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Table 2 Prediction of the potential pathogenicity of nonsynonymous variants by using five algorithms

From: Genetic and epigenetic characteristics in ovarian tissues from polycystic ovary syndrome patients with irregular menstruation resemble those of ovarian cancer

Gene

Mutation

Function

PROVEANa

SIFTb

Polyphen2 HDIVc

Polyphen2 HVARd

LRTe

MutationTaster2f

BRCA1

c.154Cā€‰>ā€‰T

p.Leu52Phe

N (āˆ’0.59)

D (0)

D (1)

D (0.985)

D

D (1)

BRCA1

c.1337Gā€‰>ā€‰T

p.Arg446Ile

D (āˆ’7.74)

D (0.007)

D (0.986)

D (0.930)

N

P (7.05e-05)

BRCA1

c.2566Tā€‰>ā€‰C

p.Tyr856His

D (āˆ’3.73)

D (0.015)

P (0.730)

P (0.733)

N

D (1)

MLH1

c.1151Tā€‰>ā€‰A

p.Val384Asp

D (āˆ’5.62)

D (0)

D (1)

D (0.998)

D

D (1)

MLH1

c.776Tā€‰>ā€‰C

p.Leu259Ser

D (āˆ’5.36)

D (0)

P (0.808)

P (0.706)

N

D (1)

MLH1

c.2135Gā€‰>ā€‰T

p.Trp712Leu

D (āˆ’7.28)

D (0.006)

P (0.576)

P (0.553)

D

D (1)

  1. aPROVEAN scoreā€‰ā‰¤ā€‰āˆ’2.5 was regarded as deleterious (D); scoreā€‰>ā€‰āˆ’ā€‰2.5 was regarded as neutral (N);
  2. bSIFT scoreā€‰ā‰¤ā€‰0.05 was regarded as deleterious (D);
  3. cPolyphen2 HDIV scoreā€‰ā‰„ā€‰0.957, probably damaging (D); 0.453ā€‰<ā€‰Polyphen2 HDIV scoreā€‰<ā€‰0.957, possibly damaging (P);
  4. dPolyphen2 HVAR scoreā€‰ā‰„ā€‰0.909, probably damaging (D); 0.447ā€‰<ā€‰Polyphen2 HVAR scoreā€‰<ā€‰0.909, possibly damaging (P);
  5. eDeleterious (D), Neutral (N);
  6. fPolymorphism (P), Disease causing (D)