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Table 3 In silico analysis of the identified non-synonymous variants in SLC4A11

From: Identification and in silico analysis of a spectrum of SLC4A11 variations in Indian familial and sporadic cases of congenital hereditary endothelial dystrophy

Sr. No

Variants Identified

Residue Conservation Score

(ConSurf)

Pathogenicity Score

(Predict SNP pathogenicity %)

[SIFT, PolyPhen2 score]

Homology modelling based analysis

   

Predict

SNP

Ph.D

SNP

PolyPhen2

SIFT

SNAP

H-bond interactions

(5A region around the mutation site)

Protein Stability

(DUET)

Protein local flexibility

(DynaMut)

1

c.1514C > G (p.Ser489Trp)

Highly conserved across 147 species

SCORE = 9

72%

82%

81%

[1]

53%

[0.002]

81%

Decreased from 136 to 116

(ΔΔG):

-0.516 kcal/mol (Destabilizing)

ΔΔSVib ENCoM: -1.717 kcal.mol−1.K−1

(Decrease of molecule flexibility)

2

c.1487G > T

(p.Ser480Ile)

Highly conserved across 132 species

87%

88%

81%

[1]

79%

[0.003]

81%

Decreased from 15 to 13

ΔΔG:

-0.17 (Destabilizing)

ΔΔSVib ENCoM: -0.557 kcal.mol−1.K−1 (Decrease of molecule flexibility)

3

c.2653C > T (p.Arg869Cys)

Highly conserved across 150 species

SCORE = 8

87%

82%

81%

[1]

79%

[0.000]

85%

Decreased from 15 to 13

ΔΔG

-1.012 kcal/mol (Destabilizing)

ΔΔSVib ENCoM: 0.188 kcal.mol−1.K−1 (Increase of molecule flexibility)

  1. SIFT score – 0–0.05: deleterious; 0.05–1: tolerated
  2. PolyPhen2 score- 0–0.05: benign; 0.15–0.85: possibly damaging; 0.85–1: damaging