Table 3 of Sodi, Mol Vis 2014; 20:1717-1731.


Table 3. Pathogenicity clues of the missense variant found in USH2A gene in this study.

DNA Level (cDNA)
Protein Level (p.) Conserved nucleotide (phyloP: −14.1;6.4) Physico
chemical difference Grantham
[0–215] Variation is in protein domain Align GVGD SIFT Mutation
Taster
c.1729T>C (p.Cys577Arg) Moderately
(phyloP: 3.92) Large
(Grantham
dist.: 180) EGF-like,
laminin C65
(GV:0.00 –
GD: 179.53) Deleterious
(score: 0,
median: 3.85) disease causing
(p value: 1)
c.4144T>C (p.Trp1382Arg) Moderately
(phyloP: 3.76) Moderate
(Grantham
dist.: 101) Fibronectin,
type III C0
(GV:268.54 –
GD: 82.54) Deleterious
(score: 0,
median: 3.83) disease causing
(p value: 1)
c.11831C>A p.Ala3944Asp Highly
(phyloP: 5.61) Moderate
(Grantham
dist.: 126) Fibronectin,
type III C65
(GV:0.00 –
GD: 125.75) Deleterious
(score: 0,
median: 3.85) disease causing
(p value: 1)
c.1040A>G(p.Asp347Gly) Moderately
(phyloP: 3.35) Moderate
(Grantham
dist.: 94) Laminin,
N-terminal GVGD: C0
(GV:213.16 –
GD: 64.73) Deleterious
(score: 0,
median: 3.85) disease causing
(p value: 1)
c.7246A>G (p:Asn2416Asp) Moderately
(phyloP: 3.68) Small
(Grantham
dist.: 23) Fibronectin,
type III C0
(GV:213.69 –
GD: 22.66) Deleterious
(score: 0,
median: 3.85) disease causing
(p value: 1)