Unique variants in gene GAA

Information The variants shown are described using the NM_000152.3 transcript reference sequence.

755 entries on 8 pages. Showing entries 1 - 100.
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Effect     

Reported     

Exon     

AscendingDNA change (cDNA)     

RNA change     

Protein     

Enzyme activity     

Classification method     

Clinical classification     

DNA change (genomic) (hg19)     

DNA change (hg38)     

Published as     

ISCN     

DB-ID     

Variant remarks     

Reference     

ClinVar ID     

dbSNP ID     

Origin     

Segregation     

Frequency     

Re-site     

VIP     

Methylation     

Owner     
+/. 6 17i_18i c.(2481+1_2482-1)_(2646+1_2647-1)del r.? p.? - - pathogenic (recessive) g.(78091549_78091991)_(78092157_78092451)del g.(80117750_80118192)_(80118358_80118652)del del ex18 - MYH2_000008 - PubMed: Vanherpe 2020 - - Germline - - - - - Johan den Dunnen
+/. 1 _1_20_ c.? r.0 p.0 - - pathogenic (recessive) g.? - - - GAA_000000 second allele expressing no GAA mRNA PubMed: Zhong 1991 - - Germline - - - - - Arnold Reuser
-/. 2 - c.-4670T>C r.(?) - - - benign g.78071052T>C g.80097253T>C CCDC40(NM_017950.3):c.3030T>C (p.D1010=) - CCDC40_000091 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Groningen, VKGL-NL_Rotterdam
-?/. 1 - c.-4654G>A r.(?) p.(=) - - likely benign g.78071068G>A g.80097269G>A CCDC40(NM_017950.3):c.3046G>A (p.(Val1016Ile)) - CCDC40_000092 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Leiden
+/. 1 - c.-4571del r.(?) - - - pathogenic g.78071151del g.80097352del - - CCDC40_000166 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Nijmegen
-/. 2 - c.-2367A>G r.(?) - - - benign g.78073355A>G g.80099556A>G CCDC40(NM_017950.3):c.3210A>G (p.T1070=) - CCDC40_000093 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Rotterdam, VKGL-NL_Groningen
?/. 1 - c.-2237G>A r.(?) p.(=) - - VUS g.78073485G>A g.80099686G>A CCDC40(NM_017950.3):c.3340G>A (p.V1114M) - CCDC40_000094 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Rotterdam
?/. 1 - c.-2222C>T r.(?) p.(=) - - VUS g.78073500C>T g.80099701C>T CCDC40(NM_017950.3):c.3355C>T (p.(Pro1119Ser)) - CCDC40_000097 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Leiden
-/. 2 - c.-2160A>G r.(?) - - - benign g.78073562A>G g.80099763A>G CCDC40(NM_017950.3):c.3417A>G (p.P1139=) - CCDC40_000099 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Rotterdam, VKGL-NL_Groningen
-/. 2 - c.-2133T>C r.(?) p.(=) - - benign g.78073589T>C g.80099790T>C CCDC40(NM_017950.3):c.*15T>C - CCDC40_000101 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Groningen, VKGL-NL_Rotterdam
-/., ?/. 3 1 c.-82G>C r.(?) p.(=), p.(?) - ACMG benign, VUS g.78075640G>C g.80101841G>C - - GAA_000001 in 5'UTR, no 2nd variant reported, no patient data reported, 1 more item PubMed: Martiniuk 1990, Pompe disease database 567 - - Germline, SUMMARY record - MAF not reported - - - Arnold Reuser, Pim Pijnappel
+/., +?/., ?/. 328 1i c.-32-13T>G r.spl, r.(=), r.[=, -32_546del, -32_486del], r.(?) p.(=), p.[=, 0] - ACMG pathogenic (recessive), pathogenic, likely pathogenic, VUS g.78078341T>G g.80104542T>G GAA(NM_000152.3):c.-32-13T>G, GAA(NM_001079803.1):c.-32-13T>G (p.(=)) - GAA_000029 8 heterozygous, no homozygous; Clinindb (India), no second variant, leaky splice site, 11 more items PubMed: Laforet 2000, PubMed: Joshi 2008, PubMed: Montalvo 2006, PubMed: Oba-Shinjo 2009, 70 more items - rs386834236 Germline, CLASSIFICATION record, SUMMARY record - 8/2793 individuals, MAF <0.01 - - - Pim Pijnappel, Mohammed Faruq, Madhuri Hegde, VKGL-NL_Rotterdam, VKGL-NL_AMC, VKGL-NL_Leiden, VKGL-NL_Utrecht, Marianne Hoogeveen-Westerveld, Gabriel Torrealba Acosta, Arnold Reuser, Johan den Dunnen, Miguel Angel Alcántara-Ortigoza, VKGL-NL_Nijmegen, Gerard C.P. Schaafsma, Andreas Laner, Helen Latsoudis
+/. 10 1i c.-32-3C>A r.spl?, r.[-32_486del, -32_546del] p.?, p.0? - ACMG pathogenic (recessive), pathogenic, NA g.78078351C>A g.80104552C>A IVS1-3C>A - GAA_000204 functional analysis using expression cloning in minigene splicing assay, 1 more item PubMed: Oba-Shinjo 2009, PubMed: Grzesiuk 2010, PubMed: Turaca 2015, Pompe disease database 570, 3 more items - - Germline, SUMMARY record, In vitro (cloned) - MAF not reported - - - Pim Pijnappel, Andrea Elena Dardis
+?/., +/. 3 1i c.-32-3C>G r.spl?, r.[-32_486del, -32_546del] p.?, p.0? - ACMG likely pathogenic, NA g.78078351C>G g.80104552C>G - - GAA_000491 functional analysis using expression cloning in minigene splicing assay, 1 more item Pompe disease database 569, PubMed: Bergsma 2015, Dardis 2019, submitted - - SUMMARY record, Germline, In vitro (cloned) - MAF not reported - - - Pim Pijnappel, Andrea Elena Dardis
+/. 3 1i c.-32-2A>G r.spl, r.[-32_486del, -32_546del] p.?, p.0? - ACMG pathogenic, pathogenic (recessive), NA g.78078352A>G g.80104553A>G - - GAA_000354 functional analysis using expression cloning in minigene splicing assay, 1 more item Pompe disease database 571, PubMed: Nino 2013, Dardis 2019, submitted - - SUMMARY record, Germline, In vitro (cloned) - MAF not reported - - - Pim Pijnappel, Andrea Elena Dardis
+/. 2 _1_20_ c.0 r.0 p.0 - ACMG pathogenic, pathogenic (recessive) g.78056048_78094853delinsTGTGGTGGCTCATG g.80082249_80121054delinsTGTGGTGGCTCATG del GAA and part of CCDC40 - GAA_000489 1 more item Pompe disease database 566, PubMed: Aminoso 2013 - - SUMMARY record, Germline - MAF not reported - - - Pim Pijnappel
+/. 1 - c.1-45T>G r.spl p.? - - pathogenic (recessive) g.78078341T>G g.80104542T>G - - GAA_000029 1 more item PubMed: Vanherpe 2020 - - Germline - - - - - Johan den Dunnen
+/. 2 2 c.1A>G r.(?) p.0? no protein on western blot ACMG pathogenic, pathogenic (recessive) g.78078386A>G g.80104587A>G - - GAA_000355 1 more item Pompe disease database 573, PubMed: Bali 2012 - - SUMMARY record, Germline - MAF not reported - - - Pim Pijnappel
+/. 3 2 c.1A>T r.(?), r.[1a>u, -32_486del, -32_546del] p.0? gives 0% residual activity in expression study ACMG pathogenic, NA, pathogenic (recessive) g.78078386A>T g.80104587A>T - - GAA_000284 functional analysis using expression cloning in minigene splicing assay, 2 more items Pompe disease database 572, Dardis 2019, submitted - - SUMMARY record, In vitro (cloned), Germline - MAF not reported - - - Pim Pijnappel, Andrea Elena Dardis
+?/., +/. 3 2 c.2T>C r.(?), r.2u>c p.0? gives 0% residual activity in expression study ACMG likely pathogenic, NA g.78078387T>C g.80104588T>C - - GAA_000356 Asian pseudodeficiency allele, functional analysis using expression cloning in minigene splicing assay, 1 more item PubMed: Yang 2011, Pompe disease database 574, Dardis 2019, submitted - - Germline, SUMMARY record, In vitro (cloned) - MAF not reported - - - Pim Pijnappel, Andrea Elena Dardis
+/. 2 2 c.3G>A r.(?) p.0? - ACMG pathogenic (recessive), pathogenic g.78078388G>A g.80104589G>A - - GAA_000357 1 more item PubMed: Bali 2012, Pompe disease database 575 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel
?/. 1 2 c.5G>C r.(?) p.(Gly2Ala) - - VUS g.78078390G>C g.80104591G>C - - GAA_000362 no second variant PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
?/. 1 2 c.11G>A r.(?) p.(Arg4Lys) - - VUS g.78078396G>A g.80104597G>A - - GAA_000363 no second variant PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
?/. 1 2 c.17C>T r.(?) p.(Pro6Leu) - - VUS g.78078402C>T g.80104603C>T - - GAA_000364 no second variant PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
+/. 2 2 c.18_25del r.(?) p.(Cys8Profs*24) - ACMG pathogenic, pathogenic (recessive) g.78078403_78078410del g.80104604_80104611del - - GAA_000358 1 more item Pompe disease database 576, PubMed: Oba-Shinjo 2009 - - SUMMARY record, Germline - MAF not reported - - - Pim Pijnappel
+/. 2 2 c.25del r.(?) p.(Ser9Profs*34) - ACMG pathogenic (recessive), pathogenic g.78078410del g.80104611del - - GAA_000359 1 more item PubMed: Nascimbeni 2008, Pompe disease database 577 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel
?/., -?/., +/. 5 2 c.32G>A r.(?), r.[32g>a, -32_486del, -32_546del] p.(Arg11Gln), p.[Arg11Gln, 0?] gives 115% residual activity in expression study ACMG VUS, likely benign, NA g.78078417G>A g.80104618G>A - - GAA_000365 functional analysis using expression cloning in minigene splicing assay, 1 more item PubMed: Nallamilli 2018, Pompe disease database 1075, Dardis 2019, submitted - - Germline, SUMMARY record, In vitro (cloned) - MAF <0.01 - - - Madhuri Hegde, Pim Pijnappel, Andrea Elena Dardis
?/., +/. 3 2 c.54C>T r.(?), r.[54c>u, -32_486del, -32_546del] p.(=), p.[Leu18=, 0?] - ACMG VUS, NA g.78078439C>T g.80104640C>T - - GAA_000492 functional analysis using expression cloning in minigene splicing assay, 1 more item Pompe disease database 1076, Dardis 2019, submitted - - Germline, SUMMARY record, In vitro (cloned) - MAF not reported - - - Pim Pijnappel, Andrea Elena Dardis
?/. 1 2 c.70G>A r.(?) p.(Ala24Thr) - - VUS g.78078455G>A g.80104656G>A - - GAA_000366 - PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
?/. 1 2 c.74C>T r.(?) p.(Ala25Val) - - VUS g.78078459C>T g.80104660C>T - - GAA_000367 no second variant PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
?/. 1 2 c.83G>T r.(?) p.(Gly28Val) - - VUS g.78078468G>T g.80104669G>T - - GAA_000368 no second variant PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
+/. 9 2 c.118C>T r.(?) p.(Arg40*) 0.30 ACMG pathogenic (recessive), pathogenic g.78078503C>T g.80104704C>T - - GAA_000056 GAA activity allele in parent fibroblasts 0.30 (combined 0.08), 1 more item PubMed: Kroos 1997, PubMed: McCready 2007, Pompe disease database 578, PubMed: Laforet 2000, 4 more items - rs767409395 Germline, SUMMARY record - MAF <0.01 - - - Pim Pijnappel, Marianne Hoogeveen-Westerveld, Arnold Reuser, Johan den Dunnen
?/. 1 - c.134C>T r.(?) p.(Ser45Phe) - - VUS g.78078519C>T g.80104720C>T - - CCDC40_000176 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Nijmegen
?/. 2 2 c.136T>C r.(?) p.(Ser46Pro) gives 100% residual activity in expression study ACMG VUS g.78078521T>C g.80104722T>C - - GAA_000056 1 more item Pompe disease database 579, PubMed: Oba-Shinjo 2009 - rs777215354 SUMMARY record, Germline - MAF <0.01 - - - Pim Pijnappel
+/. 3 2_4i c.148_859-11del r.spl? p.(Glu50_Profs*27) no protein on western blot ACMG pathogenic (recessive), pathogenic g.78078533_78081588del g.80104734_80107789del - - GAA_000446 Asian pseudodeficiency allele, 1 more item PubMed: McCready 2007, Pompe disease database 580, PubMed: Kishnani 2006 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel
+/. 3 2 c.172C>T r.(?) p.(Gln58*) - ACMG pathogenic (recessive), pathogenic g.78078557C>T g.80104758C>T - - GAA_000076 1 more item PubMed: Huie 1999, Pompe disease database 581 - rs201185475 Germline, SUMMARY record - MAF <0.01 - - - Pim Pijnappel, Arnold Reuser
+/., ?/. 4 2 c.186_196dup r.(?) p.(Arg66HisfsTer80), p.(Arg66Hisfs*80) - ACMG pathogenic, VUS, pathogenic (recessive) g.78078571_78078581dup g.80104772_80104782dup GAA(NM_000152.3):c.186_196dupACCAGGGCCCC (p.R66Hfs*80), 186dup11 - GAA_000447 VKGL data sharing initiative Nederland, no 2nd variant reported, no patient data reported, 1 more item Pompe disease database 582, PubMed: Vanherpe 2020 - - CLASSIFICATION record, SUMMARY record, Germline - MAF not reported - - - VKGL-NL_Rotterdam, Pim Pijnappel, Johan den Dunnen
?/. 3 2 c.199G>A r.(?), r.199g>a p.(Asp67Asn), p.Arg67Asn - ACMG VUS, NA g.78078584G>A g.80104785G>A - - GAA_000493 functional analysis using expression cloning in minigene splicing assay, 1 more item Pompe disease database 1077, Dardis 2019, submitted - - Germline, SUMMARY record, In vitro (cloned) - MAF not reported - - - Pim Pijnappel, Andrea Elena Dardis
?/. 1 2 c.212A>G r.(?) p.(His71Arg) - - VUS g.78078597A>G g.80104798A>G - - GAA_000369 - PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
-/., -?/. 3 2 c.221G>A r.(?) p.(Arg74His) gives 103% residual activity in expression study ACMG benign, likely benign g.78078606G>A g.80104807G>A GAA(NM_000152.3):c.221G>A (p.R74H) - GAA_000250 VKGL data sharing initiative Nederland, 1 more item Pompe disease database 1078 - - CLASSIFICATION record, Germline, SUMMARY record - MAF not reported - - - VKGL-NL_Rotterdam, Pim Pijnappel
+/. 4 2 c.236_246del r.(?) p.(Pro79Argfs*13) no protein on western blot ACMG pathogenic (recessive), pathogenic g.78078621_78078631del g.80104822_80104832del - - GAA_000240 1 more item PubMed: Palmer 2007, Pompe disease database 583, PubMed: Banugaria 2013, PubMed: Oba-Shinjo 2009 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel, Marianne Hoogeveen-Westerveld
+/. 3 2 c.241C>T r.(?), r.[241g>u, -32_486del, -32_546del] p.(Gln81*), p.[Gln81*, 0?] - ACMG pathogenic (recessive), pathogenic, NA g.78078626C>T g.80104827C>T - - GAA_000448 functional analysis using expression cloning in minigene splicing assay, 1 more item PubMed: Liu 2014, Pompe disease database 584, Dardis 2019, submitted - - Germline, SUMMARY record, In vitro (cloned) - MAF not reported - - - Pim Pijnappel, Andrea Elena Dardis
?/. 2 2 c.247G>A r.(?) p.(Asp83Asn) - - VUS g.78078632G>A g.80104833G>A - - GAA_000370 no second variant PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
+/. 14 2 c.258dup r.(?) p.(Asn87Glnfs*9), p.(Asn87GlnfsTer9) - ACMG pathogenic (recessive), pathogenic g.78078643dup g.80104844dup GAA(NM_000152.3):c.258dupC (p.N87Qfs*9), 258dupC - GAA_000060 VKGL data sharing initiative Nederland, no second variant, 1 more item PubMed: Montalvo 2006, PubMed: Nallamilli 2018, PubMed: Bali 2011, Pompe disease database 585, 2 more items - rs886042496 Germline, CLASSIFICATION record, SUMMARY record - MAF <0.01 - - - Pim Pijnappel, VKGL-NL_AMC, Madhuri Hegde, VKGL-NL_Rotterdam, Marianne Hoogeveen-Westerveld, Arnold Reuser, Johan den Dunnen
-?/. 1 - c.265C>T r.(?) p.(Arg89Cys) - - likely benign g.78078650C>T g.80104851C>T - - CCDC40_000177 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Nijmegen
?/. 5 2 c.266G>A r.(?) p.(Arg89His) gives 43.5% residual activity in expression study ACMG VUS g.78078651G>A g.80104852G>A GAA(NM_000152.3):c.266G>A (p.R89H) - GAA_000251 no second variant, VKGL data sharing initiative Nederland, no 2nd variant reported, 1 more item PubMed: Nallamilli 2018, Pompe disease database 586, PubMed: Hahn 2015 - rs200586324 Germline, CLASSIFICATION record, SUMMARY record - MAF <0.01 - - - Madhuri Hegde, VKGL-NL_Utrecht, Pim Pijnappel
+/. 4 2 c.271del r.(?) p.(Asp91Ilefs*51) - ACMG pathogenic (recessive), pathogenic g.78078656del g.80104857del - - GAA_000061 1 more item PubMed: Vorgerd 1998, PubMed: Kroos 2006, Pompe disease database 588 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel, Arnold Reuser
+/., -/., -?/., ?/. 64 2 c.271G>A r.(?), r.[271g>a, -32_486del, -32_546del] p.(Asp91Asn), p.[Asp91=, 0?] lowers affinity for glycogen (GAA2) ACMG benign, likely benign, VUS, NA g.78078656G>A g.80104857G>A GAA(NM_000152.3):c.271G>A (p.D91N, p.(Asp91Asn)) - GAA_000003 no second variant, 34 heterozygous, no homozygous; Clinindb (India), variant basis of GAA*2 allozyme, 3 more items PubMed: Nallamilli 2018, Faruq 2020, submtted, PubMed: Hermans 1998, Pompe disease database 587, 2 more items - rs1800299 Germline, CLASSIFICATION record, SUMMARY record, In vitro (cloned) - 34/2795 individuals, MAF >0.01 TaqI- - - Madhuri Hegde, Mohammed Faruq, Pim Pijnappel, VKGL-NL_Nijmegen, VKGL-NL_Utrecht, Johan den Dunnen, VKGL-NL_Rotterdam, VKGL-NL_Leiden, Arnold Reuser, Gerard C.P. Schaafsma, Andrea Elena Dardis
?/. 1 2 c.271_272delinsAG r.(?) p.(Asp91Ser) - - VUS g.78078656_78078657delinsAG g.80104857_80104858delinsAG 271_272delGAinsAG - GAA_000371 - PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
?/. 1 2 c.280C>A r.(?) p.(Pro94Thr) - - VUS g.78078665C>A g.80104866C>A - - GAA_000372 - PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
?/., +/. 3 2 c.307T>C r.(?), r.[307u>c, –32_486del, -32_546del] p.(Cys103Arg), p.[Cys103Arg, 0?] 0% residual activity, affects secretion & processing in expression study ACMG VUS, NA g.78078692T>C g.80104893T>C - - GAA_000449 no 2nd variant reported, no patient data reported, 2 more items Pompe disease database 589, Dardis 2019, submitted - - Germline, SUMMARY record, In vitro (cloned) - MAF not reported - - - Pim Pijnappel, Andrea Elena Dardis
+?/., +/., ?/. 10 2 c.307T>G r.(?), r.307u>g p.(Cys103Gly), p.Cys103Gly gives 1,5% (4MU) and 0% (glycogen) residual activity in expression study ACMG likely pathogenic, pathogenic, pathogenic (recessive), NA g.78078692T>G g.80104893T>G GAA(NM_000152.3):c.307T>G (p.C103G) - GAA_000119 VKGL data sharing initiative Nederland, 2 more items PubMed: Schneider 2013, PubMed: Joshi 2008, PubMed: Pittis 2008, PubMed: Muller-Felber 2007, 4 more items - - Germline, SUMMARY record, CLASSIFICATION record, In vitro (cloned) - MAF not reported - - - Pim Pijnappel, Marianne Hoogeveen-Westerveld, VKGL-NL_Rotterdam, Arnold Reuser, Andrea Elena Dardis
+/. 3 2 c.309C>A r.(?) p.(Cys103*) - ACMG pathogenic (recessive), pathogenic g.78078694C>A g.80104895C>A - - GAA_000120 1 more item PubMed: Hermans 2004, Pompe disease database 591 - - Germline, SUMMARY record - MAF not reported - - - Arnold Reuser, Pim Pijnappel
?/. 1 2 c.310G>A r.(?) p.(Glu104Lys) - - VUS g.78078695G>A g.80104896G>A - - GAA_000373 no second variant PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
?/. 2 2 c.322T>G r.(?) p.(Cys108Gly) 8.2% residual activity, affects secretion & processing in expression study ACMG VUS g.78078707T>G g.80104908T>G - - GAA_000450 no 2nd variant reported, no patient data reported, 1 more item Pompe disease database 592 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel
?/. 3 2 c.323G>A r.323g>a, r.(?) p.Cys108Ser, p.(Cys108Ser) - ACMG NA, VUS g.78078708G>A g.80104909G>A - - GAA_000451 functional analysis using expression cloning in minigene splicing assay, 1 more item Dardis 2019, submitted, PubMed: Liu 2014, Pompe disease database 593 - - In vitro (cloned), Germline, SUMMARY record - MAF not reported - - - Andrea Elena Dardis, Pim Pijnappel
-/. 7 2 c.324T>C r.(?) p.(=), p.(Cys108=) - ACMG benign g.78078709T>C g.80104910T>C GAA(NM_000152.3):c.324T>C (p.C108=), 324C>T - GAA_000002 VKGL data sharing initiative Nederland, 1 more item Pompe disease database 594, PubMed: Martiniuk 1990, PubMed: Hoefsloot 1990 - rs1800300 Germline, CLASSIFICATION record, SUMMARY record - MAF >0.05 - - - Pim Pijnappel, VKGL-NL_Nijmegen, Marianne Hoogeveen-Westerveld, VKGL-NL_Utrecht, VKGL-NL_Groningen, Arnold Reuser
+/. 5 2 c.340_341insT r.(?) p.(Lys114Ilefs*32), p.(Lys114IlefsTer32) no protein on western blot ACMG pathogenic, pathogenic (recessive) g.78078725_78078726insT g.80104926_80104927insT 340insT, GAA(NM_000152.3):c.340_341insT (p.K114Ifs*32), 341insT - GAA_000121 VKGL data sharing initiative Nederland, 1 more item Pompe disease database 1124, PubMed: Hermans 2004, PubMed: Messinger 2012 - - SUMMARY record, CLASSIFICATION record, Germline - MAF not reported - - - Pim Pijnappel, VKGL-NL_Rotterdam, Arnold Reuser
+/. 5 2 c.343C>T r.[343c>u, -32_486del, -32_546del], r.(?) p.[Gln115*, 0?], p.(Gln115*), p.(Gln115Ter) - ACMG NA, pathogenic (recessive), pathogenic g.78078728C>T g.80104929C>T GAA(NM_000152.3):c.343C>T (p.Q115*) - GAA_000254 functional analysis using expression cloning in minigene splicing assay, 2 more items Dardis 2019, submitted, PubMed: Gort 2007, Pompe disease database 596 - - In vitro (cloned), Germline, CLASSIFICATION record, SUMMARY record - MAF not reported - - - Andrea Elena Dardis, Pim Pijnappel, VKGL-NL_Rotterdam
+/. 2 2 c.352C>T r.(?) p.(Gln118*) no protein on western blot ACMG pathogenic, pathogenic (recessive) g.78078737C>T g.80104938C>T - - GAA_000452 no 2nd variant reported, 1 more item Pompe disease database 597, PubMed: Bali 2012 - - SUMMARY record, Germline - MAF not reported - - - Pim Pijnappel
?/. 1 2 c.362A>G r.(?) p.(Gln121Arg) - - VUS g.78078747A>G g.80104948A>G - - GAA_000374 - PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
-/., ?/. 3 2 c.363G>A r.363g>a, r.(?) p.Gln12=, p.(=) - ACMG NA, VUS g.78078748G>A g.80104949G>A - - GAA_000494 functional analysis using expression cloning in minigene splicing assay, 1 more item Dardis 2019, submitted, Pompe disease database 1079 - - In vitro (cloned), Germline, SUMMARY record - MAF not reported - - - Andrea Elena Dardis, Pim Pijnappel
?/., -/. 3 2 c.364A>G r.(?) p.(Met122Val) - ACMG VUS, benign g.78078749A>G g.80104950A>G GAA(NM_000152.3):c.364A>G (p.M122V) - GAA_000255 VKGL data sharing initiative Nederland, 1 more item PubMed: Rozdzynska-Swiatkowska 2016, Pompe disease database 598 - - Germline, SUMMARY record, CLASSIFICATION record - MAF not reported - - - Pim Pijnappel, VKGL-NL_Rotterdam
+/. 7 2 c.377G>A r.(?) p.(Trp126*) - ACMG pathogenic (recessive), pathogenic g.78078762G>A g.80104963G>A - - GAA_000242 1 more item PubMed: Palmer 2007, PubMed: Turaca 2015, PubMed: Oba-Shinjo 2009, Pompe disease database 599 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel, Marianne Hoogeveen-Westerveld
+/. 2 2 c.378G>A r.(?) p.(Trp126*) - ACMG pathogenic (recessive), pathogenic g.78078763G>A g.80104964G>A - - GAA_000453 1 more item PubMed: Fu 2014, Pompe disease database 600 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel
+/. 5 2 c.379_380del r.(?) p.(Cys127Leufs*18), p.(Cys127LeufsTer18) no protein on western blot ACMG pathogenic (recessive), pathogenic g.78078764_78078765del g.80104965_80104966del GAA(NM_000152.3):c.379_380delTG (p.C127Lfs*18) - GAA_000062 VKGL data sharing initiative Nederland, 1 more item PubMed: Muller-Felber 2007, PubMed: Kroos 1998, Pompe disease database 601, PubMed: Kroos 1998 - - Germline, SUMMARY record, CLASSIFICATION record - MAF not reported - - - Pim Pijnappel, Marianne Hoogeveen-Westerveld, VKGL-NL_Rotterdam, Arnold Reuser
?/., +/. 3 2 c.380G>T r.(?) p.(Cys127Phe) 1.5% residual activity, affects secretion & processing in expression study ACMG VUS, pathogenic g.78078765G>T g.80104966G>T GAA(NM_000152.3):c.380G>T (p.C127F) - GAA_000256 VKGL data sharing initiative Nederland, 1 more item PubMed: Loureiro Neves 2013, Pompe disease database 602 - - Germline, CLASSIFICATION record, SUMMARY record - MAF not reported - - - Pim Pijnappel, VKGL-NL_Rotterdam
?/. 1 - c.384C>G r.(?) p.(Phe128Leu) - - VUS g.78078769C>G g.80104970C>G GAA(NM_000152.3):c.384C>G (p.(Phe128Leu)) - GAA_000257 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Leiden
+/. 3 2 c.399C>A r.(?) p.(Tyr133*) - ACMG pathogenic (recessive), pathogenic g.78078784C>A g.80104985C>A - - GAA_000124 1 more item PubMed: Montalvo 2004, Pompe disease database 603 - - Germline, SUMMARY record - MAF not reported - - - Arnold Reuser, Pim Pijnappel
?/. 2 2 c.412C>G r.(?) p.(Leu138Val) - - VUS g.78078797C>G g.80104998C>G - - GAA_000375 no second variant PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
?/., -?/. 2 2 c.420C>A r.(?) p.(Asn140Lys) - - VUS, likely benign g.78078805C>A g.80105006C>A GAA(NM_000152.3):c.420C>A (p.(Asn140Lys)) - GAA_000376 VKGL data sharing initiative Nederland PubMed: Nallamilli 2018 - - Germline, CLASSIFICATION record - - - - - Madhuri Hegde, VKGL-NL_Leiden
?/. 2 2 c.421C>A r.(?) p.(Leu141Met) - ACMG VUS g.78078806C>A g.80105007C>A - - GAA_000454 1 more item PubMed: Wan 2008, Pompe disease database 604 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel
+/. 3 2 c.424_440del r.(?) p.(Ser142Lleufs*29) - ACMG pathogenic (recessive), pathogenic g.78078809_78078825del g.80105010_80105026del - - GAA_000455 Asian pseudodeficiency allele, 1 more item PubMed: Chien 2011, PubMed: Labrousse 2010, Pompe disease database 605 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel
+/. 2 2 c.444C>G r.(?) p.(Tyr148*) - ACMG pathogenic (recessive), pathogenic g.78078829C>G g.80105030C>G - - GAA_000456 1 more item PubMed: Fu Liong 2014, Pompe disease database 606 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel
-?/., -/. 5 2 c.447G>A r.(?) p.(=), p.(Thr149=) - ACMG likely benign, benign g.78078832G>A g.80105033G>A GAA(NM_000152.3):c.447G>A (p.T149=, p.(=)) - GAA_000457 VKGL data sharing initiative Nederland, 1 more item Pompe disease database 607 - rs2289536 Germline, CLASSIFICATION record, SUMMARY record - MAF >0.01 - - - Pim Pijnappel, VKGL-NL_Rotterdam, VKGL-NL_Leiden, VKGL-NL_Utrecht
?/. 1 2 c.460C>T r.(?) p.(Arg154Cys) - - VUS g.78078845C>T g.80105046C>T - - GAA_000377 no second variant PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
+?/. 2 2 c.460_465del r.(?) p.(Arg154_Thr155del) - ACMG likely pathogenic g.78078845_78078850del g.80105046_80105051del - - GAA_000458 no 2nd variant reported, 1 more item Pompe disease database 608, PubMed: Bali 2012 - - SUMMARY record, Germline - MAF not reported - - - Pim Pijnappel
?/. 2 2 c.461G>C r.(?) p.(Arg154Pro) - ACMG VUS g.78078846G>C g.80105047G>C - - GAA_000459 1 more item PubMed: Nascimbeni 2008, Pompe disease database 609 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel
+?/. 2 2 c.461_469del r.(?) p.(Arg154_Thr156del) 0.5% residual activity, affects secretion & processing in expression study ACMG likely pathogenic g.78078846_78078854del g.80105047_80105055del - - GAA_000460 1 more item PubMed: van der Beek 2008, Pompe disease database 610 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel
+/. 1 - c.465dup r.(?) p.(Thr156HisfsTer21) - - pathogenic g.78078850dup g.80105051dup GAA(NM_000152.3):c.465dupC (p.T156Hfs*21) - CCDC40_000170 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Rotterdam
+/. 7 2 c.482_483del r.(?) p.(Pro161Glnfs*15) - ACMG pathogenic (recessive), pathogenic g.78078867_78078868del g.80105068_80105069del 482_483delCC - GAA_000055 1 more item PubMed: Nicolino 1997, PubMed: Laforet 2000, PubMed: Orlikowski 2011, Pompe disease database 611, 2 more items - rs764750389 Germline, SUMMARY record - MAF <0.01 - - - Pim Pijnappel, Marianne Hoogeveen-Westerveld, Arnold Reuser, Johan den Dunnen
?/. 2 2 c.483dup r.(?) p.(Lys162Glnfs*15) - ACMG VUS g.78078868dup g.80105069dup - - GAA_000461 no 2nd variant reported, no patient data reported, 1 more item Pompe disease database 612 - - Germline, SUMMARY record - MAF not reported - - - Pim Pijnappel
?/., +?/. 4 2 c.503G>A r.503g>a, r.(?) p.Arg168Gln, p.(Arg168Gln) - ACMG NA, likely pathogenic g.78078888G>A g.80105089G>A - - GAA_000232 functional analysis using expression cloning in minigene splicing assay, 1 more item Dardis 2019, submitted, PubMed: Liu 2014, PubMed: Liu 2013, Pompe disease database 613 - rs376685205 In vitro (cloned), Germline, SUMMARY record - MAF <0.01 - - - Andrea Elena Dardis, Pim Pijnappel, Marianne Hoogeveen-Westerveld
+/., +?/. 4 2 c.503G>C r.[503g>c, -32_486del, -32_546del], r.(?) p.[Arg168Pro, 0?], p.(Arg168Pro) - ACMG NA, likely pathogenic g.78078888G>C g.80105089G>C - - GAA_000462 functional analysis using expression cloning in minigene splicing assay, 1 more item Dardis 2019, submitted, PubMed: Liu 2013, PubMed: Liu 2014, Pompe disease database 614 - - In vitro (cloned), Germline, SUMMARY record - MAF not reported - - - Andrea Elena Dardis, Pim Pijnappel
?/. 3 2 c.506T>C r.506u>c, r.(?) p.Leu169Pro, p.(Leu169Pro) - ACMG NA, VUS g.78078891T>C g.80105092T>C - - GAA_000463 functional analysis using expression cloning in minigene splicing assay, 1 more item Dardis 2019, submitted, PubMed: Gort 2007, Pompe disease database 615 - - In vitro (cloned), Germline, SUMMARY record - MAF not reported - - - Andrea Elena Dardis, Pim Pijnappel
-?/., -/., ?/. 5 2 c.510C>T r.(?) p.(Asp170=), p.(=) - ACMG likely benign, benign, VUS g.78078895C>T g.80105096C>T GAA(NM_000152.3):c.510C>T (p.D170=) - GAA_000122 VKGL data sharing initiative Nederland, 1 more item PubMed: Hermans 2004, PubMed: Nallamilli 2018, Pompe disease database 1080 - - CLASSIFICATION record, Germline, SUMMARY record - MAF <0.01 - - - VKGL-NL_Rotterdam, Arnold Reuser, Pim Pijnappel, Madhuri Hegde
?/. 1 2 c.524C>G r.(?) p.(Thr175Ser) - - VUS g.78078909C>G g.80105110C>G c-524C>G - GAA_000171 - - - - Germline - - - - - Johan den Dunnen
+/., ?/. 53 2 c.525del r.(?), r.525del p.(Glu176Argfs*45), p.(Glu176ArgfsTer45), p.Glu176Argfs*45 no protein on western blot ACMG pathogenic (recessive), pathogenic, VUS g.78078910del g.80105111del 525delT, GAA(NM_000152.3):c.525del (p.(Glu176ArgfsTer45)), GAA(NM_000152.3):c.525delT (p.E176Rfs*45) - GAA_000028 VKGL data sharing initiative Nederland, 2 more items PubMed: Wokke 1995, PubMed: Joshi 2008, PubMed: Alejaldre 2012, PubMed: Nino 2013, PubMed: Kroos 1995, 24 more items - rs386834235 Germline, CLASSIFICATION record, SUMMARY record - MAF <0.01 - - - Pim Pijnappel, Madhuri Hegde, VKGL-NL_Nijmegen, Marianne Hoogeveen-Westerveld, VKGL-NL_Leiden, VKGL-NL_Rotterdam, Arnold Reuser, Gerard C.P. Schaafsma, Johan den Dunnen
+/. 3 2 c.525_526del r.(?) p.(Asn177Profs*11) no protein on western blot ACMG pathogenic, pathogenic (recessive) g.78078910_78078911del g.80105111_80105112del - - GAA_000464 1 more item Pompe disease database 617, PubMed: Banugaria 2013, PubMed: Vill 2015 - rs767882689 SUMMARY record, Germline - MAF <0.01 - - - Pim Pijnappel
-?/. 2 2 c.532C>T r.(?) p.(Arg178Cys) gives 134% residual activity in expression study ACMG likely benign g.78078917C>T g.80105118C>T - - GAA_000495 1 more item Pompe disease database 1081 - - Germline, SUMMARY record - MAF <0.01 - - - Pim Pijnappel
?/. 3 2 c.533G>A r.(?), r.533g>a p.(Arg178His), p.Arg78His - ACMG VUS, NA g.78078918G>A g.80105119G>A - - GAA_000465 Asian pseudodeficiency allele, functional analysis using expression cloning in minigene splicing assay, 1 more item PubMed: Chien 2011, Dardis 2019, submitted, Pompe disease database 618 - rs762267535 Germline, In vitro (cloned), SUMMARY record - MAF <0.01 - - - Pim Pijnappel, Andrea Elena Dardis
?/. 1 - c.538C>A r.(?) p.(His180Asn) - ACMG VUS g.78078923C>A g.80105124C>A - - GAA_000793 - - - - Germline - - - - - Xueying Su
?/. 1 2 c.545C>G r.(?) p.(Thr182Arg) - - VUS g.78078930C>G g.80105131C>G - - GAA_000378 no second variant PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
+/., +?/. 9 2 c.546G>A r.-32_546del, r.(?), r.[spl, 546g>] p.0?, p.(=), p.(=), p.(?), p.(Thr182=), p.[?, Thr182=] - ACMG NA, pathogenic, likely pathogenic, pathogenic (recessive) g.78078931G>A g.80105132G>A GAA(NM_000152.3):c.546G>A (p.T182=) - GAA_000123 functional analysis using expression cloning in minigene splicing assay; complete skipping of exon 2, 4 more items Dardis 2019, submitted, PubMed: Nallamilli 2018, PubMed: Hermans 2004, PubMed: Bali 2011, 1 more item - rs143523371 In vitro (cloned), Germline, CLASSIFICATION record, SUMMARY record - MAF <0.01 - - - Andrea Elena Dardis, Madhuri Hegde, Pim Pijnappel, VKGL-NL_Rotterdam, Arnold Reuser
+/., +?/. 3 2 c.546G>C r.-32_546del, r.(?) p.0?, p.(=), p.(?) - ACMG NA, likely pathogenic g.78078931G>C g.80105132G>C - - GAA_000467 functional analysis using expression cloning in minigene splicing assay; complete skipping of exon 2, 1 more item Dardis 2019, submitted, PubMed: Gort 2007, Pompe disease database 621 - - In vitro (cloned), Germline, SUMMARY record - MAF not reported - - - Andrea Elena Dardis, Pim Pijnappel
+/. 6 2 c.546G>T r.-32_546del, r.(?) p.0?, p.(=), p.(?) - ACMG NA, pathogenic (recessive), pathogenic g.78078931G>T g.80105132G>T - - GAA_000466 functional analysis using expression cloning in minigene splicing assay; complete skipping of exon 2, 1 more item Dardis 2019, submitted, PubMed: Kobayashi 2010, PubMed: Maimaiti 2009, PubMed: Park 2015, 2 more items - - In vitro (cloned), Germline, SUMMARY record - MAF not reported - - - Andrea Elena Dardis, Pim Pijnappel
+/. 3 2, 2i c.546+1G>T r.-32_546del, r.spl p.0?, p.? - ACMG NA, pathogenic (recessive), pathogenic g.78078932G>T g.80105133G>T - - GAA_000468 functional analysis using expression cloning in minigene splicing assay; complete skipping of exon 2, 1 more item Dardis 2019, submitted, PubMed: Nascimbeni 2008, Pompe disease database 622 - - In vitro (cloned), Germline, SUMMARY record - MAF not reported - - - Andrea Elena Dardis, Pim Pijnappel
+/. 3 2i c.546+2T>C r.-32_546del, r.spl p.0?, p.? no protein on western blot ACMG NA, pathogenic, pathogenic (recessive) g.78078933T>C g.80105134T>C - - GAA_000469 functional analysis using expression cloning in minigene splicing assay; complete skipping of exon 2, 1 more item Dardis 2019, submitted, Pompe disease database 623, PubMed: Banugaria 2013 - - In vitro (cloned), SUMMARY record, Germline - MAF not reported - - - Andrea Elena Dardis, Pim Pijnappel
+/. 3 2i c.546+2_546+5del r.-32_546del, r.spl p.0?, p.? no protein on western blot ACMG NA, pathogenic (recessive), pathogenic g.78078933_78078936del g.80105134_80105137del - - GAA_000470 functional analysis using expression cloning in minigene splicing assay; complete skipping of exon 2, 1 more item Dardis 2019, submitted, PubMed: Khallaf 2013, Pompe disease database 624 - - In vitro (cloned), Germline, SUMMARY record - MAF not reported - - - Andrea Elena Dardis, Pim Pijnappel
?/. 1 2i c.546+3G>A r.spl? p.? - - VUS g.78078934G>A g.80105135G>A - - GAA_000379 no second variant PubMed: Nallamilli 2018 - - Germline - - - - - Madhuri Hegde
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