In silico Analysis of a Nonsense Mutation Linked to Autosomal Recessive Hypercholesterolemia Type 4

Autosomal recessive familial hypercholesterolemia-4 (FHCL4) is a genetic disorder caused by mutations in LDLRAP1, a gene encoding a protein that allows the LDL receptor to be endocytosed and degraded in the liver. In silico tools were used to examine the rs121908325 variant linked to FHCL-4. The variant protein LDLRAP1Q136X affects the coding region of LDLRAP1, resulting in a glutamine amino acid being changed into a stop codon, truncating the protein at amino acid 136. Phylogenetic analysis of ten different animal species demonstrated that glutamine 136 is 100% conserved in the LDLRAP1 protein from the human protein to flies and frogs. An NCBI Conserved Domain Search for LDLRAP1 indicated that the LDLRAP1Q136X variant truncates the protein within a peptide binding domain, a phosphoinositol binding domain, as well as a domain that specifies the Pleckstrin protein superfamily of signaling proteins. IntFold 3D rendering of wild type (WT) and LDLRAP1Q136X proteins showed that the variant has a significant alteration in 3D structure, based on the loss of 172 amino acids. Further in silico analysis using amino acid interaction software showed that the LDLRAP1Q136X protein was missing its phosphotyrosine binding pocket. The rs121908325 mutation is rare, and none of the 70 genomes analyzed during a nutrition course at a large research I university carried this allele. These in silico studies demonstrate that the nonsense mutation at position glutamine 136 would impact specific domains of LDLRAP1, ultimately inhibiting the protein’s ability to perform its function of facilitating removal of the LDL receptor from cell surfaces, leading to increased circulating cholesterol levels and potential cardiovascular health complications. KEYWORDS: Cholesterol; Hypercholesterolemia; Low density lipoprotein; LDL; LDLR; LDLRAP1; Autosomal recessive hypercholesterolemia-4 (FHCL4); heart disease