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So, I know on a higher level what an SNP is but I'm a bit confused about the details.

Firstly, our professor said that an SNP has to have at least a prevalence of 1% in the general population to be considered an SNP and not just a mutation. Wikipedia says the prevalence needs to be 0.5%. Is this actually a strictly followed cutoff? And which of the two values is correct?

Secondly, he said that SNPs never cause a disease but can only predispose you to one. However, the wikipedia article mentions thier role in diseases that are clearly caused by single mutations (cystic fibrosis, sickel cell anemia, and beta thalassemia). So, can SNPs cause a disease or not?

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  • $\begingroup$ 1% v. 0.5% is unimportant and arbitrary. The databases of SNPs need an actual cutoff. If you think of the millions of SNPs added to database by automated genome sequencing projects, the idea of weeding out any related to a mono-genic disease seems improbable, $\endgroup$ – David May 15 at 11:22
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In genetics, a SNP (Single Nucleotide Polymporphism) is the substitution of a nucleotide with a different one. A SNP can have phenotypic effects or not.

A mutation, in genetics, is any kind of inherited change in DNA. Mutation types are: SNPs, indels, structural variants, translocations and so on.

Sometimes researchers (especially in the field of medical genetics) call "mutation" (meaning "pathogenic mutation") a SNP which is responsible of a disease (especially in case of a Mendelian disease). Since mutations causing severe Mendelian diseases are usually rare, several people use the arbitrary threshold of 1% to discriminate between a "SNP" and a "mutation".

So, probably your professor is stating that SNPs cannot cause a Mendelian disease because he uses the last definition I gave. However, while this definition may be useful for medical genetics purposes (i.e. I also agree that a very common variant is unlikely to be causing a rare Mendelian disease), it is arbitrary, if not wrong.

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Single nucleotide polymorphism is the most common type of alteration in DNA, this occurs when a single nucleotide is replaced with another. SNPs are normally present in our genome, with prevalence of one in every 1,000 nucleotides, making approximately 5 million SNPs in a our genome.

These variations are commonly found in the DNA present in between the genes and act as markers for locating different genes. But when SNPs are present in gene sequence or in the regulatory region, this directly effects functioning of genes and can result in disease. It is reported that SNPs effect person's susceptibility for developing various diseases like heart disease, diabetes, and cancer.

SNPs can also be used to track the inheritance of disease genes within families. These alterations also controls individual's response to environmental factors and response to various drugs.

Reference

https://www.snpedia.com/index.php/SNPedia

https://www.sciencedirect.com/topics/medicine-and-dentistry/single-nucleotide-polymorphism)

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