Table 2.
A list of novel hemizygous RPGRORF15 variants detected in the study.
| Genomic Start Position (hg19) | cDNA RPGRORF15: NM_001034853.2 |
Protein Change | ACMG Classification (Criteria) |
|---|---|---|---|
| chrX-38145574 | c.2678G>T | p.(Gly893Val) | Uncertain significance (PM2, PP3, BP1) |
| chrX-38145533 | c.2719G>T | p.(Glu907*) | Likely Pathogenic (PVS1, PM2) |
| chrX-38145521 | c.2731del | p.(Glu911Argfs*178) | Pathogenic (PVS1, PM2, PP1) |
| chrX-38145321 | c.2931_2932ins AAGGAAAAGGGGAGAAGGGGAAGGGGAGGAAGGA | p.(Glu978Lysfs*121) | Likely Pathogenic (PVS1, PM2) |
| chrX-38145296 | c.2956G>T | p.(Gly986*) | Likely Pathogenic (PVS1, PM2) |
| chrX-38145286 | c.2966del | p.(Glu989Glyfs*100) | Likely Pathogenic (PVS1, PM2) |
| chrX-38145259 | c.2985_2993delinsAGAAGGGG | p.(Glu997Glyfs*92) | Likely Pathogenic (PVS1, PM2) |
| chrX-38145172 | c.3071_3080del | p.(Glu1024Glyfs*62) | Likely Pathogenic (PVS1, PM2) |
| chrX-38145171 | c.3077_3081del | p.(Glu1026Glyfs*51) | Likely Pathogenic (PVS1, PM2) |
| chrX-38145132 | c.3119_3120del | p.(Glu1040Glyfs*38) | Likely Pathogenic (PVS1, PM2) |
| chrX-38145115 | c.3134_3137del | p.(Glu1045Glyfs*43) | Likely Pathogenic (PVS1, PM2) |
| chrX-38145115 | c.3134_3138del | p.(Glu1045Glyfs*32) | Likely Pathogenic (PVS1, PM2) |
| chrX-38145105 | c.3146_3147del | p.(Glu1049Glyfs*29) | Likely Pathogenic (PVS1, PM2) |
| chrX-38145105 | c.3146_3149del | p.(Glu1049Glyfs*39) | Likely Pathogenic (PVS1, PM2) |
| chrX-38145040 | c.3212dup | p.(Thr1072Aspfs*7) | Pathogenic (PVS1, PM2, PP1) |
| chrX-38145000 | c.3248_3252del | p.(Glu1083Valfs*17) | Likely Pathogenic (PVS1, PM2) |
| chrX-38144991 | c.3261del | p.(Val1088*) | Likely Pathogenic (PVS1, PM2) |
| chrX-38144976 | c.3276del | p.(Gly1093Aspfs*3) | Likely Pathogenic (PVS1, PM2) |
| chrX-38144918 | c.3334C>T | p.(Gln1112*) | Likely Pathogenic (PVS1, PM2) |
| chrX-38144857 | c.3395dup | p.(Asn1132Lysfs*12) | Likely Pathogenic (PVS1, PM2) |
The American College of Medical Genetics (ACMG) criteria for this study: PVS1: null variant (nonsense, frameshift, canonical ± 1 or 2 splice sites or initiation codon); PM2: frequency on gnomAD < 0.5% and no homozygous cases (if not: BS1); PP1: Cosegregation with disease verified; PP3: At least 1 predictive algorithm suggests pathogenicity (for splice variants, score ≤ −10%), if not: BP4; BP1: Missense variant in a gene for which primarily truncating variants are known to cause disease.