Classification of Single-Nucleotide Polymorphisms (SNPs): Tips from the Basic Knowledge to the Clinical Outcomes

Single-nucleotide polymorphisms (SNPs) are the cornerstone of individuals' variations in sensitivity to cancer and drugs. The necessity of understanding how SNPs work is an urgent requirement before knowing the possibility of their interactions with clinical disorders. Despite the accumulated pieces of evidence about the SNP association with cancer, no parallel light is shed on the other portions of the SNP story. Therefore, this chapter is concerned with combining the basic knowledge available on SNPs as well as the recent innovations in this field to assess how SNPs achieve their scheduled roles in life based on their positions within genomes. Inside genes, SNPs were grouped according to their positions into coding and noncoding. Within the coding sequences, SNPs exhibited three patterns of effects with three different consequences on protein structure, function, and stability. Silent SNPs do not change the amino acid sequences, while missense SNPs change amino acid sequences with acceptable, partially acceptable, or unacceptable consequences. Nonsense codon SNP causes a premature termination of the nascent polypeptide. Noncoding SNPs include intron SNPs, untranslated region (UTR) SNPs, and promoter-enhancer SNPs with variable subsequent effects on splicing, mRNA stability, and transcription factor binding sites, respectively. Intergenic SNPs, in turn, perform different effects on the gene due to their distant positions outside genes. This chapter provided numerous proofs to demonstrate that each particular SNP function is based on the type of DNA sequence in which it is located. This chapter indicated that deep knowledge of the mechanisms of SNPs actions within their positions could greatly resolve the reason behind their possible involvement in clinical disorders. Based on the data presented, it is feasible for researchers to root out many misconceptions surrounding SNP identity, category, mechanism of action, and effect. In this chapter, various confusions were clarified, and misconceptions related to the accurate classification of SNPs were addressed and resolved.