Predict Pathogenicity of Mutations in ALSoD

Gene
Mutation

In ALSoD, out of  580  mutations, there are  227 positive pathogenic mutations.




 


Bioinformatics Analysis
Three (3) freely available online bioinformatics tools were utilized to predict the possible effect of mutations in humans. The use of these programs help to evaluate the pathogenicity of missence mutations available in ALSoD. These are:
1. PANTHER (Protein Analysis Through Evolutionary Relationships)
Damaging: score is -5.0 or lower Not damaging: score is higher than -5.0
Website: http://www.pantherdb.org/tools/csnpScoreForm.jsp
Reference: Thomas PD, Kejariwal A, Campbell MJ, et al. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res. 2003;31(1):334-41. Pubmed

2. SIFT (Sorting Intolerant From Tolerant)
Damaging: score is 0.05 or lower Not damaging: score is higher than 0.05
Website: http://sift.jcvi.org/www/SIFT_BLink_submit.html
Reference: Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31(13):3812-4. Pubmed

3. PolyPhen (Polymorphism Phenotyping)
Damaging: score is 1.5 or higher Not damaging: score is lower than 1.5
Website: http://genetics.bwh.harvard.edu/pph/
Reference: Sunyaev S, Ramensky V, Koch I, et al. Prediction of deleterious human alleles. Hum Mol Genet. 2001;10(6):591-7. Pubmed


Results:Mutations not included in the dropdown list have no values in the prediction tools. The Pathogenic result is determined by combining the predictions of each tool and rating them in binary form. A combination producing 3 or 2 or 1 in the result column is predicted as a 'Yes' in the pathogenic column but a 0 is 'No'.