what is the difference between polymorphism and mutation and variant?

Question

[nabiyari1]

what is the difference between polymorphism and mutation and variant?

[Kevin Blighe]

Have you searched for an answer yourself? This is quite a basic (yet, thought-provoking...) question, as if it were just taken from an assignment / exam. Please provide some context.

Answer 1

[finswimmer]

Hello nabiyari1 ,

the differences depends on the person who uses this terms :)

In general a variant is every difference to the given reference.

The term "polymorphism" and "mutation" are usually used in a clinical environment. "mutation" often means "this is the variant that causes (most likely) our clinical phenotype". "Polymorphism" often means: "This variant have a frequency over 1% in the population, so we don't think it causes the clinical phenotype."

But there's a problem with this definition. Even variants that are quite often can cause the clinical phenotype (thing of lactose intolerance). And we have lot variants we know nothing/not enough about whether they causes the clinical phenotype.

So whenever possible one should avoid the term "polymorphism" and "mutation". Instead just say "variant".

If possible try to classify them based on the ACMG Guidelines on "benign", "likely benign", "uncertain significance", "likely pathogenic" and "pathogenic".

fin swimmer

[Joe]

I think your answer focuses too much on clinical definitions. It's not clear whether this is what OP is asking (question is very open). For example, certainly in the circles I move in academically, "variant" would probably be the vague term and you wouldn't get very far using it. It doesn't tell you anything about the type of variation (INDEL vs SNP for instance). I agree with the definition of mutant, with the exception of the clinical term. Mutant is just any "-omic" change which is different to some reference/control state or phenotype, and is a very broad term too.

If its a single base pair change, I would call that a polymorphism, but would more likely just refer to it as an SNP (single nucleotide polymorphism). If its an INDEL, it gets a little more complicated depending on the type of mutation specifically.

This might just be a 'regional'/'by discipline' difference, but I think its probably important to point out, especially if the words have significantly different meanings.

[WouterDeCoster]

If its a single base pair change, I would call that a polymorphism, but would more likely just refer to it as an SNP (single nucleotide polymorphism).

I'd say it's a single nucleotide variant of SNV. I largely agree with the distinction finswimmer made, that's also how my "field" generally uses these terms.

If its an INDEL, it gets a little more complicated depending on the type of mutation specifically.

Insertion-deletions below 50bp are "small indels" which can be "indel variant", "indel mutation" or "indel polymorphism". If it's larger than 50bp it magically becomes a "structural variant" and no longer a small variant.

[Joe]

It's definitely a by-field distinction then. I don't think I've heard anyone in my microbiology group use "SNV"!

[nabiyari1]

Thank you for participating in the discussion

Answer 2

[Michael]

Let me give it a try too :) -> : is_a

Mutation -> Variant
Polymorphism -> Variant
Mutation !<=> Polymorphism

Variant is the most general term, it refers to any genetic difference (e.g. sequence difference)

The other two terms refer to type and origin of the variation with respect to a population.

A mutation is a 'spontaneous' variation caused e.g. by a simple error in duplication, cell-division, strand-break, radiation, toxins, etc. It does not need to exist in the population, ancestry, or even the population of all cells in the organism. It is inheritable, if it affects the germ-line, but not necessarily inherited.

A polymorphism is a variation that exists in or becomes fixated within a population, e.g. if it is neutral or benefical. Therefore, at least two genotypes exist wrt. to the given variation/locus for which a prevalence can be assigned.

All existing polymorphisms must have started (some time ago) as a heritable mutation, but not all mutations become a polymorphism.

The orthogonal axis of the definition of variation is what is actually affected: from a single nucleotide, insertions/deletions, to chromosome re-arrangements.