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ALSoD is a joint project of World Federation of Neurology and European Network to Cure ALS
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16th May 2013
Predict Pathogenicity of Mutations in ALSoD
In ALSoD, out of 494 mutations, there are 195 positive pathogenic mutations.
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
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.
2. SIFT (Sorting Intolerant From Tolerant)
Damaging: score is 0.05 or lower
Not damaging: score is higher than 0.05
Reference: Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res.
3. PolyPhen (Polymorphism Phenotyping)
Damaging: score is 1.5 or higher
Not damaging: score is lower than 1.5
Reference: Sunyaev S, Ramensky V, Koch I, et al. Prediction of deleterious human alleles. Hum Mol Genet.
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'.