Table 4.
Detection of Variants and Mutations Following Target Enrichment
| Patient No. | Gene | Exon/intron | Mutation | Amino acid change/consequence (frameshift/del) | Status (Homo/Het) | RDT detected | RDT mutation coverage | SS detected | SS mutation coverage | Sanger confirmed | Notes |
|---|---|---|---|---|---|---|---|---|---|---|---|
| C11 | COL6A1 | 30 | c.1931G>A | p.R644Q | Het | − | 11 | + | 66 | + | VUS |
| COL6A2 | 23 | c.1770G>A | p.T590 | Het | + | 8 | − | 20 | + | VUS⁎ | |
| COL6A2 | 28 | c.2994C>T | p.H998 | Het | + | 20 | + | 42 | + | VUS⁎ | |
| C12 | COL6A1 | 29 | IVS29-8G>A | Het | + | 7 | + | 34 | + | VUS | |
| FKTN | 9 | IVS9-40C>A | Het | − | − | − | − | + | VUS† | ||
| LAMA2 | 14 | c.2084C>T | p.D695V | Het | + | 82 | + | 63 | + | VUS | |
| LAMA2 | 39 | c.5614G>T | p.D1872Y | Het | + | 29 | + | 88 | + | VUS | |
| SEPN1 | 5 | IVS5+39C>T | Het | − | − | − | − | + | VUS† | ||
| SEPN1 | 11 | IVS11-31C>T | p.V549 mol/L | Het | − | − | − | − | + | VUS† | |
| SEPN1 | 13 | c.1645G>A | Het | + | 78 | + | 159 | + | VUS | ||
| SEPN1 | 3′UTR | c.1773+44G>T | Het | − | − | − | − | + | VUS† | ||
| C13 | COL6A1 | 26 | IVS26+50C>T | Het | − | − | − | − | + | VUS† | |
| COL6A1 | 33 | c.2424G>T | p.Q808H | Het | + | 8 | + | 17 | + | VUS | |
| COL6A2 | 24 | IVS24-3dupC | Het | − | 8 | + | 162 | + | VUS | ||
| COL6A3 | 38 | IVS38-34C>T | Homo | − | − | − | − | + | VUS† | ||
| C14 | LAMA2 | 22 | c.3154A>G | p.S1052G | Het | + | 17 | + | 40 | + | VUS |
| LAMA2 | 47 | c.6617delT | frameshift | Het | − | 1 | + | 75 | + | Del mut | |
| C15 | POMGNT1 | 7 | c.636C>T | p.F212 | Het | + | 34 | + | 30 | + | Splicing mut‡ |
| POMGNT1 | 17 | IVS17+1G>A | Het | + | 105 | + | 73 | + | Splicing mut§ | ||
| W16 | |||||||||||
| 1 | COL6A3 | 14 | IVS14-8del29 | Del | Het | + | 87 | − | − | + | Del mut |
| 3 | COL6A2 | 22 | IVS22+4G>A | p.H1337R | Het | + | 44 | + | 137 | + | |
| LAMA2 | 27 | c.4010A>G | Het | + | 10 | + | 32 | + | Possibly damaging | ||
| 7 | COL6A3 | 1 | c.53C>A | p.A18X | Homo | + | 111 | + | 35 | + | Nonsense mut |
| 8 | COL6A1 | 6 | IVS6-18CC>T | Het | + | 66 | + | 122 | + | ||
| LAMA2 | 24 | c.3412G>A | p.V1138 mol/L | Het | + | 66 | + | 132 | + | Mut-HGMD | |
| LAMA2 | 43 | IVS43+5G>C | Het | + | 66 | + | 15 | + | |||
| 9 | COL6A1 | 21 | IVS21-2A>G | Het | − | − | − | − | + | ||
| COL6A2 | 26 | c.2039G>A | p.R680H | Het | + | 8 | + | 22 | + | ||
| COL6A2 | 22 | IVS22+4G>A | Het | − | − | + | 26 | + | |||
| COL6A3 | 41 | c.9206C>T | T3069I | Het | + | 26 | + | 15 | + | ||
| LARGE | 15 | c.1949G>A | p.R650Q | Het | + | 10 | + | 49 | + | ||
| SEPN1 | 12 | c.1506C>A | p.N502K | Homo | + | 26 | + | 17 | + | ||
| 10 | COL6A1 | 14 | IVS14+1G>A | Het | + | 19 | + | 14 | + | Splicing mut |
Target enrichment achieved by RainDance Technologies and SureSelect in combination with next-generation sequencing. Out-of-frame deletion mutation predicted to result in a premature translation stop. This change is of the type predicted to cause disease.
+, present; −, not present; C, positive control samples; Del, deletion; Het, heterozygous change; Homo, homozygous change; MEB, muscle-eye-brain; Mut, mutation; UTR, untranslated region; VUS, variant of unknown clinical significance, pending functional analysis for reclassification; W, wild-type sample.
It is possible for silent changes to disrupt RNA splicing.
Mutation and/or variant of unknown clinical significance not detected because the bioinformative algorithm set to detect ±20 bases from exon/intron boundaries.
This mutation has been reported in individuals with MEB disease.
This mutation results in a G to A change in the consensus donor site of the exon 17/intron 17 boundary and is predicted to result in aberrant splicing of POMGNT1 RNA. This mutation has been reported in individuals with MEB disease.