Table 1. Selected candidate genes implicated by bioinformatics analyses.
Fifteen candidate genes implicated most consistently across various analyses. To assemble this list, each gene in a DEPICT-defined locus (Supplementary Information section 4.5) was assigned a score equal to the number of criteria it satisfies out of ten (see Supplementary Table 4.1 for details). The DEPICT prioritization P-value was used as the tiebreaker. “SNP”: the SNP in the gene's locus with the lowest P-value in the EduYears meta-analysis. “Syndromic”: which, if any, of three neuropsychiatric disorders have been linked to de novo mutations in the gene (Supplementary Information section 4.6). “Top-ranking gene sets”: DEPICT reconstituted gene sets of which the gene is a top-20 member (Supplementary Table 4.5.1). The three most significant gene sets are shown if more than three are available. ID, intellectual disability; ASD, autism spectrum disorder; SCZ, schizophrenia.
| Gene | SNP | Syndromic | Score | Top-ranking gene sets |
|---|---|---|---|---|
| TBR1 | rs4500960 | ID, ASD | 6 | Developmental biology, decreased brain size, abnormal cerebral cortex morphology |
| MEF2C | rs7277187 | ID, ASD | 5 | ErbB signaling pathway, abnormal sternum ossification, regulation of muscle cell differentiation |
| ZSWIM6 | rs61160187 | – | 5 | Transcription factor binding, negative regulation of signal transduction, PI3K events in ErbB4 signaling |
| BCL11A | rs2457660 | ASD | 5 | Dendritic spine organization, abnormal hippocampal mossy fiber morphology, SWI/SNF-type complex |
| CELSR3 | rs11712056 | SCZ | 5 | Dendrite morphogenesis, dendrite development, abnormal hippocampal mossy fiber morphology |
| MAPT | rs192818565 | ID | 5 | Dendrite morphogenesis, abnormal hippocampal mossy fiber morphology, abnormal axon guidance |
| SBNO1 | rs7306755 | SCZ | 5 | Protein serine/threonine phosphatase complex |
| NBAS | rs12987662 | – | 5 | – |
| NBEA | rs9544418 | SCZ | 4 | Developmental biology, signaling by Robo receptor, dendritic shaft |
| SMARCA2 | rs1871109 | ID | 4 | – |
| MAP4 | rs11712056 | ASD | 4 | Developmental biology, signaling by Robo receptor, SWI-SNF-type complex |
| LINC00461 | rs10061788 | – | 4 | Decreased brain size, abnormal cerebral cortex morphology, abnormal hippocampal mossy fiber morphology |
| POU3F2 | rs9320913 | – | 4 | Dendrite morphogenesis, developmental biology, decreased brain size |
| RAD54L2 | rs11712056 | SCZ | 4 | Decreased brain size, SWI/SNF-type complex, nBAF complex |
| PLK2 | rs2964197 | – | 4 | Negative regulation of signal transduction, PI3K events in ErbB4 signaling |