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.

ProbandChrBase (GRCh37)Base (GRCh38)GeneTranscriptVariant effectcDNA changeProtein changegnomAD MAFpLIPhenotype previously associated with heterozygous pLoF variantsClassification

01163099103730979716SETD1ANM_014712Frameshiftc.3930_3940del CCCTGCGCCAGp.P1313Afs1701.00Neurodevelopmental disorder and schizophrenia [47], childhood apraxia of speech [13, 14]Pathogenic
022242122172241182757PPP1R7NM_002712Frameshiftc.1017delCp.R340Gfs11100.99VUS
045145859585146480022TCERG1NM_006706Splicingc.1820-3_1822delTAGTTA?1.00VUS
06166758007367546170RIPOR1NM_024519Stop-gainc.C3501Gp.Y1167X00.95VUS
173857272240416470TOP2ANM_001067Frameshiftc.220delGp.E74Kfs1600.99VUS

Chr: chromosome; MAF: minor allele frequency; pLI: probability of being loss-of-function intolerant; VUS: variant of unknown significance.