Table 2.
Associations between speech phenotypes and rare variants.
| Class 1 variants (PTVs) | ||||||
|---|---|---|---|---|---|---|
| Gene | Speech phenotype | Total number of individuals with a variant (proportion with the phenotype) | Control frequency | P-value | OR | 95% CI |
| SMARCE1 | Aphasia | 2 (1) | 0.1 | 0.0102 | 45.21 | 1.67-Inf |
| Dysarthria | 2 (1) | 0.14 | 0.0226 | 28.55 | 1.06-Inf | |
| RERE | Receptive language delay | 4 (0.5) | 0.05 | 0.0172 | 17.59 | 1.23–245.10 |
| MAZ | Stuttering | 4 (0.5) | 0.08 | 0.0359 | 11.5 | 0.81–160.01 |
| PDPKI | Language impairment | 7 (0.57) | 0.21 | 0.0421 | 4.96 | 0.83–34.09 |
| Class 2 variants (missense with CADD > 20) | ||||||
| UQCRC1 | Expressive aphasia | 8 (0.5) | 0.02 | 1.72 × 10−5* | 50.5 | 8.26–294.37 |
| SPAST | Receptive language delay | 3 (1) | 0.05 | 1.56 × 10−4 | 128.15 | 7.32-Inf |
| NDST4 | Incomprehensible speech | 5 (0.4) | 0.004 | 3.77 × 10−4 | 159.56 | 9.16–1960.73 |
| GRID1 | Poor speech | 3 (0.66) | 0.01 | 4.08 × 10−4 | 204.57 | 8.88–10761.92 |
| Class 3 variants (PTVs and missense combined) | ||||||
| WASHC4 | Abnormality of speech or vocalization | 18 (0.39) | 0.05 | 1.84 × 10−5* | 13.02 | 3.97–39.24 |
| CEP250 | Aphasia | 16 (0.5) | 0.09 | 5.33 × 10−5 | 9.76 | 3.06–30.74 |
| NEURL4 | Aphasia | 27 (0.37) | 0.09 | 1.35 × 10−4 | 5.84 | 2.28–14.11 |
| CRYBA1 | Abnormality of speech or vocalization | 7 (0.57) | 0.05 | 2.47 × 10−4 | 25.30 | 4.06–176.82 |
| PCARE | Expressive language delay | 13 (0.46) | 0.08 | 3.92 × 10−4 | 9.68 | 2.58–34.68 |
| PCLO | Palilalia | 65 (0.23) | 0.08 | 4.14 × 10−4 | 3.44 | 1.68–6.73 |
*
If significant after the FDR correction for multiple testing.