What is the difference between SNP and a mutation ?

Question

[QAZ]

Dears,

I really confused between SNP and mutation. SNP can occur more than 1% in each column. If the SNP occurs less than 1% then it is considered as a mutation. if in the same column two nucleotides have been changed in the same position and the percentage of their occurrence together is less than 1% then there are two mutations in the same position.

Is these info correct ? Please I have searched a lot and didn't find enough answer. I am a computer science students I am not a biologist.

Thank you

Answer 1

[GiantSilverSoy]

People typically use the word “mutation” for the variations in the genome that are very rare and have phenotypic consequences, whereas “polymorphism” is used to describe those differences that are more common. “Variant” is a more neutral term that simply recognizes genetic differences between individuals.

Source: https://cjasn.asnjournals.org/content/15/2/268

Answer 2

[GenoMax]

SNP = single nucleotide polymorphism (LINK). Technically a SNP is a mutation since it has resulted in a change when compared to a reference in that individual. I guess you are referring to a requirement that the SNP be present in at least 1% of the population to be considered a mutation by some definitions (see link).

[QAZ]

So, you mean if the occurrence is less than 1% it is called SNP. If the occurrence is bigger than 1% it is called a mutation.

Or the reverse ?

Thanks a lot

[GenoMax]

A single change is called a SNP (and it is still a mutation). Some definitions seem to want it to be present at least in 1% of the individuals of a population to be considered significant. Note: This may only be relevant to SNP's present in human populations.

[QAZ]

In this link they have a comparison but I got more confused.

https://pediaa.com/what-is-the-difference-between-snp-and-mutation/#SNP

Please if these two upcoming sentences are correct then tell me.

SNPs occurs > 1% Mutations occurs < 1%

[GenoMax]

By the definition used in link you provided they are calling SNP's to be mutations that occur in >1% of the population.

SNP (single nucleotide polymorphism) is a type of DNA variant defined by the detectable with a more than 1% frequency within a population. Therefore, it is the most common genetic variation among people.

A mutation is a change in genetic material in classical genetics. There is no percentage or frequency associated with that definition. A SNP would be classified as a point mutation (LINK).

Answer 3

[Camelia]

I can confirm. Mutation is usually used for a rare variant that can have a pathogenic significance. SNPs are with a higher frequency in the general population and since they're present in the healthy people they're most likely benign, or at least don't have a complete pathogenic impact (hence the various studies which still manage to show some implications of SNPs in disease - usually complex multifactorial ones). Variant is a general term that includes both SNPs and mutations. It means a nucleotide in a specific position which is different than the reference genome.

Of note, when you read classical genetic books, you'll see that mutation is defined as a change in the genome - similar definition to variant. then the definition continues with the classification of mutations in benign, pathogenic. So this might be confusing when you start reading/studying these subjects. But for the sake of being clear especially in a medical environment, we prefer: variant = any nucleotide change different than the consensus reference genome; mutation = pathogenic variant; SNPs = variant with >1% allele frequency that can be benign or maybe can have some effect in a certain context (quick example https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2564574/)

cheers!

Answer 4

[grant.hovhannisyan]

Any SNP is a mutation, but not any mutation is a SNP (deletion, duplication, etc). There is a also a difference between SNP and point mutation (or variant) - the latter is called a SNP if its frequency is higher than 1% in a given population.

Answer 5

[4galaxy77]

In my experience nobody in everyday life every delineates SNPs and mutations based on their frequency, esepcially on some arbitrary cutoff like 1%, which IMO is quite an unhelpful criteria. Is it based on a frequency in a given population? Across all populations? How do you calculate the frequency? Working backwards and trying to figure out whether something is low or high frequency based on whether someone calls it a SNP or a mutation isn't very helpful. For example, the abstract of the 1000 genomes paper refers to singletons as SNPs, even though they are only found in a single individual (i.e. they are as low a frequency as its possible to get). https://www.nature.com/articles/nature15393

IMO the difference in terminology is far more about context than frequency. As others have suggested, 'mutations' is a common term in e.g. cancer genetics or rare disease discovery when talking about rare, singly occuring pathogenic variants which might occur in the germline. SNPs is used more often in population genetic or genetic epidemiology studies when people are talking about SNP arrays or SNP discovery in a population cohort. Of course, these often overlap.