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 (p = 1.0)
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 (p = 0.999)
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 (p = 1.0)
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 (p = 1.0)

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).