Gene mutation nomenclature??

PRPH2 gene mutation nomenclature can be a bit cryptic at first. It is a letter-number salad that makes no sense at first glance. Fortunately, that salad isn’t really that complicated. For example, a common mutation is designated as:

c.514C>T, p.Arg172Trp

Let´s talk about each of those designators.

The nomenclature that starts “c.-----“ (in this case c.514C>T) describes the mutation in the gene. Genes can be thought of as a long string of letters. And in genes, there are only four possible letters: A, G, C and T. So in the case of c.514C>T, at the 514th letter in the string, this mutation changes so that instead of being a C, instead of T. By the way, the four letters stand for adenine, guanine, cytosine, and thymine.

The nomenclature that starts “p.----“ (in this case, p.Arg172Trp) describes the mutation in the protein. Proteins can also be thought of as a string of items but for proteins, it is a string of amino acids. There are 20 amino acids and they are designated by a one or three letter abbreviations such as Arg or Trp to refer to Arginine and Tryptophan. All the amino acids are listed at the bottom of this article. So p.Arg172Trp means that at the 172nd amino acid, there should be Arginine but in this mutation, it is Tryptophan. There a numerous possible mutations. The one described above is called a missense mutation. In addition, to missense, there commonly are mutations denoted as deletions (amino acids are missing), insertions (amino acids added), and splice site (these are special cases where mutation affects the genetic machinery which then alters the protein). The nomenclature for insertion and deletions tends to be somewhat explanatory.

The following cartoon (Fig. 1) is a rough representation of the PRPH2 protein. The cartoon looks like a bunch of ping-pong balls glued together with letters on each ping-pong ball. Those ping-pong balls represent amino acids and the letters tell which amino acid it should be in an unmutated PRPH2. The numbers (where provided) indicate the position of that amino acid. The interesting thing about proteins is the actual structure. The cartoon is merrely a rough approximation but gives a sense of the protein. Attribution for this cartoon is located in caption.

List of the 20 amino acids (name, three letter abbrev, one letter abrev)

• alanine - ala - A

• arginine - arg - R

• asparagine - asn - N

• aspartic acid - asp - D

• cysteine - cys - C

• glutamine - gln - Q

• glutamic acid - glu - E

• glycine - gly - G

• histidine - his - H

• isoleucine - ile - I

• leucine - leu - L

• lysine - lys - K

• methionine - met - M

• phenylalanine - phe - F

• proline - pro - P

• serine - ser - S

• threonine - thr - T

• tryptophan - trp - W

• tyrosine - tyr - Y

• valine - val - V