Additional file 1 of In silico analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in the human GJA3 gene associated with congenital cataract

Additional file 1. The nsSNPs collections of GJA3 gene from dbSNP database, the HGMD, the ClinVar database, the DisGeNET database and literatures

I-Mutant 2.0, Mupro and INPS software predicted the change of protein free energy caused by nsSNPs.

I-Mutant 2.0, Mupro and INPS software predicted the change of protein free energy caused by nsSNPs.</p

Comparison between theoretical prediction results and biophysical experimental data available in the literature on beta crystallins.

Comparison between theoretical prediction results and biophysical experimental data available in the literature on beta crystallins.</p

Additional file 2 of In silico analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in the human GJA3 gene associated with congenital cataract

Additional file 2. Deleterious predictions of nsSNPs of GJA3 gene by eight computational in silico tools

CRYBA4 high-risk pathogenic nsSNPs that were predicted to be "pathogenic" or "harmful" by all the six pieces of software.

CRYBA4 high-risk pathogenic nsSNPs that were predicted to be "pathogenic" or "harmful" by all the six pieces of software.</p

Additional file 6 of In silico analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in the human GJA3 gene associated with congenital cataract

Additional file 6. Predicted effects of the mutations from 88 high-risk pathogenic nsSNPs of GJA3 on amino acid size, charge, hydrophobicity, spatial structure and function

Additional file 5 of In silico analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in the human GJA3 gene associated with congenital cataract

Additional file 5. Residues predictions of 67 amino acids by ConSurf

Structural domains, evolutionary conservation and protein structure analysis of CRYBA4 high-risk pathogenic nsSNPs.

A. CRYBA4 protein domain. CRYBA4 consists of "Crystall" and "XTALbg" domains. There are 84 amino acids in Crystall domain (from 13th to 96th) and 89 amino acids in XTALbg domain (from 106th to 194th). B. ConSurf software CRYBA4 protein amino acid evolutionary conservation prediction results. The black boxes indicate wild amino acids that would be affected by CRYBA4 high-risk pathogenic nsSNPs. Four motifs are marked as blue underlines. Evolutionary conserved sites get scores between 7 and 9. The letter “e” denotes the exposed residues according to the neural-network algorithm; the letter “b” denotes the buried residues according to the neural-network algorithm; the letter “f” denotes the predicted functional residues (highly conserved and exposed) and the letter “s” denotes the predicted functional residues (highly conserved and buried). C. Prediction of secondary structure of CRYBA4 protein by SOPMA software. The black boxes indicate wild amino acids that would be affected by CRYBA4 high-risk pathogenic nsSNPs. The letter “h” denotes alpha helix; the letter “e” denotes extended strand, the letter “t” denotes beta turn and the letter “c” denotes random coil.</p

The solvent accessible surface areas of the protein result calculated by GETAREA software.

A. The solvent accessible surface areas of all 189 amino acids. B. The solvent accessible surface areas of 39 CRYBA4 high-risk pathogenic nsSNPs related amino acids.</p

Evolutionary conservativeness analyses and protein structure prediction of CRYBA4 high-risk pathogenic nsSNPs.

Evolutionary conservativeness analyses and protein structure prediction of CRYBA4 high-risk pathogenic nsSNPs.</p