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Table 2 GALNS gene mutation identified in Gujarati-Indian MPS IVA patients using Sanger sequencing

From: The GALNS p.P77R variant is a probable Gujarati-Indian founder mutation causing Mucopolysaccharidosis IVA syndrome

Patient ID cDNA changea Amino acid changeb Locationc Mutation type Allele frequency (gnomADd) Ethnicity Reference PolyPhen-2 analysis DANN score ACMG-AMP classification
P20 c.121-7C > G - Intron 1 Splice site NA Indian Present study - - Uncertain significance/ likely pathogenic
P4, P19 c.107 T > G p.L36R Exon 1 Missense 0.00003 Southeast Asian- multi-ethnic, European Morrone et al. 2014 [11], Caciotti et al. 2015 [14] 1
Probably damaging
0.9889 Pathogenic
P7 c.116A > G p.D39G Exon 1 Missense NA Indian Present study 0.997
Probably damaging
0.9844 Likely pathogenic
P1-P3, P5, P9, P10, P11e, P12, P14, P17, P18, P21-P23 c.230C > G p.P77R Exon 2 Missense NA Indian, Turkish Tomatsu et al. 1995 [15], Present study 1
Probably damaging
0.9984 Pathogenic
P16 c.235 T > C p.C79R Exon 2 Missense 0.00000807 Indian, Malaysian Bidchol et al. 2014 [12], Leong et al. 2019 [9] 1
Probably damaging
0.9974 Pathogenic
P15e c.374C > T p.P125L Exon 4 Missense 0.00000399 Chinese Zhao et al. 2011 [16] 1
Probably damaging
0.9247 Pathogenic
P8 c.452C > T p.P151L Exon 5 Missense 0.0000279 Indian Bidchol et al. 2014 [12] 1
Probably damaging
0.9986 Pathogenic
P11e c.764G > C p.G255A Exon 8 Missense NA Indian Present study 1
Probably damaging
0.9979 Likely pathogenic
P15e c.839_841delACA p.N280del Exon 8 Deletion NA Indian Present study - - Likely pathogenic
P13 c.1049 T > C p.L350P Exon 10 Missense NA Indian Present study 1
Probably damaging
0.9989 Likely pathogenic
P6 c.1241_1242insA p.I416Hfse2 Exon 11 Frame shift NA Indian Present study - - Pathogenic
  1. NA Not available, DANN Deep learning approach to annotating variants
  2. acDNA numbering is based on RefSeq transcript NM_000512.5
  3. bAmino acid change is based on NP_00503.1
  4. cGenomic position is based on hg19/GCRh37 genome build
  5. dgnomAD allele frequency is based on version 2.1
  6. ePatient was heterozygous for the said variant