Proband ID | TE Type | Gene | SFARI Classificationa | pLI | Genic Region | Validation Status | Observed Phenotype | Previous Neurodevelopmental Phenotype associated with gene | Reference |
---|---|---|---|---|---|---|---|---|---|
11,859.p1 | Alu | CSDE1 | No | 1 | Exon | Validated | ASD, language delay, ID, macrocephaly, history of vision correction, normal EEG at 4 years | LGD variants associated with ASD, developmental delay, ID, seizures, macrocephaly, ADHD, anxiety, ocular abnormalities | Guo et al. 2019 [22] |
14,565.p1 | Alu | KBTBD6 | No | 0.935 | Exon | Validated | ASD, macrocephaly, uncoordinated, normal IQ, BMI Z-score − 3.91 |  |  |
12,548.p1 | Alu | APPBP2 | No | 0.999 | Intron | Validated | ASD, normal IQ, macrocephaly | Â | Â |
12,748.p1 | Alu | SYT1 | Syndromic | 0.837 | Intron | Validated | ASD, normal IQ, uncoordinated | Developmental delays, autistic features, hypotonia, ocular abnormalities, hyperkinetic movements associated with de novo missense variation | Baker et al., 2018 [23] |
13,931.p1 | Alu | OTUD7A | Suggestive evidence | 0.975 | Intron | Validated | ASD, borderline IQ, normal EEG, and brain imaging | Neurodevelopmental phenotype of ASD, developmental delay, ID, seizures associated with 15q13.3 microdeletion syndrome | |
13,107.p1 | Alu | TOX3 | No | 0.994 | Intron | Validated | ASD, normal IQ | Â | Â |
14,315.p1 | Alu | JAZF1 | No | 0.958 | Intron | Validated | ASD, borderline verbal IQ, normal nonverbal IQ, normal EEG | Â | Â |
11,196.p1 | L1 | SRGAP3 | Minimal Evidence | 1 | Intron | Validated | ASD, above average IQ, no history of seizures, heart problems reported | Case report of translocation breakpoint at loci posited to be LoF associated with hypotonia and severe ID | Endris et al. 2002 [26] |
13,684.p1 | L1 | HCN1 | Syndromic | 0.953 | Intron | NA | ASD, Tourette syndrome, above average IQ, GI problems, uncoordinated | Missense variation associated with a syndrome of seizures, intellectual disability, and autistic features, gene also implicated in Tourette syndrome, role in striatal neuronal function and enteric nervous system | |
14,080.p1 | L1 | DAB1 | Hypothesized | 0.981 | Intron | Validated | ASD, uncoordinated, GI problems | ASD, GI problems, schizophrenia, spinocerebellar ataxia-37 associated with non-coding nucleotide repeats | |
14,282.p1 | L1 | DPYD | Suggestive evidence | 0 | Intron | Not in LCL DNA, predicted blood mosaic | ASD, normal IQ | ASD, ID | |
11,234.p1 | L1 | NOTCH2 | No | 1 | Intron | NA | ASD, above average IQ | Â | Â |
13,451.p1 | L1 | DPP10 | Suggestive evidence | 1 | Intron | NA | ASD, borderline IQ | ASD | Marshall et al. 2008 [33] |
14,404.p1 | SVA | GRAMD1B | No | 0.985 | Intron | NA, predicted blood mosaic | ASD, non-verbal, IQ in profound intellectual disability range, macrocephaly | Autosomal recessive intellectual disability | Santos-Cortez et al. 2018 [34] |
14,523.p1 | SVA | ACACA | No | 1 | Intron | NA | ASD, above average IQ, macrocephaly | Acetyl-CoA carboxylase deficiency | Blom et al. 1981 [35] |