Design of efficient treatment strategies for diseases requires clarification of the nature of each mutation causing the disease. In this study, we have investigated three factors to correctly predict the correlation between genotype and phenotype on N-acetylgalactosamine-6-sulfate sulfatase (GALNS) gene responsible for one of lysosomal storage diseases, known as mucopolysaccharidosis IVA (MPS IVA); (i) evolutionary conservation of amino acid residues among family proteins, (ii) conservativeness of amino acid changes in GALNS, and (iii) structural conservation of amino acid residue. The results showed that (i) the likelihood of a missense variant causing MPS IVA was directly correlated with the level of evolutionary conservation and inversely correlated with conservativeness but not correlated with the structural conservation, (ii) the disease-causative mutations were 9 times more likely to be located on the 'highly conserved' residues than the polymorphisms, (iii) the likelihood of 'non-conservative' amino acid changes in missense mutations was 6.8 times higher than those in the polymorphisms, (iv) the degree of evolutionary conservation was nearly as predictive in phenotype as that of conservativeness of amino acid changes, and (v) the combination of the two factors, evolutionary conservation and conservativeness, provides a better association between missense variants and clinical severity with higher sensitivity (83.5-88.9%) and specificity (71.4-88.3%), than that obtained by either factor alone. These findings suggest that the combination of evolutionary conservation and conservativeness is a useful tool to predict the effect of each mutation on the clinical phenotype and can be applied to the analysis of phenotype/genotype relation in other genetic diseases.