Extended Data Table 8. Summary of observed likely-deleterious variants in ARC genes across studies.
For the 28 ARC genes, a summary of which genes had singleton disruptive, or damaging missense, variants in the current study, compiled alongside the genes with de novo CNVs or SNVs observed in Kirov et al. (2012) or Fromer et al. as well as the intellectual disability (ID) de novo genes (compiled in Fromer et al.). The P-values at the bottom indicate that in each comparison, the ARC geneset was significantly enriched.
| ARC gene (N=28) | Current study | de novo CNV (Kirov et al.) | de novo SNV (Fromer et al.) | de novo SNV in ID | ||
|---|---|---|---|---|---|---|
| Disruptive | Damaging missense (strict) | |||||
| ACTN4 | 3/1 | |||||
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| ARF5 | ||||||
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| ATP1A1 | 3/0 | |||||
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| ATP1A3 | 2/1 | |||||
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| ATP1B1 | 1/0 | 1/0 | ||||
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| BAIAP2 | 1/0 | NS(x2) | ||||
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| CAMK2A | 1/0 | 1/0 | ||||
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| CRMP1 | 1/3 | |||||
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| CYFIP1 | 1/0 | 4/1 | 2 del; 2 dup | |||
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| DLG1 | 1/0 | 2/0 | 1 del | NS | ||
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| DLG2 | 2/3 | 2 del | LoF | |||
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| DLG4 | 1/2 | NS | ||||
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| DLGAP1 | 2/0 | 1 del | ||||
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| DLGAP2 | 1/0 | |||||
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| DPYSL2 | 0/1 | |||||
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| GLUD1 | 1/0 | 1/0 | ||||
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| GLUL | 2/0 | |||||
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| GRIN1 | 2/0 | |||||
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| HSPA8 | LoF & NS | |||||
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| IQSEC1 | 4/1 | |||||
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| IQSEC2 | 1/0 | 0/1 | LoF | |||
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| MBP | 1/0 | 0/1 | ||||
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| PKM2 | ||||||
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| PLP1 | ||||||
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| SLC25A3 | 1/0 | |||||
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| SLC25A4 | ||||||
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| SLC25A5 | ||||||
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| STXBP1 | LoF, NS(x2) | |||||
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| Counts: | 9/0 | 32/15 | 8 SCNVs | 6 SNVS | 5 SNVS | |
| P-value: | 0.0016 | 0.0069 | 0.00025 | 0.0005 | 0.00002 | |