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Table 3 The functional classification and score of VSX1 variants are predicted by using various bioinformatics tools

From: Two novel missense substitutions in the VSX1 gene: clinical and genetic analysis of families with Keratoconus from India

c. DNA position

Protein change

Location of protein

Polyphen–2 humDiv

SIFT

Mutation assessor

PROVEAN

c.751 T > A

p. Ser251Thr

CVC domain

Benign (0.9)

Tolerated

Neutral

Neutral

(0.17)

(0.485)

–2.467

c.803 T > A

p. Leu268His

CVC domain

Possibly damaging for function (1.0)

Deleterious

Functional effect on protein

Deleterious

(0.05)

–6.831

(1.905)

  1. Prediction servers are Polymorphism Phenotyping v2 (PolyPhen–2), Sorting Tolerant From Intolerant (SIFT), Protein Variation Effect Analyzer (PROVEAN), CVC (Chx10/Vsx–1, and ceh–10)
  2. Polyphen–2 scores: 0: benign, 1 possibly damaging for function; 2: Probably damaging for function
  3. SIFT scores: Intolerant or deleterious: score ≤0.05, Tolerant: score >0.05
  4. Mutation Assessor scores: 0–1: no functional effect, 2–3: functional effect on protein function
  5. Provean scores: Cut off threshold = −2.5,
  6. -Variants with a score equal to or below −2.5 are considered “deleterious,”-Variants with a score above −2.5 are considered “neutral
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BMC Medical Genetics

ISSN: 1471-2350

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