Question: Where do mutations occur?
About the article "Evolution", section "Mutation".

Candidate passages:
The most common function is found during the cell cycle when mutations occur because it becomes activated without phosphorylation and turns on Cds1.
It also works with Cdk1 to get rid of the mutations that occur.
If MCR 1 is not present in the cell these check points do not work properly. 
As noted above, about 3 or 4 driver mutations and 60 passenger mutations occur in the exome (protein coding region) of a cancer.
However, a much larger number of mutations occur in the non-protein-coding regions of DNA.
The average number of DNA sequence mutations in the entire genome of a breast cancer tissue sample is about 20,000.
In an average melanoma tissue sample (where melanomas have a higher exome mutation frequency) the total number of DNA sequence mutations is about 80,000.  
Causes.
"Pax2" mutations.
The majority of mutations occur in exons 2,3 and 4, which encode the paired domain and frame shift mutations that lead to a null allele.
The missense mutations appear to disrupt hydrogen bonds, leading to decreased transactivation of "Pax2", but do not seem to effect nuclear localization, steady state mRNA levels, or the ability of "Pax2" to bind to its DNA consensus sequence.
Mutations related to the disease have also been noted in exons 7,8, and 9, with milder phenotypes than the other mutations. 
Mutagens cause changes to the DNA that can affect the transcription and replication of the DNA, which in severe cases can lead to cell death.
The mutagen produces mutations in the DNA, and deleterious mutation can result in aberrant, impaired or loss of function for a particular gene, and accumulation of mutations may lead to cancer.
Different mutagens act on the DNA differently.
Powerful mutagens may result in chromosomal instability, causing chromosomal breakages and rearrangement of the chromosomes such as translocation, deletion, and inversion.
Such mutagens are called clastogens.
Mutagens may also modify the DNA sequence; the changes in nucleic acid sequences by mutations include substitution of nucleotide base-pairs and insertions and deletions of one or more nucleotides in DNA sequences.
Although some of these mutations are lethal or cause serious disease, many have minor effects as they do not result in residue changes that have significant effect on the structure and function of the proteins.
Many mutations are silent mutations, causing no visible effects at all, either because they occur in non-coding or non-functional sequences, or they do not change the amino-acid sequence due to the redundancy of codons.
Some mutagens can cause aneuploidy and change the number of chromosomes in the cell.
In Ames test, where the varying concentrations of the chemical are used in the test, the dose response curve obtained is nearly always linear, suggesting that there is no threshold for mutagenesis.
Similar results are also obtained in studies with radiations, indicating that there may be no safe threshold for mutagens.
However, some proposed that low level of some mutagens may stimulate the DNA repair processes and therefore may not necessarily be harmful. 
  BAP1 somatic mutations were identified in a small number of breast and lung cancer cell lines, but BAP1 was first shown to act as a tumor suppressor in cultured cells, where its deubiquitinase (UCH) domain and Nuclear localization sequences were required for BAP1 to suppress cell growth.
In 2010, Exome sequencing identified inactivating mutations in BAP1 in 47% of Uveal melanomas, and BAP1 mutation was strongly associated with metastasis.
These mutations included multiple Nonsense mutations and splice site mutations throughout the gene.
missense mutations were only found within the UCH and ULD domains, further supporting the requirement for BAP1 catalytic function.
This study also identified a Germline mutation in one of the uveal melanoma patients, suggesting that, besides being a Metastasis suppressor, BAP1 could predispose certain people to more aggressive uveal melanoma tumors.
BAP1 mutations have been identified in aggressive Mesotheliomas with similar mutations as seen in melanomas.
Mutations in the tumor suppressor gene BAP1 occur in approximately 15% of clear cell renal cell carcinoma (CCRCC) cases.
Sequencing efforts demonstrated worse outcomes in patients with BAP1 mutated clear cell renal cell carcinoma.
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