OGG1 Mutations and Risk of Female Breast Cancer: Meta-Analysis and Experimental Data

Table 3

Mutations in OGG1 gene in breast cancer patients with conservation score, SIFT score, Align GVGD score, Grantham distance, and Mutation Taster prediction.

Change in nucleotide; with its conservation level PhyloP score [−14.1; 6.4]	Change in codon	Amino acid change; with its conservation level (up to 13 species)	SIFT score; (median)	Align GVGD score; (C0–C65)	Grantham dist. (for physicochemical difference b/w amino acids); (0–215)	Mutation Taster (p value)
g.9793544T>G; Highly conserved nucleotide phyloP: 4.97	GTG to GGG	Val159Gly; Moderately conserved amino acid	Deleterious 0.01 (2.95)	C0 (GV: 197.52-GD: 72.75)	109 (moderate)	Disease causing; ()
g.9796483G>A; Moderately conserved nucleotide phyloP: 2.38	GGG to AGG	Gly221Arg; Moderately conserved amino acid	Tolerated 0.28 (2.95)	C0 (GV: 161.50-GD: 19.25	125 (moderate)	Disease causing; ()
g.9798773C>G; Not conserved nucleotide phyloP: 0.28	TCC to TGC	Ser326Cys; Weakly conserved amino acid	Tolerated 0.19 (2.95)	C0 (GV: 353.86-GD: 0.00)	112 (moderate)	Polymorphism; ()
g.9807669G>A; Weakly conserved nucleotide phyloP: 0.12	TGG to TGA	Trp375STOP; Moderately conserved amino acid	Deleterious 0.01 (2.95)	C0 (GV: 197.52-GD: 72.75)	170 (large); Protein truncation	Disease causing; ()

PhyloP was used as a conservation score rating the nucleotides from “not conserved” (−14.1) to “highly conserved” (6.4). Align GVGD score: most likely deleterious (C65) to least likely deleterious (C0) GV (Grantham variation) and GD (Grantham deviation). The Grantham distance was used to evaluate physicochemical changes in amino acids (0 = no physicochemical changes; 215 = large changes). In silico predictions were performed using PolyPhen-2 (Polymorphism Phenotyping-2), SIFT (Sorting Intolerant from Tolerant) score: <0.05 deleterious, >0.05 tolerated, and Mutation Taster: disease causing variants (p value = 1.0), might not be disease causing (p value <0.99).