- databases for immunodeficiency-causing variations

   Variation registry for  X-linked agammaglobulinemia (XLA)

Patient Identification System

Immunodeficiency mutation databases (IDbases) have a unique feature, Patient Identity Number (PIN), which names the patient and mutation in a simple and comprehensive, but still unambiguous way. The name indicates the type and location of a mutation using the PIN convention. PIN is given as soon as a mutation is available to the study group. Another way used to identify patients is Accession number, which is a unique, running number that will never be changed.


PINs are formed as follows. Point mutations in the coding region are numbered according to the affected amino acids. The complete PIN contains

1) the single letter amino acid code of the wild type residue,
2) the number of the affected amino acid,
3) the single letter amino acid code of the mutated residue,
4) running number for mutations at this site,
so that eg. L11P(1) means the first listed mutation of leucine 11 to proline.
Members of the same family having the very same mutation are indicated with alphabets following the PIN, eg. L11P(1a) and L11P(1b).

Insertions, Deletions, Nonsense Mutations

Insertions are marked with sign "@" and deletions with "#" in front of the mutation site.
If mutation causes a stop codon it is marked with X and the number of the codon with the newly introduced stop codon.
Thus, #I651X652(1) means deletion at codon 651 causing frameshift mutation leading to appearance of the stop signal at codon 652.
In the rare occasion of inframe insertions or deletions the number of added or deleted residues is indicated by denoting the number of residues preceded by "+" or "-", respectively. @V103+7(1) describes the addition of seven residues inframe after valine 103.
Partially characterized gene rearrangements are listed differently, e.g. gross deletions have PINs starting from Deletion (1).

Intron, Upstream and Downstream Mutations

Due to possible variations in the size of non-coding regions causing numbering problems, the PINs for up- and downstream and intron mutations have only running numbers without giving the actual mutated nucleotide(s).
Intron mutations are indicated by the intron number followed by running number of mutations in the intron. Thus, Intron 5(7) indicates the seventh described mutation affecting intron 5. Similar notation is used for up- and downstream sequences where either "Upstream" or "Downstream" is written before number of the mutation.

Most of the entries are mutations observed in patients. Polymorphic alterations are also included.

The PIN nomenclature is suitable for both X-linked and autosomal diseases.

This site is updated by Jouni Väliaho
Last modified