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Table 1 Features of variants identified in this study

From: Clinical features and genetic spectrum in Chinese patients with recessive hereditary spastic paraplegia

Gene dbSNP ID Exon Nucleotide change Amino acid change Mutation type Predicted Impact 1000 Genomes ExAc GnomAD Family Segregation Final Classificationb
SPG11 rs312262720 4 c.733_734delATa p.M245 fsa Deletion NA/NA/NA absent 0.0001 6.133E-5 yes Pathogenic
SPG11 rs312262751 16 c.2849dupTa p.L950 fsa Insertion NA/NA/NA absent absent 4.07e-6 yes Pathogenic
SPG11 rs749652788 31 c.5934_5935insTAACCTGGAA p.V1979_L1980delinsX Insertion NA/NA/NA absent 8.26E-6 4.069E-6 yes Pathogenic
SPG11 NA 39 c.7028_7029delTT p.F2343 fs Deletion NA/NA/NA absent absent absent yes Pathogenic
CYP7B1 rs200737038 3 c.334C > Ta p.R112Xa Nonsense NA/NA/A 0.0002 0.0002 0.0001422 yes Pathogenic
ALDH18A1 NA 7 c.725G > A p.S242 N Missense T/P/D absent absent absent NA Pathogenic
GBA2 NA 11 c.1789delG p.D597fs Deletion NA/NA/D absent absent absent yes Pathogenic
AP5Z1 rs182694738 2 c.164C > T p.T55 M Missense D/D/D 0.0004 0.0001 0.0001733 NA Likely Pathogenic
AP5Z1 rs1035120004 7 c.923G > C p.S308 T Missense T/D/D absent absent absent NA Likely Pathogenic
CAPN1 NA 6 c.759 + 1G > Aa splicing NA/NA/D absent absent 4.189e-6 yes Pathogenic
ATP13A2 NA 15 c.1456C > T p.Q486X Nonsense NA/NA/A absent absent absent yes Pathogenic
  1. The impact of non-synonymous protein-coding region variants were determined using prediction software including SIFT, PolyPhen-2 and Mutation Taste. SIFT results as Tolerated (T) or Deleterious (D). PolyPhen-2 results as Unknown (UN), Benign (B), Possibly Damaging (P) or Probably Damaging (D). Mutation Taste results as Tolerated (T), Disease causing (D) and Disease causing automatic (A). 1000G, 1000 Genomes Project; ExAC, Exome Aggregation Consortium; a, Reported previously; b, Variants were finally classified with the functional data according to ACMG guidelines. NA Not available