Computational Identification and Functional Analysis of Potentially Pathogenic nsSNPs in the NLRP3 Gene Linked to Alzheimer's Disease.
PMID 39167281 | DOI 10.1007/s12013-024-01465-9 · Cell biochemistry and biophysics · 2025
Single Nucleotide Polymorphisms (SNPs) are key in understanding complex diseases. Nonsynonymous single-nucleotide polymorphisms (nsSNPs) occur in protein-coding regions, potentially altering amino acid sequences, protein structure and function. Computational methods are vital for distinguishing deleterious nsSNPs from neutral ones. We investigated the role of NLRP3 gene in neuroinflammation associated with Alzheimer's disease (AD) pathogenesis. A total of 893 missense (nsSNPs) were obtained from the dbSNP database and subjected to rigorous filtering using bioinformatics tools like SIFT, Align GVGD, PolyPhen-2, and PANTHER to identify potentially damaging variants. Of these, 18 nsSNPs were consistently predicted to have deleterious effects across all tools. Notably, 16 of these variants exhibited reduced protein stability, while only 4 were predicted to be buried within the protein structure. Among the identified nsSNPs, rs180177442 (R262L and R262P), rs201875324 (T659I), and rs139814109 (T897M) were classified as high-risk variants due to their significant deleterious impact, probable damaging effects, and association with decreased protein stability. Molecular docking and simulation analyses were conducted utilizing Memantine, a standard drug utilized in AD treatment, to investigate potential interactions with the altered protein structures. Additional clinical and genetic investigations are necessary to elucidate the underlying mechanisms that link NLRP3 polymorphisms with the initiation of AD.
Validated evidence
| Type | Entity | Source evidence | Confidence | Extractor |
|---|---|---|---|---|
| gene | NLRP3 | “Computational Identification and Functional Analysis of Potentially Pathogenic nsSNPs in the NLRP3 Gene Linked to Alzheimer's Disease.” | 0.98 | hgnc_dict_v1 |
| phenotype | Alzheimer disease | “Computational Identification and Functional Analysis of Potentially Pathogenic nsSNPs in the NLRP3 Gene Linked to Alzheimer's Disease.” | 0.93 | phenotype_alias_lexicon_v2 |
| variant | rs180177442 | “Among the identified nsSNPs, rs180177442 (R262L and R262P), rs201875324 (T659I), and rs139814109 (T897M) were classified as high-risk variants due to their significant deleterious impact, probable damaging effects, and association with decreased protein stability.” | 0.90 | hgvs_regex_v1 |
| variant | rs201875324 | “Among the identified nsSNPs, rs180177442 (R262L and R262P), rs201875324 (T659I), and rs139814109 (T897M) were classified as high-risk variants due to their significant deleterious impact, probable damaging effects, and association with decreased protein stability.” | 0.90 | hgvs_regex_v1 |
| variant | rs139814109 | “Among the identified nsSNPs, rs180177442 (R262L and R262P), rs201875324 (T659I), and rs139814109 (T897M) were classified as high-risk variants due to their significant deleterious impact, probable damaging effects, and association with decreased protein stability.” | 0.90 | hgvs_regex_v1 |
| variant | R262L | “Among the identified nsSNPs, rs180177442 (R262L and R262P), rs201875324 (T659I), and rs139814109 (T897M) were classified as high-risk variants due to their significant deleterious impact, probable damaging effects, and association with decreased protein stability.” | 0.82 | literature_variant_regex_v2 |
| variant | R262P | “Among the identified nsSNPs, rs180177442 (R262L and R262P), rs201875324 (T659I), and rs139814109 (T897M) were classified as high-risk variants due to their significant deleterious impact, probable damaging effects, and association with decreased protein stability.” | 0.82 | literature_variant_regex_v2 |
| variant | T659I | “Among the identified nsSNPs, rs180177442 (R262L and R262P), rs201875324 (T659I), and rs139814109 (T897M) were classified as high-risk variants due to their significant deleterious impact, probable damaging effects, and association with decreased protein stability.” | 0.82 | literature_variant_regex_v2 |
| variant | T897M | “Among the identified nsSNPs, rs180177442 (R262L and R262P), rs201875324 (T659I), and rs139814109 (T897M) were classified as high-risk variants due to their significant deleterious impact, probable damaging effects, and association with decreased protein stability.” | 0.82 | literature_variant_regex_v2 |