Software that were used in this study to evaluate conservation, minor allele frequency and potential damage of variants on splicing and protein structure and function
| Software | Source | Comments | |
|---|---|---|---|
| Conservation | 1. MutationAssessor 2. Exome Variant Server database | http://mutationassessor.org http://evs.gs.washington.edu/EVS | |
| Allele frequency | 1. Exome Variant Server 2. 1000 Genomes 3. Variant Effect Predictor at the Ensembl genome browser | http://evs.gs.washington.edu/EVS http://browser.1000genomes.org/index.html http://useast.ensembl.org/Homo_sapiens/UserData/UploadVariations?db=core | Known polymorphism and common variants were excluded. We used a minor allele frequency (MAF) cut-off of 0.2% for variants in genes with AD and XL disease inheritance, and 0.5% for variants in genes with AR inheritance |
| Predict potential damage of amino acid substitution on protein structure and function | 1. Polymorphism Phenotyping 2 (PolyPhen2) 2. Sorting Intolerant From Tolerant (SIFT) 3. Sorting Intolerant From Tolerant (SIFT)—Indel 4. Protein Variation Effect Analyzer (Provean) 5. MutationTaster | http://genetics.bwh.harvard.edu/pph2 http://sift.jcvi.org http://sift.bii.a-star.edu.sg/www/SIFT_indels2.html http://provean.jcvi.org http://www.mutationtaster.org | |
| Predict potential damage on splicing | 1. Human Splicing Finder 3.0 2. MutationTaster | http://www.umd.be/HSF http://www.mutationtaster.org | |
| Reported disease-causing mutations | 1. SNP effect 4.0 2. The National Center for Biotechnology Information's ClinVar database 3. the Leiden Open Variation Database (LOVD) 4. Fanconi Anemia Mutation database 5. The Telomerase Database | http://snpeffect.switchlab.org http://www.ncbi.nlm.nih.gov/clinvar http://databases.lovd.nl/shared/genes http://www.rockefeller.edu/fanconi/genes http://telomerase.asu.edu/diseases.html |