Computational protocol: Whole Exome Sequencing Reveals a BSCL2 Mutation Causing Progressive Encephalopathy with Lipodystrophy (PELD) in an Iranian Pediatric Patient

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Protocol publication

[…] Non-exonic and synonymous variants were removed. The process was followed by the removal of common variants (i.e., minor allele frequency >0.02) reported in the single nucleotide polymorphism database (dbSNP), the 1-k human genome, the ESP6500 and BGI in house databases. To evaluate the pathogenicity of the novel variants, we analyzed the potential impact of a given variant on the function or structure of the encoded protein. The analysis was carried out based on conservation, physical properties of the amino acids or possible occurrence in regulatory or splicing motifs using bioinformatic tools SIFT (sift.jcvi.org), PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2), Combined Annotation Dependent Depletion[], and MutationTaster[]. Among the prioritized variants, truncating mutations or mutations predicted to be damaging were considered to be the most promising candidates. PubMed and OMIM were reviewed for previous publications regarding candidate genes as well as functional and expression data. […]

Pipeline specifications

Software tools SIFT, PolyPhen, CADD, MutationTaster
Databases dbSNP OMIM
Application WGS analysis
Diseases Brain Diseases, Lipodystrophy, Heredodegenerative Disorders, Nervous System