Table 2.
Characteristics of the variants identified through whole exome sequencing (WES) in our cohort.
| Patient # |
Gene | Variants | CADD score |
ID |
gnomAD frequency (%) |
rs | Pathogenicity Criteria (ACMG)⁎ |
Phenotype |
|---|---|---|---|---|---|---|---|---|
| 1 | ΑΝΟ5 | p.Phe506fs⁎6 (c.1517delT) / p.Met542fs⁎11 (c.1624dupA) |
23.1 / 35.0 |
NM_01142649.2 |
0.000 / 0.004 |
794727158 / 281865480 |
PVS1, PS4, PM2, PM3 / PVS1, PS4, PM2, PM3 |
LGMD R12 (former 2L) |
| 2 | CAPN3 | p.Tyr537⁎ (c.1611C>A) / deletion of exons 2 to 8 (c.310-?_c.1115+?del) |
38.0 / - |
NM_000070.3 |
0.000 / 0.000 |
886042439 / - |
PVS1, PS3, PS4, PM2, PM3 / PM3, PM4 |
LGMD R1 (former 2A) |
| 3 | CAV3 | p.Thr78Met (c.233C>T) | 23.0 | NM_001234.5 | 0.270 | 72546668 | PS3, PS4, PM1, PM5, PP3, BS1, BP5, BP6 |
Caveolinopathy (former LGMD 1C) |
| 4 | CLCN1 | p.Phe167Leu (c.501C>G) / c.1471+1G>A |
20.3 / 34.0 |
NM_000083.3 |
0.110 / 0.002 |
149729531 / 375596425 |
PS4, PM1, PM2, PM3, PP1, PP5, BP6 / PVS1, PS3, PS4, PM2, PM3, BS2 |
Myotonia Congenita |
| 5 , 6 | CPT2 | p.Ser113Leu (c.338C>T) -Homozygous |
34.0 | NM_000098.3 | 0.140 | 74315294 | PA2, PS3, PS4, PM3, PP3, PP5, BS1, BS2 |
Metabolic Myopathy |
| 7 | DYSF | c.997-1G>A / p.Ala927fs⁎21 (c.2779delG) |
33.0 / 35.0 |
NM_003494.4 |
0.000 / 0.002 |
- / 727503909 |
PVS1, PM2 / PVS1, PS4, PM2, PM3, PP5 |
LGMD R2 (former 2B) |
| 8 | ETFDH | p.Pro483Leu (c.1448C>T) / p.Arg559⁎ (c.1675C>T) |
27.4 / 42.0 |
NM_04453.4 |
0.002 / 0.000 |
377656387 / 186023896 |
PS4, PM2, PM3, PP3, PP5 / PVS1, PS4, PM2 |
Metabolic Myopathy |
| 9 | GAA | c.32-13T>G / p.Tyr292Cys (c.875A>G) |
<10 / 28.5 |
NM_000152.5 |
0.340 / 0.001 |
386834236 / 1057516600 |
PA2, PS3, PS4, PM3, PP5, BS1, BS4, BP2, BP4 / PS3, PS4, PM1, PM2, PM3, PP3, PP5 |
Metabolic Myopathy (former LGMD 2V) |
| 10 | CRPPA (ISPD) | p.Thr238Ala (c.712A> G) -Homozygous |
24.9 |
NM_01101426.4 |
0.000 |
1038301242 |
PS4, PM1, PM2, PM5, PP3 |
LGMD R20 |
| 11 | LAMA2 | c.2208+4_2208+19delAGCTTGCAAGAATGTA / p.Ile2508fs⁎4 (c.7521dupT) |
- / - |
NM_000426.4 |
0.000 / 0.000 |
- / - |
PM2 / PVS1, PM2 |
LGMD R23 |
| 12 | LMNA | p.Arg249Gln (c.746G>A) | 27.1 | NM_170707.4 | 0.000 | 59332535 | PS4, PM1, PM2, PM6, PP3, PP5, BP2 |
Laminopathy (former LGMD 1B) |
| 13 | LMNA | c.1608+2T>C | 29.4 | NM_170707.4 | 0.000 | - | PVS1, PM2 | Laminopathy (former LGMD 1B) |
| 14 | MT-TE | m.14709T>C | <10 | NC_012920.1 | - | 121434453 | BP4 | Mitochondrial Myopathy |
| 15 | MYOT | p.Thr57fs⁎2 (c.170delC) | 33.0 | NM_006790.3 | 0.000 | - | PVS1, PM2 | Myotilinopathy (former LGMD 1A) |
| 16 | SGCA | p.Val247Met (c.739G>A) / p.Arg284Cys (c.850C>T) |
25.8 / 33.0 |
NM_000023.4 |
0.010 / 0.020 |
143570936 / 137852623 |
PS3, PS4, PM1, PM2, PM3, PP1, PP3, PP5 / PS3, PS4, PM1, PM2, PM3, PP3, PP5 |
LGMD R3 (former 2D) |
⁎
Criteria according to Richards et al, Genet Med, 2015 (Standards and Guidelines for the Interpretation of Sequence Variants) through the Ingenuity software.