Table 1.
Candidate gene variants detected by whole-exome sequencing
| Chr | Position | Gene | Transcript accession# | Exon | Nucleotide change | Amino acid change | ExAc | Gnomad | CADD |
|---|---|---|---|---|---|---|---|---|---|
| De novo | |||||||||
| 9 | 39103792 | CNTNAP3 | NM_033655.3 | 16 | c.2485G > C | p.(Val829Leu) | −1 | −1 | 23.4 |
| 2 | 202251090 | TRAK2 | NM_015049.2 | 14 | c.1814A > C | p.(Tyr605Ser) | −1 | −1 | 29.4 |
| 11 | 86947710 | TMEM135 | NM_022918.3 | 6 | c.494_498del | p.(Tyr165fs) | −1 | −1 | |
| Homozygous | |||||||||
| 3 | 127323612 | MCM2 | NM_004526.2 | 3 | c.398G > A | p.(Arg133His) | 0.003 | 0.0018 | 27 |
| X-linked | |||||||||
| X | 47060300 | UBA1 | NM_003334.3 | 6 | c.488T > C | p.(Val163Ala) | −1 | −1 | 25.5 |
WES was performed on the trio by SureSelect Clinical Research Exome (Agilent, Technologies) and NextSeq500 sequencing system (Illumina, hg 19 human reference genome). A customized pipeline based on Burrows-Wheeler Alignment tool, Genome Analysis Toolkit and ANNOVAR were used to call, annotate, filter, and prioritize variants. Variants are submitted in LOVD repository (as Lab-ID ULOele-15-22; https://databases.lovd.nl/shared/individuals/00228899).
−1: indicate absence in control dataset. Additional interpretation of these variants is provided in Supplementary material
Chr chromosome, ExAC Exome Aggregation Consortium, Gnomad Genome Aggregation Database, CADD Combined Annotation Dependent Depletion