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Table 4 Family-specific variants identified in mother and two affected children and variant annotations from ANNOVAR

From: Whole-exome sequencing of a pedigree segregating asthma

     Functional prediction program
Gene Amino acid change1 Chr2         Pos3 SIFT4 PolyPhen25 PhyloP6 Mutation taster7 LRT8
PDE4DIP I303L 1 144930802 0.47 0.45 0.75 1.00* 0.95*
FCRL6 R123Q 1 159778799 0.14 0.28 0.02 0.01 0.00
AIM2 N194D 1 159035936 0.00 0.99* 0.16 0.08 0.69
ZBTB37 M396V 1 173854936 0.00 -- -- -- --
IER5 E103K 1 181058345 0.07 0.07 0.94 0.02 0.91
CBLB D454A 3 105438937 0.37 0.78 0.99* 0.99* 0.99*
CCDC80 S95L 3 112358469 0.13 0.03 6.2E-4 0.04 6.0E-6
KALRN L1644F 3 124281690 0.00 0.83 0.99* 0.72 0.99*
GALNTL6 I160V 4 173269765 1.00* 0.00 0.99* 0.00 0.84
COMMD5 R38Q 8 146076611 0.47 0.03 0.10 0.06 0.94
  1. 1Amino acid changes are represented as the wild type amino acid, position of the amino acid in the polypeptide chain followed by the amino acid resulting from the mutation. All amino acids are represented by the single letter amino acid code.
  2. 2Chr = Chromosome.
  3. 3Pos = chromosome position.
  4. 4SIFT, prediction of a change being damaging (>0.95) or tolerated. Values >0.95 are marked with an asterisk. For all five functional prediction programs, missing values (−−) were not provided by ANNOVAR.
  5. 5PolyPhen2, prediction of a change being damaging (>0.85), possibly damaging (0.15-0.85) or benign (<0.15). Values >0.85 are marked with an asterisk.
  6. 6Phylop, prediction of a conserved (>0.95) or non-conserved site (<0.95) sites across species. Values >0.95 are marked with an asterisk.
  7. 7Mutation Taster, prediction of a disease-causing variant (1 – p-value). Values >0.95 are marked with an asterisk.
  8. 8LRT, likelihood ratio test for codon constraint. Values >0.95 are marked with an asterisk.