Research Article
Genome Sequencing of Idiopathic Speech Delay
Table 1
Rare probable loss-of-function variants in intolerant genes identified in 13 singleton cases with speech delay.
| Proband | Chr | Base (GRCh37) | Base (GRCh38) | Gene | Transcript | Variant effect | cDNA change | Protein change | gnomAD MAF | pLI | Phenotype previously associated with heterozygous pLoF variants | Classification |
| 01 | 16 | 30991037 | 30979716 | SETD1A | NM_014712 | Frameshift | c.3930_3940del CCCTGCGCCAG | p.P1313Afs17 | 0 | 1.00 | Neurodevelopmental disorder and schizophrenia [47], childhood apraxia of speech [13, 14] | Pathogenic | 02 | 2 | 242122172 | 241182757 | PPP1R7 | NM_002712 | Frameshift | c.1017delC | p.R340Gfs111 | 0 | 0.99 | — | VUS | 04 | 5 | 145859585 | 146480022 | TCERG1 | NM_006706 | Splicing | c.1820-3_1822delTAGTTA | ? | | 1.00 | — | VUS | 06 | 16 | 67580073 | 67546170 | RIPOR1 | NM_024519 | Stop-gain | c.C3501G | p.Y1167X | 0 | 0.95 | — | VUS | 17 | 38572722 | 40416470 | TOP2A | NM_001067 | Frameshift | c.220delG | p.E74Kfs16 | 0 | 0.99 | — | VUS |
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Chr: chromosome; MAF: minor allele frequency; pLI: probability of being loss-of-function intolerant; VUS: variant of unknown significance.
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