Table 2.
Biallelic PYGM variants identified in individuals in this study, with relevant population frequencies, computational predictions, and classification
| Genomic coordinates (hg19) | Ref allele | Alt allele | HGVS cDNA | HGVS protein (inheritance) | Variant classification | gnomAD (v2.1.1) allele frequency | Computational predictions | |||
|---|---|---|---|---|---|---|---|---|---|---|
| Provean | SIFT | CADD (v1.6) | REVEL | |||||||
| Chr 11: 64517943 (Individual 1) | G | T | c.2082C > A | p.Asp694Glu (paternal) | Likely pathogenic | Not found | Deleterious (score −3.86) | Damaging (score 0.000) | 14.29 | 0.707 |
| Chr 11: 64527223 (Individual 1) | G | A | c.148C > T | p.Arg50Ter (maternal) | Pathogenic | 1.4 × 10−3, no homozygotes | n/a | n/a | 33 | n/a |
| Chr 11: 64514696 (Individual 2) | C | T | c.2312G > A | p.Arg771Gln | Likely pathogenic | 7.1 × 10−6, no homozygotes | Deleterious (score −3.38) | Tolerated (score 0.165) | 35 | 0.913 |
The Refseq transcript used for annotation is NM_005609.3. Chr 11:64517943-G-T, VAF: 0.42, 134/321 total reads; Chr 11:64527223-G-A, VAF: 0.49, 127/259 total reads; Chr 11:64514696-C-T, VAF: 1, 43/43 total reads.
(VAF) Variant allele fraction.