Introduction
Materials and methods
Study design
Patients
Methods
Targeted next generation sequencing and data analysis
Sanger sequencing
Multiplex ligation-dependent probe amplification analysis/assays for microrearrangements detection
Genotyping for dynamic mutation detection
Results
Coverage and depth of sequencing
NGS results
Patient ID | Gender | Onset | Age at diagnosis (yrs) | Gene symbol | Reference sequence | Mutation nucleotide (protein) | Genotype | ACMG classification | CADD score* | REVEL score | Novel | Serum CPK levels | Muscle biopsy |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Myotonia congenita, autosomal recessive | |||||||||||||
P1 | M | childhood | 21 | CLCN1 | NM_000083.2 | c.2680C > T (p.Arg894Ter) | Homozygote | Likely pathogenic (PVS1, PM2, PP5) | 35 | N/A | No | Not done | Not done |
P2 | M | 16 | 20 | CLCN1 | NM_000083.2 | c.2680C > T (p.Arg894Ter) | Homozygote | Likely pathogenic (PVS1, PM2, PP5) | 35 | N/A | No | 213 U/L | Not done |
P3 | F | childhood | 35 | CLCN1 | NM_000083.2 | c.2680C > T (p.Arg894Ter) | Homozygote | Likely pathogenic (PVS1, PM2, PP5) | 35 | N/A | No | 63 U/L | Not done |
P4 | F | 10 | 36 | CLCN1 | NM_000083.2 | c.2680C > T (p.Arg894Ter) | Homozygote | Likely pathogenic (PVS1, PM2, PP5) | 35 | N/A | No | Not done | Not done |
P5 | M | childhood | 41 | CLCN1 | NM_000083.2 | c.2680C > T (p.Arg894Ter) | Homozygote | Likely pathogenic (PVS1, PM2, PP5) | 35 | N/A | No | Not done | Not done |
P6 | F | 24 | 29 | CLCN1 | NM_000083.2 | c.871G > A (p.Glu291Lys) | Heterozygote compound | Pathogenic (PM3, PP3, PM2, PM1, PP2, PS3, PP1, PP5) | 33 | Deleterious (Strong) | No | Not available | Not available |
c.2680C > T (p.Arg894Ter) | Likely pathogenic (PVS1, PM2, PP5) | 35 | N/A | No | |||||||||
P7 | F | Not available | 25 | CLCN1 | NM_000083.2 | c.899G > A (p.Arg300Gln) | Heterozygote compound | Benign (PP3, PP2, BP6, BS1, BS2) | 28.9 | Deleterious (Moderate) | No | Not available | Not available |
c.1238 T > G (p.Phe413Cys) | Pathogenic (PS4, PM2, PM1, PP3, PP2, PS3, PP1, PP5) | 27.7 | Deleterious (Moderate) | No | |||||||||
P8 | F | early childhood | 45 | CLCN1 | NM_000083.2 | c.899G > A (p.Arg300Gln) | Heterozygote compound | Benign (PP3, PP2, BP6, BS1, BS2) | 28.9 | Deleterious (Moderate) | No | 148 U/L | Not done |
c.1231G > T (p.Gly411Cys) | Pathogenic (PS4, PP3, PM2, PM1, PP2, PP5) | 32 | Deleterious (Strong) | No | |||||||||
c.2680C > T (p.Arg894Ter) | Likely pathogenic (PVS1, PM2, PP5) | 35 | N/A | No | |||||||||
P9 | M | childhood | 18 | CLCN1 | NM_000083.2 | c.1238 T > G (p.Phe413Cys) | Heterozygote compound | Pathogenic (PS4, PM2, PM1, PP3, PP2, PS3, PP1, PP5) | 27.7 | Deleterious (Moderate) | No | Not available | Not available |
c.2680C > T (p.Arg894Ter) | Likely pathogenic (PVS1, PM2, PP5) | 35 | N/A | No | |||||||||
P10 | F | 6 | 13 | CLCN1 | NM_000083.2 | c.1437_1450del (p.Pro480HisfsTer24) | Heterozygote compound | Pathogenic (PVS1, PM3, PM2, PP5) | 36 | N/A | No | 86 U/L | Not done |
c.2680C > T (p.Arg894Ter) | Likely pathogenic (PVS1, PM2, PP5) | 35 | N/A | No | |||||||||
P11 | M | Not available | 30 | CLCN1 | NM_000083.2 | c.1697C > T (p.Ala566Val) | Heterozygote compound | Pathogenic (PM3, PP3, PM2, PM1, PP2, PP5) | 29.6 | Deleterious (Strong) | No | Not available | Not available |
c.2680C > T (p.Arg894Ter) | Likely pathogenic (PVS1, PM2, PP5) | 35 | N/A | No | |||||||||
Myotonia congenita, autosomal dominant | |||||||||||||
P12 | F | since birth | 1 | SCN4A | NM_000334.4 | c.190C > G (p.Leu64Val) | Heterozygote | VUS (PM2, PP3) | 22.1 | Deleterious (Supporting) | No | Not available | Not available |
P13 | F | since birth | 65 | SCN4A | NM_000334.4 | c.4298 T > G (p.Leu1433Arg) | Heterozygote | Pathogenic (PS4, PP3, PM2, PM1, PP5) | 25.2 | Deleterious (Strong) | No | Not done | Not done |
P14 | F | since birth | 2 | SCN4A | NM_000334.4 | c.4324G > A (p.Val1442Met) | Heterozygote | Likely pathogenic (PM2, PM1, PP3, PM5) | 28.6 | Deleterious (Moderate) | No | Not available | Not available |
Muscular dystrophy, limb-girdle type 2A (recessive) | |||||||||||||
P15 | F | early childhood | 44 | CAPN3 | NM_000070.2 | c.550del (p.Thr184ArgfsTer36) | Homozygote | Pathogenic (PVS1, PM3, PM2, PS3, PP5) | 23.8 | N/A | No | Not done | the section contained mainly tissue fat overgrown by fibrous connective tissue, in which very few preserved striated muscle fibers were found small diameter and enlarged centrally located nucleus |
P16 | F | early childhood | 66 | CAPN3 | NM_000070.2 | c.550del (p.Thr184ArgfsTer36) | Homozygote | Pathogenic (PVS1, PM3, PM2, PS3, PP5) | 23.8 | N/A | No | 100,3 IU/L | primarily muscular changes (biceps) |
P171 | M | early childhood | 16 | CAPN3 | NM_000070.2 | c.550del (p.Thr184ArgfsTer36) | Homozygote | Pathogenic (PVS1, PM3, PM2, PS3, PP5) | 23.8 | N/A | No | 5320 U/L | primarily muscle changes of mild intensity (quadriceps femoris muscle) |
P18 | M | 14 | 37 | CAPN3 | NM_000070.2 | c.598_612del (p.Phe200_Leu204del) | Heterozygote compound | Pathogenic (PM3, PM2, PM4, PM1, PP5) | 23.4 | N/A | No | Not available | Not available |
c.985G > A (p.Gly329Arg) | Pathogenic (PS1, PM3, PM2, PP3, PM1, PP2, PS3, PP5) | 29.5 | Deleterious (Moderate) | No | |||||||||
P192 | M | Not available | 57 | CAPN3 | NM_000070.2 | c.(309 + 1_310–1)_(1115 + 1_1116-1)del (exon 2–8 del) | Heterozygote | Pathogenic | N/A | N/A | No | Not available | Not available |
c.319G > A (p.Glu107Lys) | Homozygote | Benign (PP2, BS1, BS2, BP6, BA1) | 19.92 | Uncertain | No | ||||||||
Muscular dystrophy, limb-girdle type 2D (recessive) | |||||||||||||
P20 | F | Not available | 5 | SGCA | NM_000023.3 | c.190G > A (p.Ala64Thr) | Heterozygote compound | Likely pathogenic (PM2, PM1, PP2, PP5) | 25.2 | Uncertain | No | ~ 30000 U/L | Not available |
c.574C > T (p.Arg192Ter) | Pathogenic (PVS1, PM3, PM2, PP5) | 43 | N/A | No | |||||||||
c.662G > A (p.Arg221His) | Benign (PP3, PM5, PP2, BP6, BS1, BS2) | 28.3 | Deleterious (Moderate) | No | |||||||||
P21 | M | 3 months | 8 | SGCA | NM_000023.3 | c.747G > A (p.Leu249 =) | Heterozygote compound | VUS (PP3, PM2) | 21.5 | N/A | Yes | 23582 U/L 10750 U/L | Not done |
c.790_791dup (p.Gly265GlnfsTer57) | Pathogenic (PVS1, PM3, PM2, PP5) | 26.3 | N/A | Yes | |||||||||
P22 | M | 14 | 38 | SGCA | NM_000023.3 | c.748G > T (p.Val250Leu) | Heterozygote compound | VUS (PM2, PP3, PP2) | 24.3 | Uncertain | No | 12575 U/L | atrophic fibers of various diameters were found, internalization of the nucleus, excess connective and fatty tissue from degenerative changes, normal dystrophin expression, reduced expression of alpha and gamma sarcoglycans |
c.850C > T (p.Arg284Cys) | Pathogenic (PM3, PM2, PM5, PP3, PP2, PS3, PP1, PP5) | 27.4 | Deleterious (Supporting) | No | |||||||||
Muscular dystrophy, limb-girdle type 2B (recessive) | |||||||||||||
P233 | F | Not available | 46 | DYSF | NM_001130987.2 | c.1276 + 5G > A | Heterozygote compound | Pathogenic (PM3, PP3, PM2, PP5) | N/A | N/A | No | 6856,3 U/L | features of primarily muscular damage without inflammatory features, changes typical of muscular dystrophy (left quadriceps muscle) |
c.5356del (p.Glu1786ArgfsTer77) | Likely pathogenic (PVS1, PM2) | 33 | N/A | Yes | |||||||||
Muscular dystrophy, limb-girdle type 1B (autosomal dominant | |||||||||||||
P24 | F | Not available | 50 | LMNA | NM_170707.3 | c.162_163del (p.Asn56ArgfsTer11) | Heterozygote | Pathogenic (PVS1, PM2, PS4, PP5) | 35 | N/A | No | Not available | Not available |
Muscular dystrophy, Duchenne/Becker muscular dystrophies (X-linked) | |||||||||||||
P25 | M | Not available | 12 | DMD | NM_004006.2 | c.4846-1G > C | Hemizygote | Likely pathogenic (PVS1, PM2, PP5) | 33 | N/A | Yes | Not available | Not available |
P26 | M | Not available | 9 | DMD | NM_004006.2 | c.6630del (p.Asn2211IlefsTer10) | Hemizygote | Likely pathogenic (PVS1, PM2) | 35 | N/A | Yes | Not available | Not available |
Ullrich congenital muscular dystrophy (AD) | |||||||||||||
P27 | M | 6 | 51 | COL6A1 | NM_001848.2 | c.1029_1032delins | Heterozygote | Likely pathogenic | N/A | N/A | Yes | Not done | fibers of different diameters intermingle, irregularly arranged in bunches. In single fibers nucleus centralization. In a single bunch of lesions under the form overgrowth of connective tissue between fibers, atrophied in this bunch the fibers have rounded shapes |
Myopathies | |||||||||||||
P284 | M | 30 | 45 | RYR1 | NM_000540.2 | c.131G > A (p.Arg44His) | Heterozygote compound | Likely pathogenic (PP3, PM2, PM5, PM1, PP2) | 28.5 | Deleterious (Strong) | No | 2797 U/L 4194 U/L | no diagnostic material was obtained for evaluation (right quadriceps muscle) |
c.6523_6525del (p.Glu2175del) | VUS (PM2, PM4, PM1) | 20.4 | N/A | No | |||||||||
P29 | F | 62 | 73 | RYR1 | NM_000540.2 | c.8027G > A (p.Arg2676Gln) | Heterozygote compound | Likely pathogenic (PM2, PM5, PP2, PP5) | 23.6 | Uncertain | No | 769 U/L | features resembling the central core (left quadriceps muscle) |
c.14920C > A (p.His4974Asn) | Likely pathogenic (PM2, PM1, PP3, PP2) | 24.1 | Deleterious (Supporting) | No | |||||||||
Nemaline myopathy 6 (AD) | |||||||||||||
P30 | M | Not available | 42 | KBTBD13 | NM_001101362.2 | c.1304C > T (p.Ser435Phe) | Heterozygote | VUS (PM2) | 25.5 | Uncertain | No | Not available | Not available |