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Table 3 Non-synonymous SNPs predicted to impact protein function either by Polyphen-2, SIFT or PROVEAN

From: Non-synonymous genetic variation in exonic regions of canine Toll-like receptors

Canine gene Position SNP dbSNP ID AA Subst Protein domain a Polyphen-2 result SIFT result Provean result Variant freq (dog) b Variant freq (wolf) b
EXTRACELLULAR TLRs
TLR1 3:73542337 G/T rs23585044 S29I ncp Pos. damaging Tolerated Neutral 0,36 0,77
  3:73543092 T/G new S281A ncp Pos. damaging Tolerated Neutral 0,06 0,00
  3:73543825 C/T new A525V LRRCT2 Pos. damaging Tolerated Deleterious 0 0,11
TLR2 15:51463020 C/A rs22410121 S46Y ncp Pos. damaging Tolerated Neutral 0,10 0,00
  15:51464430 C/T new S516L ncp Prob. damaging Aff. function Deleterious 0,14 0
TLR3 16:44623632 C/G new E176D ncp Pos. damaging Tolerated Neutral 0,16 0,12
TLR4 11:71356420 C/T reference1 A8V ncp Prob. damaging Tolerated Neutral 0,77 0,57
  11:71360887 G/A new V82M ncp Pos. damaging Tolerated Neutral 0,09 0,15
  11:71364581 T/C rs22145736 L167P ncp Prob. damaging Aff. function Deleterious 0,15 0
  11:71364681 A/C reference1 Q200H ncp Pos. damaging Aff. function Neutral 0,88 0,23
  11:71365810 A/G new T577A LRRCT3 Pos. damaging Aff. function Neutral 0,01 0
TLR5 38:23702837 C/T rs9070447 R269C ncp Prob. damaging Aff. function Neutral 0,19 0,01
  38:23702918 G/A new V296I ncp Pos. damaging Tolerated Neutral 0,05 0,26
  38:23703629 G/A new G533S ncp Prob. damaging Tolerated Neutral 0,02 0
  38:23704331 G/T new D767Y ncp Prob. damaging Tolerated Deleterious 0,04 0
  38:23704531 C/G new N833K LRRCT Pos. damaging Tolerated Deleterious 0 0,06
  38:23704562 C/T new R844C LRRCT Pos. damaging Tolerated Neutral 0,04 0,39
  38:23704581 C/T reference 1 S850L LRRCT Prob. damaging Aff. function Deleterious 0,68 0,02
  38:23704695 T/G new F888C low complexity Prob. damaging Aff. function Deleterious 0,04 0
  38:23705081 C/T new H1017Y TIR Benign Aff. function Neutral 0,02 0
  38:23705264 G/A new A1078T TIR4 Pos. damaging Aff. function Neutral 0,07 0,00
TLR6 3:73521250 A/G new Y182C ncp Prob. damaging Tolerated Deleterious 0,01 0,09
  3:73522074 C/T new L457F ncp Prob. damaging Aff. function Deleterious 0,03 0
  3:73522242 G/A rs23570247 D513N ncp Pos. damaging Tolerated Neutral 0,73 1,00
  3:73522441 C/T new P579L LRRCT Pos. damaging Aff. function Deleterious 0,01 0,07
TLR10 3:73569402 C/T rs23518574 T361M ncp Prob. damaging Aff. function Deleterious 0,13 0,12
  3:73570681 T/A new F787L TIR5 Pos. damaging Low confidence Neutral 0,00 0,39
INTRACELLULAR TLRs
TLR8 X:9397240 T/C new V157A ncp Pos. damaging Aff. function Deleterious 0,06 0
TLR9 20:37544129 G/A new V87I ncp Benign Aff. function Neutral 0,02 0
  20:37546230 C/T new P787L ncp Pos. damaging Tolerated Neutral 0,22 0,24
  20:37546454 C/T new R862W ncp Prob. damaging Tolerated Neutral 0,2 0
  1. In italics, SNPs that are predicted to have an effect on protein function by the three algorithms. ancp, no confident prediction. bObserved frequency by massive sequencing. 1reference allele tested as the alternative in the SNP. 2Leucine Rich Repeat C-terminal (LRRCT) domain predicted from aminoacid 528 to 582. 3LRRCT domain predicted from aminoacid 579 to 629. 4TIR domain predicted from aminoacid 927 to 1074. 5TIR domain predicted from aminoacid 641 to 784.