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Table 1 Variants detected in the NBS program for Pompe disease

From: Current status of newborn screening for Pompe disease in Japan

  Variant No rs IDs Nucleic acid Amino acid Location Classification
Pompe disease GAA variant database ClinVar Miner PolyPhen-2 (score)
Disease-associated variants 2 rs772534106 c.317G > A p.R106H Exon 2 Potentially less severe Uncertain significance Probably damaging (1.000)
  4 c.439G > A p.G147S Exon 2 NR NR Probably damaging (0.989)
  5 rs376685205 c.503G > C p.R168P Exon 2 Unknown Uncertain significance Possibly damaging (0.795)
  6 c.539_543delACTTC p.F181Dfs*6 Exon 2 NR NR
  7 rs143523371 c.546G > T p.T182 =  Exon 2 Potentially mild Likely pathogenic
  8 rs756024023 c.546 + 5G > T Intron 2 Unknown Conflicting interpretations of pathogenicity
  14 c.547-27A > G Intron 2 NR NR ##
  21 rs200856561 c.752C > T p.S251L Exon 4 Presumably non-pathogenic Conflicting interpretations of pathogenicity Benign (0.004)
  22 rs577915581 c.761C > T p.S254L Exon 4   Pathogenic/Likely pathogenic Probably damaging (0.997)
  23 rs1555599667 c.796C > T p.P266S Exon 4 Potentially mild Likely pathogenic Benign (0.001)
  28 c.1082C > A p.P361Q Exon 7 Potentially less severe NR Probably damaging (1.000)
  29 rs142752477 c.1124G > A p.R375H Exon 7 Unknown Uncertain significance Probably Damaging (1.000)
  31 c.1170delC p.N390Kfs*2 Exon 7 NR NR
  32 rs776008078 c.1190C > T p.P397L Exon 7 Less severe Uncertain significance Probably damaging (1.000)
  35 c.1244C > T p.T415M Exon 8 Potentially less severe NR Probably damaging (1.000)
  36 rs770610356 c.1309C > T p.R437C Exon 8 Less severe Pathogenic/likely pathogenic Probably damaging (0.995)
  37 rs747610090 c.1316 T > A p.M439K Exon 8 Potentially mild Pathogenic/likely pathogenic Benign (0.096)
  43 c.1494G > A p.W498* Exon 10 Very severe NR
  46 c.1562A > T p.E521V Exon 11 Unknown Uncertain significance Probably damaging (1.000)
  50 rs747150965 c.1669A > T p.I557F Exon 12 Very severe Conflicting interpretations of pathogenicity Benign (0.069)
  52 rs764670084 c.1798C > T p.R600C Exon 13 Less severe Pathogenic probably damaging (1.000)
  53 rs914396317 c.1857C > G p.S619R Exon 13 Less severe Likely pathogenic Probably damaging (1.000)
  55 rs28940868 c.1935C > A p.D645E Exon 14 Potentially less severe Pathogenic Probably damaging (1.000)
  56 rs1555601633 c.2003A > G p.Y668C Exon 14 Potentially less severe Uncertain significance Probably damaging (1.000)
  58 c.2055C > G p.Y685* Exon 15 Very severe NR
  62 rs121907938 c.2173C > T p.R725W Exon 15 Less severe Pathogenic Probably damaging (1.000)
  64 rs1800312 c.2238G > C p.W746C Exon 16 Potentially mild Pathogenic/likely pathogenic Probably damaging (1.000)
  71 rs121907943 c.2560C > T p.R854* Exon 18 Very severe Pathogenic
  72 rs192679574 c.2647-7G > A Intron 18 Potentially mild Pathogenic/likely pathogenic
non-pathogenic variants 1 c.-260G > C Exon 1 Non-pathogenic Likely benign
  3 c.324 T > C p.C108 =  Exon 2 Non-pathogenic Benign
  9 rs34746710 c.546 + 293G > A Intron 2 Non-pathogenic Benign
  10 rs8065426 c.547-243C > G Intron 2 Non-pathogenic Benign
  11 rs12452263 c.547-238 T > C Intron 2 Non-pathogenic Benign
  12 c.547-67C > G Intron 2 Non-pathogenic Benign
  13 rs12452721 c.547-39 T > G Intron 2 Non-pathogenic Benign
  15 rs3816256 c.547-4C > G Intron 2 non-pathogenic benign
  16 rs1042393 c.596A > G p.H199R Exon 3 Non-pathogenic Benign 0.000 (benign)
  17 rs1042395 c.668G > A p.R223H Exon 3 Non-pathogenic Benign 0.206 (benign)
  18 c.692 + 38C > T Intron 3 Non-pathogenic NR
  19 rs11150844 c.693-216 T > C Intron 3 Non-pathogenic Benign
  20 rs2304846 c.705G > A p.T235 =  Exon 4 Unknown Conflicting interpretations of pathogenicity
  24 c.858 + 5_858 + 6ins7GCAGCGG Intron 4 Unknown NR
  25 rs5822325 c.858 + 8G > A Intron 4 NR Benign/likely benign
  26 rs2304845 c.858 + 30 T > C Intron 4 Non-pathogenic Benign
  27 rs2252455 c.955 + 12G > A Intron 5 Non-pathogenic Benign
  30 rs111832449 c.1143C > G p.T381 =  Exon 7 NR Conflicting interpretations of pathogenicity
  33 c.1194 + 19_1194 + 20insA Intron 7 NR NR
  34 rs1800304 c.1203G > A p.Q401 =  Exon 8 Non-pathogenic Benign
  38 rs6565641 c.1327-269A > G Intron 8 Non-pathogenic Benign
  39 rs2278620 c.1327-179G > A Intron 8 Non-pathogenic Benign
  40 rs2278619 c.1327-18A > G Intron 8 Non-pathogenic Benign
  41 rs2278618 c.1438-220A > G Intron 9 Non-pathogenic Benign
  42 rs2304844 c.1438-19G > C Intron 9 Non-pathogenic Benign
  44 rs2304843 c.1551 + 49C > A Intron 10 Non-pathogenic Benign
  45 c.1552-52C > A Intron 10 NR NR #
  47 rs1042396 c.1581G > A p.R527 =  Exon 11 Non-pathogenic Benign
  48 rs2304842 c.1636 + 43G > T Intron 11 Non-pathogenic Benign
  49 rs79487884 c.1636 + 210G > A Intron 11 Non-pathogenic Benign
  51 rs1800307 c.1726G > A† p.G576S Exon 12 Presumably non-pathogenic Benign Probably damaging (1.000)
  54 rs2304837 c.1888 + 21G > A Intron 13 Non-pathogenic Benign
  57 rs2304836 c.2040 + 20A > G Intron 14 Non-pathogenic Benign
  59 c.2065G > A† p.E689K Exon 15 Non-pathogenic Benign, other 0.092 (benign)
  60 rs1555601773 c.2132C > G p.T711R Exon 15 Non-pathogenic Conflicting interpretations of pathogenicity 0.999
(Probably damaging)         
  61 rs1800310 c.2133A > G p.T711 =  Exon 15 Non-pathogenic Benign
  63 rs7221604 c.2189 + 263G > A Intron 15 Non-pathogenic Benign
  65 rs2304832 c.2331 + 20G > A Intron 16 Non-pathogenic Benign
  66 rs2304831 c.2331 + 24 T > C Intron 16 Non-pathogenic Likely benign
  67 rs2304830 c.2332-198A > T Intron 16 Non-pathogenic Benign  
  68 rs1126690 c.2338G > A p.V780I Exon 17 Non-pathogenic Benign 0.000 (benign)
  69 rs1800314 c.2446G > A p.V816I Exon 17 Non-pathogenic Benign 0.008 (benign)
  70 rs1042397 c.2553G > A p.G851 =  Exon 18 Non-pathogenic benign
  73 rs9890469 c.2800-227C > T Intron 19 Non-pathogenic benign
  74 c.2859G > A p.*953 =  Exon 20 NR NR #
  75 rs1800317 c.*3G > A Exon 20 Non-pathogenic Benign
  76 rs865903736 c.*139dup Exon 20 NR Likely benign
  77 rs8132 c.*223C > T Exon 20 Non-pathogenic Benign
  78 rs7567 c.*419G > T Exon 20 NR Benign
  1. NR, not registered
  2. Pseudodeficiency alleles; Human Splicing Finder: #No impact on splicing; ##Potential alteration of splicing