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What is the difference between a Single Nucleotide Polymorphism (SNP) and a point mutation? I am quite confused in understanding these term as both of them refer to one base difference from the reference sequence?

Daniel Standage
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Zheng Keong Ng
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1 Answers1

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The difference between the two depends on to whom you talk ;)

You are right: both refer to one base difference from the sequence. Usually the term "mutation" is used if the change has an impact on the phenotype. The "P" in "SNP" means "polymorphism". A lot of people use this term if more than 1% of the individual in a given population have this variant.

My recommendation: only use "mutation" if you are sure that your variant has an important impact on the phenotype. Only use "SNP" if you are sure that it is a commonly occurring variant. In any other case just use "variant". It is slowly becoming more common to talk about "SNV" (Single Nucleotide Variant) than about "SNP".

Daniel Standage
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finswimmer
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    I would add that "mutation" is best used when it has an important negative impact on the phenotype. There's a lot of baggage that goes along with the word "mutation", so even when we talk about patients we usually prefer "deleterious variant" or something like that. – Devon Ryan Jan 15 '19 at 08:08
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    Personally, I only use "mutation" when talking about it actually happening. So somatic mutations are mutations, or de novo mutations where the child had a variant but the parent doesn't are mutations. But if it's germline, I always call it a variant. The other advantage of saying "variant" over "SNP" is that "variant" can be used to describe insertions and deletions larger than one base. – Emily_Ensembl Jan 15 '19 at 08:54
  • @DevonRyan But consider "silent mutation" or "adaptive mutation", these are not negative in their impact and people studying molecular evolution would not consider that the default; indeed most mutations are neutral – Chris_Rands Jan 15 '19 at 13:05
  • I think SNP is only really used at the population level while a point mutation may imply either population level (SNP) or between-species (substitution). Also sometimes, a point mutation is used for a single base pair insertion/deletion (although personally I wouldn't use it like that), while SNP is never an indel – Chris_Rands Jan 15 '19 at 13:06
  • @Chris_Rands I suspect this comes more from my human genetics background, where we worry about how patients will interpret what we're saying. – Devon Ryan Jan 15 '19 at 13:16
  • @Chris_Rands When I was working on comparative genomics and sequence evolution, I and those around me would use "SNP" for any form of single nucleotide change. Using the term specifically for common ones is something I only saw when I started looking at NGS data in a clinical context. I think this is one of those things that really change depending on your specific sub-field. – terdon Jan 15 '19 at 13:44