I'm looking to know when the variation is deemed mutation or polymorphism and why? In the case of polymorphism, it may be associated with disease so that variation should be called mutation or not?
I'm not going to repeat myself here - in addition to the links Sabine posted above, the same question was asked a few months ago and has a lot of answers: https://www.researchgate.net/post/What_is_the_difference_between_polymorphism_and_a_mutation
Short answer: individuals have mutations, populations have polymorphisms and you should always add qualifiers such as "disease-causing" or "low frequency" for clarity if it is important. The terms have fairly precise meanings in genetics but are used quite lazily in the literature - particularly popular science - with discipline-specific nuances, so when reading "mutation" or "polymorphism", you always have to defer to the context to work out what is meant - and sometimes, even then, it will not be clear.
There is a contradiction going on in order to differentiate these terms that's why scientists are preferring to use the word variation instead of mutation or polymorphism
Genetic changes that occur in more than 1 percent of the population are called polymorphisms and less than that is a mutation. Mutation applies to all "GENETIC" changes or variations (nucleotide substitutions, indels, changes in genomic location of transposable genetic elements and chromosome rearrangements etc). Polymorphisms are common enough to be considered a normal variation in the DNA.
Polymorphism and mutation are not equivalent terms. A polymorphism is a detectable difference occurring among individuals within a population, which means that the variants coexist in the population. Thus, it excludes changes observed among evolutionarily related species or changes occurring in geographically-isolated populations. Since it is a detectable difference, the presence of polymorphism would depend on how it is detected. It could be a morphological variant (eye color), indels or change of a single base in a DNA sequence (SNP).
A mutation in a coding sequence for an enzyme, for instance, if it produces a codon that codes for the same amino acid, it could be a SNP if detected by sequencing, but would not be a polymorphism if detected by isozyme approach (no change/variation would be detected in that case).
I must add to my previous comment that a mutation is ANY change in the DNA sequence, and it could be beneficial, deleterious (associated to a disease) or neutral. So, you can call mutation to this change even if not associated to a disease. If you are able to detect variants of this change whithin a population, then you can call it a polymorphism.
Terminology is not exact and there is usually further context, which is why we often have additional qualifiers, e.g. "germline mutation" versus "somatic mutation", the latter of which is not inherited from the parents (e.g. in cancer). In layman's term "mutation" has a negative context, but the point was made above that in its scientific context, the word simply denotes a change, whether good, bad, or neutral.
I'm not going to repeat myself here - in addition to the links Sabine posted above, the same question was asked a few months ago and has a lot of answers: https://www.researchgate.net/post/What_is_the_difference_between_polymorphism_and_a_mutation
Short answer: individuals have mutations, populations have polymorphisms and you should always add qualifiers such as "disease-causing" or "low frequency" for clarity if it is important. The terms have fairly precise meanings in genetics but are used quite lazily in the literature - particularly popular science - with discipline-specific nuances, so when reading "mutation" or "polymorphism", you always have to defer to the context to work out what is meant - and sometimes, even then, it will not be clear.
As I see it (and in a very simplw way to explain it), Polymorphism is a pool of options for a gene, you can expect an A or a B version of that gene.
Mutation is a change in that gene, it can be any type of mutation(invertion, deletion, etc) and is not "registred" or predictable.
If you exposes a cell to UV light, you know it will mutate, but you cant know how will be the mutation or the efects. but if you are looking for polymorphism, you know that you can get an A or a B version of it.
Recent papers tend to differentiate Polymorphism from Mutation just by terms of occurrence ratio and penetrance .. Polymorphism is defined as allelic variation of more than 1% of the population being studied while many mutational events are quite less. Many of the other features could be claimed for both for example about 55% of the polymorphic variants recorded in HGMD are ‘disease-associated’!!!!
A very useful tool to understand the difference is the HGMD designed by colegeus in Cardiff ..
Mutation is a quantitative and qualitative change in the structure of an organism's DNA. Mutations or are not compatible with life or lead to inefficient functioning of the genome. The principal difference between mutation and polymorphism, in consequences changes DNA.
In summary can be said: A mutation is a genetic change that has occurred in an individual organism (e.g., an A is changed to a G in a cell of an organism.). A polymorphism is the existence of multiple genetic varieties within a population (e.g., At a particular place in the genome, some organisms within a population have A's and other organisms within the population have G's.)
Mutations and polymorphisms can be advantageous, deleterious, or neutral. All polymorphisms began their existence as mutations. A mutation always occurs in an individual, but can become a polymorphism if it is heritable (i.e., if the mutation affected the germ line) and if it succeeds in spreading through a significant proportion of the population.
Genetic information exists as the DNA base sequence. A range of chemical substances and radiation can alter bases and may further cause errors in DNA replication. Changes in genetic information are termed mutations. Genetic mutations are of many types, ranging from a single base substitution to the deletion of a large region containing multiple genes. A difference in the sequence that is observed in less than 1% of the population is termed a mutation. Mutations known to cause genetic diseases are generally observed at extremely low frequency. In contrast, if this difference is observed in more than 1% of the population, then it is termed polymorphism.
When a single base of a gene is substituted, it may result in no change in the amino acids comprising the protein (silent mutation); it may result in a change of one amino acid to another (missense mutation), or it may result in a termination codon (nonsense mutation). Proteins encoded by genes with silent and missense mutations are usually not dysfunctional or are slightly dysfunctional. Therefore, these changes do not have a major positive or negative effect onsurvival. (In some cases, large changes in function are also observed.) Thus, many individuals within populations of living organisms may have altered sequences. This type of mutation is called single nucleotide polymorphism. If two types of sequences are each observed in a 50% ratio in the population, we refer to them as polymorphisms, without being able to determine the mutated form.
As a non-geneticist what i could understand is...All Polymorphisms are Mutations but all mutations are NOT polymorphisms. Polymorphism is a feature/property which may or may not be exhibited by a particular mutation. Also, As Richards says....Polymorphism is the phenomenon of prevalence of a mutation in context of a population only.