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Table 2 Summary of PolyPhen and PANTHER annotations of missense SNPs

From: Mouse SNP Miner: an annotated database of mouse functional single nucleotide polymorphisms

Strains   Functional Predictions Total SNP(%) Genes Affected(%)
C57BL/6J vs. DBA/2J PolyPhen Deleterious 1,755 (19.4%) 954 (26.1%)
   Benign 6,757 (74.5%) 2,343 (64%)
   Unknown 567 (6.3%) 367 (10.1%)
   Total 9,079 3,664
  PANTHER Deleterious 1,285 (14.2%) 632(17.1%)
   non-deleterious 4,678 (51.6%) 1,736 (47%)
   Unknown 3,116 (34.4%) 1,329 (36%)
   Total 9,079 3,697
C57BL/6J vs. 129S1/SvImJ PolyPhen Deleterious 796 (19.5%) 480 (24.9%)
   Benign 2,995 (73.4%) 1,270(65.7%)
   Unknown 293 (7.2%) 185 (9.6%)
   Total 4,084 1,935
  PANTHER Deleterious 568 (14%) 327(16.9%)
   non-deleterious 2,049 (50.2%) 913 (47.1%)
   Unknown 1,467 (36%) 701 (36.2%)
   Total 4,084 1,941
C57BL/6J vs. A/J PolyPhen Deleterious 2,350 (18.9%) 1,197(26.1%)
   Benign 9,220 (74.2%) 2,889 (63%)
   Unknown 865 (7%) 504 (11%)
   Total 12,435 4,590
  PANTHER Deleterious 1,785 (14.4%) 798(17.1%)
   non-deleterious 6,443 (51.9%) 2,154(46.1%)
   Unknown 4,207 (33.9%) 1,724 (36.9%)
   Total 12,435 4,676
  1. According to PolyPhen, 20% of missense mutations contained in the database are predicted to be deleterious (either 'possibly' or 'probably' damaging) to protein function. According to PANTHER, 14% of missense mutations contained in the database are predicted to be deleterious to protein function.