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Table 7 Characterization of the seven predicted deleterious SNPs annotated in PCGs for internal organ traits in chickens

From: Genome-wide association scan for QTL and their positional candidate genes associated with internal organ traits in chickens

Gene Symbol SNP ID GGA Position1 Amino acid change SIFT score2
TNFSF11 rs312442403 1 166,510,185 Arg/Gln Deleterious low confidence3 (0.03)
NR4A2 g.36224286 > C/T 7 36,224,286 Val/Met Deleterious (0)
g.36225242 > G/T 36,225,242 Arg/Ser Deleterious (0)
g.36225278 > C/T 36,225,278 Val/Met Deleterious (0.01)
ITGB4 rs313279811 18 4,785,491 His/Tyr Deleterious (0.01)
rs316340790 4,787,392 Asp/Asn Deleterious (0.04)
rs732847450 4,790,177 Met/Ile Deleterious (0.03)
  1. 1Position based on Gallus_gallus 5.0 assembly
  2. 2SIFT (Sorting Intolerant From Tolerant) score
  3. 3Deleterious low confidence: little sequence diversity in this position affecting the substitution model, and consequently the averages of conservation value [35]