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Table 2 The predicted effects of the ATM variants using SIFT, PolyPhen2 and Mutation taster Phylop algorithms

From: Genetic variants in ATM, H2AFX and MRE11 genes and susceptibility to breast cancer in the polish population

 

SIFT

PolyPhen 2

Mutation taster Phylop

ATM

 c.6067G > A; G2023R

damaging; 0.03

benign,0.340

disease causing base on

• amino acid sequence changed

• heterozygous in tgp or exac

• protein features (might be) affected

 c.6095G > A; R2032K

tolerated; 0.1

possibly damaging with a score of 0.859

disease causing base on

• amino acid sequence changed

• known disease mutation at this position (hgmd cm990215)

• known disease mutation at this position (hgmd cs961479)

• known disease mutation: rs139770721 (pathogenic)

• protein features (might be) affected

• splice site changes

 c.8187A > T; Q2729H

damaging; 0

probably damaging with a score of 1.000

disease causing base on

• amino acid sequence changed

• protein features (might be) affected

• splice site changes

 c.8314G > A; G2772R

damaging; 0.04

probably damaging with a score of 0.998

disease causing base on

• amino acid sequence changed

• protein features (might be) affected

• splice site changes

 c.6083A > G; Q2028R

damaging; 0.03

benign with a score of 0.232

polymorphism base on

• amino acid sequence changed

• protein features (might be) affected

• splice site changes

 c.8787-55C > T

intronic variant

polymorphism base on

• homozygous in TGP or ExAC