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 | |