Table 1 Detected mutations increasing severity of granular corneal dystrophy 2 as a compound heterozygote with p.(Arg124His) in this study.

From: Compound heterozygous mutations in TGFBI cause a severe phenotype of granular corneal dystrophy type 2

Family

Nucleotide changea

Amino acid change

Amino acid sequence conservationb

Frequencies in the dbSNP databasec

Frequencies in the gnomAD databased

PP2e

MTf

PRO-VEANg

SIFTh

YUGCDF-1

YUGCDF-2

YUGCDF-3

c.520C > G

p.(His174Asp)

D. rerio

NA

0.000012

Dam

(0.999)

DC

(0.999)

Del

(-7.81)

Dam

(0.000)

YUGCDF-4

c.740 T > A

p.(Ile247Asn)

D. rerio

rs376340498

C = 0.000008/1 (ExAC)

A = NA

C = 0.00001444

A = NA

Dam

(0.804)

DC

(0.999)

Del

(-5.14)

Dam

(0.000)

YUGCDF-5

c.263A > G

p.(Tyr88Cys)

D. rerio

NA

NA

Dam

(0.863)

DC

(0.999)

Del

(-6.93)

Dam

(0.000)

YUGCDF-6

c.770G > C

p.(Arg257Pro)

D. rerio

rs377709778

A = 0.00003/4 (ExAC)

C = NA

A = 0.00002890

C = NA

Dam

(0.977)

DC

(0.999)

Del

(-2.86)

Dam

(0.010)

YUGCDF-7

c.1631A > G

p.(Asn544Ser)

D. rerio

rs777288957

G = 0.00008/10 (ExAC)

0.000053

Benign

(0.281)

DC

(0.999)

Del

(-2.97)

Dam

(0.003)

YUGCDF-8

c.535C > T

p.(Arg179*)

D. rerio

rs886059924

(MAF = NA)

A = 0.000008133

T = NA

NA

DC

(1.000)

NA

NA

YUGCDF-9

c.1404 T > A

p.(Tyr468*)

X. tropicalis

rs781643226

C = 0.000008/1 (ExAC)

A = NA

C = 0.000004064

A = NA

NA

DC

(1.000)

NA

NA

  1. Abbreviations: Dam, damaging; DC, disease causing; Del, deleterious; MAF, minor allele frequency; MT, mutation taster; NA, not available; PP2, PolyPhen-2 prediction score Humvar; PROVEAN, Protein Variation Effect Analyzer; SIFT, Sorting Intolerant from Tolerant; SNP, single nucleotide polymorphism.
  2. acDNA mutations are numbered according to the human cDNA reference sequence NM_004183; + 1 corresponds to the A of ATG translation initiation codon.
  3. bAmino acid residue is continually conserved throughout evolution including the species as indicated.
  4. cdbSNP database (http://www.ncbi.nlm.nih.gov/SNP).
  5. dgnomAD browser (http://gnomad.broadinstitute.org/).
  6. ePolyPhen-2 prediction score HumVar ranges from 0 to 1.0; 0 = benign, 1.0 = probably damaging (http://genetics.bwh.harvard.edu/pph2/).
  7. fMutation taster (http://www.mutationtaster.org/). gPROVEAN (http://provean.jcvi.org/index.php). hSIFT (http://sift.jcvi.org/).
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