–Inf) | DNV&dnLGD |
| KIF1A | 42 (0/42) | 0 (0/0) | 5.52e–8 | 2.21e–4 | Inf (5.5–Inf) | DNV&dnMIS |
| CHD7 | 51 (31/20) | 6 (0/6) | 7.36e–6 | 1.64e–2 | Inf (4–Inf) | dnLGD only |
Two-sided Fisher’s exact test for DNV counts was performed comparing ASD (n = 15,560) and DD (n = 31,052) patients. This table shows the 18 genes with significant DNV burden in DD compared to ASD patients, while no gene with significant burden is identified in ASD patients. The significance threshold (FDR 5%) was corrected for 20,000 genes (Benjamini-Hochberg). OR: odds ratio; CI: confidence interval; Inf: infinity.