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Table 2 OPA1 variants identified from 11 unrelated Chinese ADOA families and pathogenicity analyses

From: Autosomal dominant optic atrophy caused by six novel pathogenic OPA1 variants and genotype–phenotype correlation analysis

family ID

Position

Nucleotide change

Protein

variant

Mutation

type

SIFT

MutationTaster

PROVEAN

Net Gene2

CADD

gnomAD

ExAc

1000 Genomes

ACMG

Evidence

Novel

NM_015560.2

NM_130837.2

F1

Exon 27

c.2787_2794del

c.2952_2959del

p.T929Tfs

frameshift deletion

-

DC(1)

-

-

-

-

-

-

P

PVS1 + PM2 + PP1

Y

F2

Exon 27

c.2708_2711del

c.2873_2876del

p.V903Gfs

frameshift deletion

-

DC(1)

-

-

-

3.658E-5

3.369E-5

-

P

PVS1 + PS4 + PM1 + PM2

N

F3

Exon 24

c.2496G > A

c.2661G > A

p.L832L

splicing

-

DC(1)

-

SSC

D(28)

-

-

-

VUS

PM2 + PP3 + PP4

Y

F4

Intron 9

c.984 + 1_984 + 2del

c.1149 + 1_1149 + 2del

-

splicing

-

DC(1)

-

SSC

-

-

-

-

P

PVS1 + PM6 + PM2

Y

F5

Exon 13

c.1283A > C

c.1448A > C

p.N428T

missense

D(0.003)

DC(1)

D(-5.74)

-

D(27.7)

-

-

-

VUS

PM2 + PP3 + PP4

Y

F6

Exon 28

c.2830G > T

c.2995G > T

p.E944X

stop-gain

-

DC(1)

-

-

D(54)

-

-

-

P

PVS1 + PM2 + PP4

Y

F7

Intron 10

c.1065 + 5G > C

c.1230 + 5G > C

-

splicing

-

DC(1)

-

SSC

D(26.3)

-

-

-

VUS

PM2 + PP3 + PP4

Y

F8

Exon 20

c.1937 C > G

c.2102C > G

p.S646X

stop-gain

-

DC(1)

-

-

D(41)

-

-

-

P

PVS1 + PM2 + PP4

Y

F9

Intron 12

c.1194 + 2 T > C

c.1305 + 2 T > C

-

splicing

-

DC(1)

-

SSC

D(32)

-

-

-

P

PVS1 + PM2 + PP4

Y

F10

Exon 2

c.112C > T

c.112C > T

p.R38X

stop-gain

-

DC(1)

-

-

D(38)

-

-

-

P

PVS1 + PM2 + PP1 + PP4

N

F11

Intron 13

C.1316-10 T > G

c.1478-10 T > G

-

splicing

-

DC(1)

-

SSC

D(29)

-

-

-

LP

PM6 + PM2 +  + PP3 + PP4

Y

  1. D deleterious (<0.05), DC disease causing, SSC splicing site change, P pathogenic, LP, likely pathogenic, VUS variant of uncertain significance, − not available
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