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Table 2 Genotypes and Clinical Phenotypes Carrying the Mutations of VPS50

From: The rare mutation in the endosome-associated recycling protein gene VPS50 is associated with human neural tube defects

Nucleotide changea Amino acid changeb Case no. Control no. SIFTc PolyPhen2d Sex Age (weeks) NTD type MAF in cohort MAF in CHB
c.G506 T p. Gly169Val 1 0 0.04 1 F 12 anencephalus 0.001845 not reported
c.A1104T p. Glu368Asp 1 1 0.25 0.003 F 24 anencephalus 0.00369 0.0049
  1. aFor nucleotide numbering, + 1 corresponds to the A of ATG of mRNA sequence 2. NM_017667.3
  2. bReference protein sequence NP_060137.2
  3. cThe threshold for intolerance is 0.05 and ranges from 0 to 1. The amino-acid substitution was predicted to be damaging if the score was <=0.05 and tolerated if the score was > 0.05
  4. dThe score is from 0 to 1; the amino-acid substitution was appraised qualitatively as benign or damaging based on pairs of false positive rate thresholds and optimized separately for each model