ArticlePloS one2018
Accurate prediction of functional, structural, and stability changes in PITX2 mutations using in silico bioinformatics algorithms.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 48 citations in OpenAlex.
- In Silico Characterization of Pathogenic Homeodomain Missense Mutations in the PITX2 Gene.Biochemical genetics · 2025Article
- A systematic in-silico functional and structural analysis reveals deleterious missense nsSNPs in the humanMolecular biology research communications · 2025Article
- Restoring adapter protein complex 4 function with small molecules: an in silico approach to spastic paraplegia 50.Protein science : a publication of the Protein Society · 2025Article
- Using computational approaches to enhance the interpretation of missense variants in the PAX6 gene.European journal of human genetics : EJHG · 2024Article
- Structure-based network analysis predicts pathogenic variants in human proteins associated with inherited retinal disease.NPJ genomic medicine · 2024Article
- Predicting the effects of rare genetic variants on oncogenic signaling pathways: A computational analysis of HRAS protein function.Frontiers in chemistry · 2023Article
- Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure.Nature communications · 2022Article
- Article
- PSnpBind: a database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow.Journal of cheminformatics · 2022Article
- Glaucoma Syndromes: Insights into Glaucoma Genetics and Pathogenesis from Monogenic Syndromic Disorders.Genes · 2021Review
- Article
- Novel mutations in the PITX2 gene in Pakistani and Mexican families with Axenfeld-Rieger syndrome.Molecular genetics & genomic medicine · 2020Article
- Large scale analyses of genotype-phenotype relationships of glycine decarboxylase mutations and neurological disease severity.PLoS computational biology · 2020Article
- A novel human Cdh1 mutation impairs anaphase promoting complex/cyclosome activity resulting in microcephaly, psychomotor retardation, and epilepsy.Journal of neurochemistry · 2019Article
- Extracting Complementary Insights from Molecular Phenotypes for Prioritization of Disease-Associated Mutations.Current opinion in systems biology · 2018Article
- Homology modeling identified for purported drug targets to the neuroprotective effects of levodopa and asiaticoside-D in degenerated cerebral ganglions ofIndian journal of pharmacologyArticle
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mutations in PITX2 have been implicated in several genetic disorders, particularly Axenfeld-Rieger syndrome. In order to determine the most reliable bioinformatics tools to assess the likely pathogenicity of PITX2 variants, the results of bioinformatics predictions were compared to the impact of variants on PITX2 structure and function. The MutPred, Provean, and PMUT bioinformatic tools were found to have the highest performance in predicting the pathogenicity effects of all 18 characterized missense variants in PITX2, all with sensitivity and specificity >93%. Applying these three programs to assess the likely pathogenicity of 13 previously uncharacterized PITX2 missense variants predicted 12/13 variants as deleterious, except A30V which was predicted as benign variant for all programs. Molecular modeling of the PITX2 homoedomain predicts that of the 31 known PITX2 variants, L54Q, F58L, V83F, V83L, W86C, W86S, and R91P alter PITX2's structure. In contrast, the remaining 24 variants are not predicted to change PITX2's structure. The results of molecular modeling, performed on all the PITX2 missense mutations located in the homeodomain, were compared with the findings of eight protein stability programs. CUPSAT was found to be the most reliable in predicting the effect of missense mutations on PITX2 stability. Our results showed that for PITX2, and likely other members of this homeodomain transcription factor family, MutPred, Provean, PMUT, molecular modeling, and CUPSAT can reliably be used to predict PITX2 missense variants pathogenicity.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.