Pompe disease GAA variant database
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Link to variant Link to patients Location DNA nomenclature RNA nomenclature Protein nomenclature Predicted severity Phenotype with null allele CRIM status Number of patients
Variant info Patients:1 GAA and part of CCDC40 Ch37/hg19:g.78,056,048_ 78,094,854delins14bp r.(-212_*551del) p.(0) Very severe Classic infantile Negative 1
Variant info Patients:1 CCDC40 and GAA exon 1 Ch37/hg19 chr17:78,059,821_ 78,076,592del r.0 p.? very severe Classic infantile Unknown 1
Variant info Patients:0 exon 1A, 5' UTR c.-338C>G r.(-338c>g) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 exon 1A, 5' UTR c.-260G>C r.(-260g>c) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 exon 1A, 5' UTR c.-178G>A r.(-178g>a) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:3 intron 1A c.-113+2T>C r.spl p.? Very severe Unknown (disease-associated) Unknown 3
Variant info Patients:0 exon 1B, 5' UTR c.-82G>C r.(-82g>c) p.? Unknown Unknown Positive 0
Variant info Patients:0 exon 1B, 5' UTR c.-75C>G r.(-75c>g) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-33+219G>C r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-33+316C>A r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-33+317C>T r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-33+671A>C r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-33+757G>A r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-33+903A>C r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-33+1104A>G r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-33+1172G>A r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-33+1190G>T r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-33+1309T>C r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-32-1298G>C r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-32-1124C>T r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-32-884T>C r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-32-793C>G r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-32-721G>C r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-32-686A>G r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-32-640C>T r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-32-521G>T r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-32-494C>G r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:0 intron 1B c.-32-462G>A r.(=) p.? Non-pathogenic Unknown Positive 0
Variant info Patients:1 intron 1B c.-32-17_-32-10delins(30) r.? p.? very severe Classic infantile Unknown 1
Variant info Patients:733 intron 1B c.-32-13T>G r.[=,-32_546del,-32_486del] p.[=,0] Potentially mild Childhood or Adult Positive 733
Variant info Patients:2 intron 1B c.-32-3C>G r.(=) p.? Less severe Unknown (disease-associated) Unknown 2
Variant info Patients:14 intron 1B c.-32-3C>A r.(=) p.? Less severe Childhood Unknown 14
Variant info Patients:3 intron 1B c.-32-2A>G r.spl p.? Very severe Childhood or Adult Unknown 3
Variant info Patients:1 intron 1B c.-32-1G>C r.spl p.? very severe Unknown (disease-associated) Unknown 1
Variant info Patients:0 exon 2 c.1A>T r.(1a>u) p.(0) Potentially less severe Unknown Negative 0
Variant info Patients:6 exon 2 c.1A>G r.(1a>g) p.(0) Very severe Classic infantile or Childhood Negative 6
Variant info Patients:2 exon 2 c.2T>C r.(2u>c) p.(0) Potentially less severe Childhood Negative 2
Variant info Patients:1 exon 2 c.3G>A r.(3g>a) p.(0) Very severe Classic infantile or Childhood Negative 1
Variant info Patients:1 exon 2 c.18_25del r.(18_25del) p.(Cys8Profs*24) Very severe Classic infantile Negative 1
Variant info Patients:1 exon 2 c.25del r.(25del) p.(Ser9Profs*34) Very severe Unknown (disease-associated) Negative 1
Variant info Patients:1 exon 2 c.40_47del r.(40_47del) p.(Ala14Argfs*18) very severe Classic infantile Negative 1
Variant info Patients:0 exon 2 c.32G>A r.(32g>a) p.(Arg11Gln) Non-pathogenic Unknown Positive 0
Variant info Patients:0 exon 2 c.54C>T r.(54c>u) p.(=) Non-pathogenic Unknown Positive 0
Variant info Patients:1 exon 2 c.104T>C r.(104u>c) p.(Phe35Ser) Potentially less severe Classic infantile Positive 1
Variant info Patients:18 exon 2 c.118C>T r.(118c>u) p.(Arg40*) Very severe Classic infantile Negative 18
Variant info Patients:1 exon 2 c.136T>C r.(136u>c) p.(Ser46Pro) Non-pathogenic Classic infantile Positive 1
Variant info Patients:3 exon 2 c.147_859-12del r.spl p.? Very severe Classic infantile Negative 3
Variant info Patients:1 exon 2 c.169C>T r.(169c>u) p.(Gln57*) very severe Classic infantile Negative 1
Variant info Patients:3 exon 2 c.172C>T r.(172c>u) p.(Gln58*) Very severe Classic infantile Negative 3
Variant info Patients:0 exon 2 c.186_196dup r.(186_196dup) p.(Arg66Hisfs*80) Very severe Unknown Negative 0
Variant info Patients:1 exon 2 c.205C>T r.(205c>u) p.(Gln69*) very severe Unknown (disease-associated) Negative 1
Variant info Patients:0 exon 2 c.199G>A r.(199g>a) p.(Asp67Asn) Non-pathogenic Unknown Positive 0
Variant info Patients:0 exon 2 c.221G>A r.(221g>a) p.(Arg74His) Non-pathogenic Unknown Positive 0
Variant info Patients:13 exon 2 c.236_246del r.(236_246del) p.(Pro79Argfs*13) Very severe Classic infantile Negative 13
Variant info Patients:3 exon 2 c.241C>T r.(241c>u) p.(Gln81*) Very severe Unknown (disease-associated) Negative 3
Variant info Patients:4 exon 2 c.258dup r.(258dup) p.(Asn87Glnfs*9) Very severe Unknown (disease-associated) Negative 4
Variant info Patients:0 exon 2 c.258C>A r.(258c>a) p.? Unknown Unknown (disease-associated) Positive 0
Variant info Patients:0 exon 2 c.265C>T r.(265c>u) p.(Arg89Cys) potentially less severe Unknown (disease-associated) Positive 0
Variant info Patients:2 exon 2 c.266G>A r.(266g>a) p.(Arg89His) Presumably non-pathogenic Classic infantile Positive 2
Variant info Patients:2 exon 2 c.271G>A r.271g>a p.(Asp91Asn) Presumably non-pathogenic Unknown (disease-associated) Positive 2
Variant info Patients:3 exon 2 c.271del r.(271del) p.(Asp91Ilefs*51) Very severe Unknown (disease-associated) Negative 3
Variant info Patients:1 exon 2 c.295_314del r.(295_314del) p.(Thr99Profs*40) very severe Unknown (disease-associated) Negative 1
Variant info Patients:0 exon 2 c.307T>C r.(307u>c) p.(Cys103Arg) Potentially less severe Unknown Positive 0
Variant info Patients:19 exon 2 c.307T>G r.(307u>g) p.(Cys103Gly) Potentially less severe Classic infantile Positive 19
Variant info Patients: exon 2 c.309C>G r.(309c>g) p.(Cys103Trp) Potentially less severe Unknown Positive
Variant info Patients:1 exon 2 c.309C>A r.(309c>a) p.(Cys103*) Very severe Classic infantile Negative 1
Variant info Patients:1 exon 2 c.317G>A r.(317g>a) p.(Arg106His) potentially less severe Unknown (found only in NBS) Positive 1
Variant info Patients:0 exon 2 c.322T>G r.(322u>g) p.(Cys108Gly) Potentially less severe Unknown Unknown 0
Variant info Patients:2 exon 2 c.323G>A r.(323g>a) p.(Cys108Ser) Unknown Unknown (disease-associated) Positive 2
Variant info Patients:1 exon 2 c.323G>C r.(323g>c) p.(Cys108Ser) Potentially less severe Unknown (disease-associated) Positive 1
Variant info Patients:0 exon 2 c.324T>C r.324u>c p.(=) Non-pathogenic Unknown Positive 0
Variant info Patients:2 exon 2 c.340_341insT r.(340_341insu) p.(Lys114Ilefs*32) Very severe Classic infantile Negative 2
Variant info Patients:2 exon 2 c.343C>T r.(343c>u) p.(Gln115*) Very severe Childhood or Adult Negative 2
Variant info Patients:1 exon 2 c.352C>T r.(352c>u) p.(Gln118*) Very severe Unknown (disease-associated) Negative 1
Variant info Patients:0 exon 2 c.363G>A r.(363g>a) p.(=) Non-pathogenic Unknown Positive 0
Variant info Patients:4 exon 2 c.364A>G r.(364a>g) p.(Met122Val) Less severe Unknown (disease-associated) Unknown 4
Variant info Patients:0 exon 2 c.365del r.(365del) p.(Met122Argfs*20) very severe Unknown (disease-associated) Negative 0
Variant info Patients:1 exon 2 c.365T>A r.(365u>a) p.(Met122Lys) unknown Unknown (found only in NBS) Positive 1
Variant info Patients:9 exon 2 c.377G>A r.(377g>a) p.(Trp126*) Very severe Classic infantile Negative 9
Variant info Patients:1 exon 2 c.378G>A r.(378g>a) p.(Trp126*) Very severe Classic infantile Negative 1
Variant info Patients:11 exon 2 c.379_380del r.(379_380del) p.(Cys127Leufs*18) Very severe Classic infantile Negative 11
Variant info Patients:1 exon 2 c.380G>A r.(380g>a) p.(Cys127Tyr) Potentially less severe Unknown (disease-associated) Unknown 1
Variant info Patients:1 exon 2 c.380G>T r.(380g>u) p.(Cys127Phe) Potentially less severe Unknown (disease-associated) Positive 1
Variant info Patients:1 exon 2 c.397T>G r.(397u>g) p.(Tyr133Asp) potentially less severe Unknown (disease-associated) Positive 1
Variant info Patients:1 exon 2 c.399C>A r.(399c>a) p.(Tyr133*) Very severe Classic infantile Negative 1
Variant info Patients:1 exon 2 c.421C>A r.(421c>a) p.(Leu141Met) Potentially less severe Classic infantile Positive 1
Variant info Patients:3 exon 2 c.424_440del r.(424_440del) p.(Ser142Lleufs*29) Very severe Unknown (found only in NBS) Negative 3
Variant info Patients:2 exon 2 c.437del r.(437del) p.(Met146Argfs*7) very severe Classic infantile Negative 2
Variant info Patients:1 exon 2 c.444C>G r.(444c>g) p.(Tyr148*) Very severe Unknown (disease-associated) Negative 1
Variant info Patients:1 exon 2 c.445A>C r.(445a>c) p.(Thr149Pro) Potentially less severe Unknown (disease-associated) Positive 1
Variant info Patients:0 exon 2 c.447G>A r.(447g>a) p.(=) Non-pathogenic Unknown Positive 0
Variant info Patients:2 exon 2 c.460_465del r.(460_465del) p.(Arg154_Thr155del) Unknown Classic infantile Positive 2
Variant info Patients:1 exon 2 c.461G>C r.(461g>c) p.(Arg154Pro) Less severe Unknown (disease-associated) Positive 1
Variant info Patients:1 exon 2 c.461_469del r.(461_469del) p.(Arg154_Thr156del) Potentially less severe Unknown (disease-associated) Positive 1
Variant info Patients:5 exon 2 c.482_483del r.(482_483del) p.(Pro161Glnfs*15) Very severe Unknown (disease-associated) Negative 5
Variant info Patients:2 exon 2 c.483dup r.(483dup) p.(Lys162Glnfs*15) Very severe Classic infantile Negative 2
Variant info Patients:2 exon 2 c.484A>C r.(484a>c) p.(Lys162Gln) Potentially less severe Classic infantile Unknown 2
Variant info Patients:1 exon 2 c.502C>T r.(502c>u) p.(Arg168Trp) Potentially less severe Unknown (disease-associated) Positive 1
Variant info Patients:3 exon 2 c.503G>A r.(503g>a) p.(Arg168Gln) Unknown Childhood Unknown 3
Variant info Patients:2 exon 2 c.503G>C r.(503g>c) p.(Arg168Pro) Unknown Childhood Positive 2

The Pompe disease GAA variant database represents an effort to collect all known variants in the GAA gene and is maintained and provide by the Pompe center, Erasmus MC.

We kindly ask you to reference one of the following articles if you use this database for research purposes:

de Faria, DOS, in 't Groen, SLM, Bergsma, AJ, et al. Update of the Pompe variant database for the prediction of clinical phenotypes: Novel disease-associated variants, common sequence variants, and results from newborn screening.
Human Mutation. 2021; 42: 119-134. https://doi.org/10.1002/humu.24148

Niño, MY, in 't Groen, SLM, Hoogeveen-Westerveld, M, et al. Extension of the Pompe mutation database by linking disease‐associated variants to clinical severity. Human Mutation. 2019; 40: 1954–1967. https://doi.org/10.1002/humu.23854

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