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Table 3 Pathogenicity prediction of five variants using bioinformatics tools

From: Novel mutations identified in Chinese families with autosomal dominant congenital cataracts by targeted next-generation sequencing

Family (proband)

Gene

Transcript

Nucleotide change

Amino acid change

SIFT

Polyphen2

MutationTaster

M-CAP

PROVEAN

Pathogenicity (ACMG)

Evidence (ACMG)

Family 1 (II:1)

GJA8

NM_005267.4

c.154 T > C

p.F52 L

Deleterious

Possibly damaging

Disease causing

Possibly Pathogenic

Deleterious

Likely Pathogenic

PM1 PM2 PP3 PP4

0.00

0.478

–

0.513

−5.81

–

–

Family 2 (II:1)

GJA3

NM_021954.3

c.1152_1153insG

p.S385Efs*83

Not predicted

Not predicted

Disease causing

Not predicted

Not predicted

Pathogenic

PVS1 PP1 PP4 BP4

Family 3 (IV:1)

BFSP1

NM_001195.3

c.1804G > C

p.G602R

Deleterious

Possibly damaging

Polymorphism

Possibly Pathogenic

Neutral

Uncertain significance

PM2 PP1 PP4

0.02

0.472

–

0.308

−1.03

–

–

Family 4 (IV:1)

EPHA2

NM_004431.3

c.1532C > T

p.T511 M

Deleterious

Probably damaging

Disease causing

Possibly Pathogenic

Deleterious

Uncertain significance

PM1 PM2 PP1 PP3 PP4 BS1 BS2 BP6

0.00

1.00

–

0.04

−4.80

–

–

Family 5 (IV:12)

HSF4

NM_001538.3

c. 356G > A

p. R119H

Deleterious

Probably damaging

Disease causing

Possibly Pathogenic

Deleterious

Pathogenic

PM1 PM2 PP1 PP2 PP3 PP4 BP1

0.00

1.00

–

0.259

−4.81

–

–