Deletions - Deletions occur when the nucleotides are left out of the gene, and they also usually cause a shift in the reading frame that will ultimately truncate the protein. Deletions are named by listing the nucleotide number of the first deleted nucleotide - del (short for deletion) - the nucleotides deleted. If there are more than two nucleotides deleted then the number of nucleotides is listed.
Example: 6174delT in BRCA2 is a T that is deleted at nucleotide position 6174. This frame shift causes a stop codon at amino acid position 2003, truncating the protein.
Insertions - Insertions are additional nucleotides that are inserted and usually cause a shift in the reading frame that will ultimately truncate the protein. Insertions are named by listing the nucleotide number of the last wild type nucleotide before the insertion - ins (short for insertion) - the nucleotides inserted. If there are more than two nucleotides inserted then the number of nucleotides is listed.
Example: 5385insC in BRCA1 is a C nucleotide inserted after the nucleotide position 5385. This frame shift will result in generation a stop codon at amino acid position 1829, truncating the protein.
Intronic Mutations - Intronic mutations occur in the regions between exons (the coding regions). Introns are important for the correct splicing of the mRNA. A single base change, insertion or deletion could cause incorrect splicing of the mRNA and lead to an abnormal size protein. These mutations are named IVS (intervening sequence) - intron number (same as the exon number preceding it) - location of the mutation relative to the nearest exon (+ if upstream, - if downstream) mutation description (ins or del as described above).
Example: IVS1-2A>G in MSH2. This is a wild type A that is changed to a G, two nucleotides (-2) from the beginning of exon 2.
Missense Mutations - Missense mutations are alterations in the DNA that change one amino acid in the protein. These mutations are denoted by a one-letter abbreviation for the wild type (or normal) amino acid - then the codon number - and finally the one letter abbreviation for the mutated amino acid.
Example: C77Yin MLH1. At nucleotide position 230, G is the wild type base. When this base is changed to an A, codon 77 changes from TGT, which codes for cysteine (C), to TAT, which codes for tyrosine (Y).
Nonsense Mutations - Nonsense mutations are alterations in the DNA that insert a stop codon prematurely instead of an amino acid, so the protein is truncated. These mutations are named with the one letter abbreviation for the wild type amino acid - the codon number - X, signifying the stop codon.
Example: L385X in BRCA2, nucleotide position 1381, A is the wild type base. When this base is changed to a T, codon 385 changes from AAG, which codes for lysine (K), to TAG, which codes for a stop codon (X).