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Table 1 GAA variants detected in the patients sequenced by the MYO-SEQ project

From: Identification of GAA variants through whole exome sequencing targeted to a cohort of 606 patients with unexplained limb-girdle muscle weakness

Patient Location Reported Polymorphism Variant Predicted deleteriousness ClinVar clinical significance ExAC v3 allele frequency
Chromosome Coding Protein SIFT PolyPhen-2 MutationTaster2 FATHMM
10 chr17:78,078,411 c.26C > G p.Ser9Cys No Missense Damaging Benign Polymorphism Damaging No data 0.00000
13 chr17:78,078,484 c.99 T > C No rs144736309 Synonymous No data No data No data No data No data 0.00002
2 chr17:78,078,671 c.286A > G p.Lys96Glu No Missense Tolerated Benign Polymorphism Tolerated No data 0.00001
28 chr17:78,078,805 c.420C > A p.Asn140Lys No Missense Tolerated Benign Polymorphism Damaging No data 0.00002
18 and 32* chr17:78,078,909 c.525delT p.Glu176ArgfsTer45 Yes Frameshift No data No data No data No data Pathogenic 0.00007
9 chr17:78,078,930 c.545C > G p.Thr182Arg No rs200524747 Missense Tolerated Benign Disease-causing Tolerated No data 0.00006
35* chr17:78,079,570 c.569G > A p.Arg190His Yes Missense Deleterious Probably damaging Disease-causing Damaging Likely pathogenic 0.00001
31 chr17:78,079,591 c.590C > A p.Thr197Asn No Missense Tolerated Benign Polymorphism Damaging No data 0.00001
24 chr17:78,079,677 c.676C > G p.Leu226Val No rs113085339 Missense Tolerated Benign Polymorphism Damaging Likely benign; uncertain significance 0.00070
15 chr17:78,081,352 c.693-4G > T No rs200088236 Splice region No data No data No data No data No data 0.00031
30 chr17:78,081,518 c.855C > G No Synonymous No data No data No data No data No data 0.00000
14 chr17:78,081,653 c.913G > A p.Gly305Arg No rs200154987 Missense Deleterious Probably damaging Disease-causing Damaging No data 0.00025
12 and 34 chr17:78,081,655 c.915G > A Yes rs150343359 Synonymous No data No data No data No data Uncertain significance 0.00113
16 chr17:78,082,117 c.984 T > C No Synonymous No data No data No data No data No data 0.00000
6 chr17:78,082,180 c.1047C > T No rs138262940 Synonymous No data No data No data No data No data 0.00002
17* chr17:78,082,399 c.1192delC p.Leu398TrpfsTer42 No Frameshift No data No data No data No data No data 0.00000
26 chr17:78,083,737 c.1327-7 T > G No Splice region No data No data No data No data No data 0.00001
21 chr17:78,083,769 c.1352C > G p.Pro451Arg No rs7215458 Missense Tolerated Possibly damaging Disease-causing Damaging No data 0.00043
21 chr17:78,084,516 c.1438-7_1438-5delTGT No Splice region No data No data No data No data No data 0.00002
25 chr17:78,085,800 c.1655 T > C p.Leu552Pro Yes Missense Deleterious Probably damaging Disease-causing Damaging No data 0.00002
20 and 29 chr17:78,086,452 c.1830C > T Yes rs61736896 Synonymous No data No data No data No data No data 0.00151
4 and 27 chr17:78,086,706 c.1920 T > G Yes rs144090460 Synonymous No data No data No data No data No data 0.00032
35* chr17:78,086,806 c.2020C > G p.His674Asp No Missense Deleterious Probably damaging Disease-causing Damaging No data 0.00000
8* chr17:78,087,027 c.2051C > G p.Pro684Arg No Missense Deleterious Probably damaging Disease-causing Damaging No data 0.00000
5* chr17:78,087,039 c.2066_2070dupAGCCG p.Ala691SerfsTer7 Yes Frameshift No data No data No data No data No data 0.00000
19 chr17:78,087,046 c.2070G > A No Synonymous No data No data No data No data No data 0.00003
33 chr17:78,087,131 c.2155G > A p.Ala719Thr No Missense Tolerated Benign Polymorphism Damaging No data 0.00004
1 chr17:78,087,133 c.2157G > A No rs201523530 Synonymous No data No data No data No data Uncertain significance 0.00014
7* chr17:78,090,846 c.2269C > T p.Gln757Ter Yes rs200483245 Stop gained No data No data No data No data No data 0.00000
23 chr17:78,090,907 c.2330C > T p.Thr777Met No Missense Tolerated Benign Polymorphism Damaging No data 0.00002
3* chr17:78,090,910 c.2331 + 2 T > A Yes Splice donor No data No data No data No data No data 0.00000
11 chr17:78,091,525 c.2458G > T p.Ala820Ser No Missense Tolerated Benign Polymorphism Damaging No data 0.00002
17* chr17:78,092,521 c.2716G > A p.Val906Ile No Missense Tolerated Benign Disease-causing Damaging No data 0.00000
22 chr17:78,092,562 c.2757C > T No Synonymous No data No data No data No data No data 0.00005
3, 5, 7, 8, 18, 32 chr17:78,078,341 c.-32-13 T > G Yes Intronic No data No data No data No data No data 0.00360
  1. Rows 1-34: all rare (< 1%) coding variants detected. Those highlighted with an asterisk (*) were classified as disease-causing and occurred in combination with the c.-32-13 T > G intronic variant for all but patients 17 and 35. Row 35: intronic c.-32-13 T > G transversion considered to contribute to disease pathology. Reported variants are listed in the Pompe Disease Mutation Database [6]