Fig. 3

Long-read sequencing identified a deletion in the G6PC gene. (a) IGV screen shot of reads at the G6PC locus. Four reads carry a deletion (chr17 g.41049904_41057049del7125 that starts from the first intron of the LINC00671 gene to intron 2 of the G6PC gene. (b) Quantitative PCR validation of the deletion in the trio. Relative quantitation (RQ) of copy number was analyzed by the ΔΔCT method, and error bars represent standard deviation. The deletion includes exon 1F (5′-Flanking introns), exon 1 and exon 2, and the patient and his father are mutation carriers while his mother is normal. (c) Sanger validation of the deletion breakpoints. The first sequence shows the mutated genomic segment, while the second and third sequences show expected genomic segments if deletion is not present. The red arrow refers to the breakpoint, and a 7125 bp sequence is deleted based on the human reference genome (GRCh37). (d) Depiction of the protein domains that were targeted by the non-synonymous mutation and the 7.1 kb deletion. (e) Illustration of the genomic contexts of the two breakpoints, which are both located in known Alu elements. (f) Gel electrophoresis of the PCR product designed to detect the deletion. The lane marked with M represent GeneRuler 50 bp DNA Ladder (Thermo Scientific™), and all lanes (except “-“lane) include an ~ 800 bp internal control (β-Globin gene). A 418 bp fragment can be amplified from the father and the proband