Table 2 Allele frequencies in various population databases and in silico analysis of novel candidate variants detected in SGCA, SGCB, and SGCG
From: Clinical and genetic spectrum of sarcoglycanopathies in a large cohort of Chinese patients
Gene | c.DNA position | Global AF in all subpopulation | FATHMM | Mutation Taster | PolyPhen-2 HumVar | SIFT | GERP* | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
gnomAD | ESP6500 | TGP | ExAC | 100 HC | |||||||
SGCA | c.218C > G | absent | absent | absent | absent | absent | Deleterious | Disease_causing | Probably damaging | Deleterious | 4.53 |
SGCA | c.218C > T | 0.00000815 | absent | absent | absent | absent | Deleterious | Disease_causing | Probably damaging | Deleterious | 4.53 |
SGCA | c.158-10_160del | absent | absent | absent | absent | absent | – | – | – | – | – |
SGCA | c.234C > A | absent | absent | absent | absent | absent | Deleterious | – | – | – | −1.04 |
SGCA | c.427C > T | absent | absent | absent | absent | absent | Deleterious | Disease_causing | Possibly damaging | Tolerated | 4.35 |
SGCA | c.956G > A | absent | absent | absent | absent | absent | Deleterious | Disease_causing | Benign | Tolerated | 1.19 |
SGCA | c.1A > G | absent | absent | absent | absent | absent | Deleterious | Disease_causing | Possibly damaging | Deleterious | 3.78 |
SGCA | c.687delT | absent | absent | absent | absent | absent | – | – | – | – | – |
SGCA | Exons 1–7 duplication | – | – | – | – | – | – | – | – | – | – |
SGCA | Exons 4–8 deletion | – | – | – | – | – | – | – | – | – | – |
SGCB | Exons 5–6 deletion | – | – | – | – | – | – | – | – | – | – |
SGCB | c.29_33delAACAG | absent | absent | absent | absent | absent | – | – | – | – | – |
SGCB | c.273_292del | absent | absent | absent | absent | absent | – | – | – | – | – |
SGCB | c.366_367delTT | absent | absent | absent | absent | absent | – | – | – | – | – |
SGCB | c.543C > A | absent | absent | absent | absent | absent | Deleterious | Disease_causing | Probably damaging | Deleterious | 3.3 |
SGCG | c.320C > T | 0.00000813 | absent | absent | 0.000008 | absent | Deleterious | Disease_causing | Probably damaging | Deleterious | 5.39 |