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Table 3 Coding Sequence Variants Predicted by Syzygy and Verified by Sanger Sequencing in the ANOP1 and ANOP2 Libraries

From: Targeted 'Next-Generation' sequencing in anophthalmia and microphthalmia patients confirms SOX2, OTX2 and FOXE3 mutations

Gene

Position (hg18)

Nucleotide

Alterationa

Predicted Effect on

Protein

dbSNP/1000 Genomes

Sanger Sequencing

Het./

Homo.b

Interpretation

ANOP1

       

FOXE3

chr1:47655084

c.510C > T

p.Ala170Ala

rs34082359

Yes; verified

Het.

SNP

FOXE3

chr1:47655175

c.601 G > A

p.Val201Met

-

Yes; verified10

Het.

SNP

FOXE3

chr1:47655192

c.618C > G

p.Ala206Ala

-

Yes; verified10

Homo.

SNP

SIX3

chr2:45022837

c.90 G > T

p.Ala30Ala

rs78018362

Not done

Het.

SNP

SIX3

chr2:45025346

c.942A > G

p.Ala314Ala

rs62840660

Not done

Het.

SNP

SOX2

chr3:182913381

c.539A > D c

Predicted FS d

-

Yes; c.542delC verified

Het.

Mutation

GDF6

chr8:97242073

c.24C > G

p.Leu8Leu

-

Yes, verified

Het.

Unknown

PAX2

chr10:102558862

c.867C > T

p.Asn289Asn

rs1800897

Not done

Het.

SNP

PAX2

chr10:102558973

c.978A > C

p.Pro326Pro

rs1800898

Not done

Het.

SNP

BMP4

chr14:53487272

c.455T > C

p.Val152Ala

rs17563

Not done

Het.

SNP

OTX2

chr14:56338763

c.313C > T

p.Glu105X

-

Yes; verified 8

Het.

Mutation

VSX2

chr14:73781636

c.471C > T

p.Ser157Ser

rs35435463

Not done

Het.

SNP

CRYBA4

chr22:25351457

c.171C > T

p.Phe57Phe

rs5761637

Not done

Het.

SNP

ANOP2

       

FOXE3

chr1:47655084

c.510C > T

p.Ala170Ala

rs34082359

Yes; verified

Het.

SNP

FOXE3

chr1:47655294

c.720C > A

p.Cys240X

-

YES; verified 10

Homo.

Mutation

SIX3

chr2:45023323

c.576C > T

p.Arg192Arg

rs182881

Not done

Het.

SNP

PAX2

chr10:102558862

c.867C > T

p.Asn289Asn

rs1800897

Not done

Het.

SNP

PAX2

chr10:102558973

c.978A > C

p.Pro326Pro

rs1800898

Not done

Het.

SNP

PAX6

chr11:31768060

c.1268A > T

p.X423Leu

extX*15

-

YES; not verified 24

Het.

Mutation

BMP4

chr14:53487272

c.455T > C

p.Val152Ala

rs17563

Not done

Het.

SNP

VSX2

chr14:73781636

c.471C > T

p.Ser157Ser

rs35435463

Not done

Het.

SNP

VSX2

chr14:73797160

c.871 G > A

p.Asp291Asn

rs75395981

YES; verified

Het.

SNP

CRYBA4

chr22:25349282

c.124 G > A

p.Glu42Lys

-

YES; verified

Het.

Unknown

CRYBA4

chr22:25351457

c.171T > C

p.Phe57Phe

rs5761637

Not done

Het.

SNP

  1. aNucleotide numbering is according to dbSNP (Database of Single Nucleotide Polymorphisms; http://www.ncbi.nlm.nih.gov/projects/SNP/). Het./Homo.b = heterozygous or homozygous sequence alteration; Dc = predicted deletion; FSd = frameshift.