FH aHUS Mutation Database ©
Help Page
Searches
  • You can carry out a variety of different searches varying from simply returning the mutations within a domain to complex queries that retrieve mutations of a certain phenotype, amino acid type and from specific authors over a range of domains
  • The results of each search are shown as a HTML interface, where patient data can either be displayed or omitted at the touch of a button. An excel spreadsheet of the results is available by clicking the "Excel Results" link at the top right corner of the page. The user can choose whether to include or not include different data fields
  • Alongside this Excel link are printable versions of the search results.
  • The quicksearch feature on the home page can be used to retrieve data on mutations for a specific codon number within a protein.
Mutation Data
  • The nucleotide description for each mutation includes the nucleotide number, where, following HGVS guidelines c. represents cDNA. Sequences are numbered from +1 starting with the A of the ATG initiation codon, taken from RefSeq files accesion #: NM_000186.1 (FH), #:NP_000195.1 (FI) and #:NM_002389.3 (MCP).
  • Following HGVS guidelines, amino acids are numbered starting from the ATG initiation codon and include the signal peptide. The number of the codon with respect to the mature protein is shown alongside in parenthesis.
  • The sequence used for MCP represents Isoform A. For more information read MCP info pages
  • The position field describes the location of the residue within the homology models of the protein domains using the consensus set of Β-Sheets for SCR domains and other domains. They are given as DSSP assignments (B = etc) and the cysteine and Β strands are indicated by numbers. The six conserved Βstrands within each SCR of FH are numbered 1-6 in the order they occur in the sequence, and similarly the four conserved cysteine residues are numbered 1-4 in the order they occur in the sequence. The secondary structures and cysteine residues in the FI and MCP domains are also numbered in the order that they occur in the sequence.
Patient Data
  • Patient data can be displayed for each mutation on the results page by using the expand button under the Patient Data column.
  • The patient data in this database is taken where possible from the literature reporting the mutations. It includes the results of mutant protein and C3 assays for the reported patients and also has comments on any experimental data on the mutant protein.
  • If the patient and/or mutation have only been entered in the database and not fully reported in a peer reviewed journals - these will be flagged as hving no reference.
  • The Type field indicates the phenotypic classification of the mutation using the reported levels of mutant protein from patient plasma. Levels are given as low (L), normal (N) or high (H).
    • A low level of protein indicates a Type I phenotype where the mutant protein is not available in normal amounts, and therefore the mutation must have a structural effect on the mutant protein affecting stability, for example leading to problems with secretion.
    • A normal or high level of protein indicates a Type II phenotype where the mutant protein is available in normal amounts, and so must be dysfunctional.
  • A number of the patients are compound heterzygous for different mutations, and this can effect the analysis of these mutations. Wherever this occurs, patient data displays a genotype of CH and the corresponding entry for the other mutation can be displayed.
  • The data for mutant protein and C3 levels is taken from the references where possible and is quoted as L (low) , N (normal) or H (high) using the normal benchmark used in the original study from the paper. Details of the assays have been added to the records for clarity when comparing different mutations from different studies.
References
  • Each patient record has a reference field quoting the reference that originally discussed the patient and mutation. References are quoted in full using the reference link and the pubmed entry for the mutation can be displayed be clicking the link.
Structural Analysis
  • Detailed analysis of any possible point mutation can be carried out using the homology models of the FH, FI or MCP domains. The mutations can be displayed on each relevant domain and also in the lowest energy structure from the full FH solution scattering model 1haq.pdb.
  • Caution must be taken when using this analysis with homology models because DSSP assignments and accessibility scores may not be so accurate in unconserved loop regions of the models.
  • The structural analysis displays the model using the JMol java applet (http://jmol.sourceforge.net/index.html). This requires a Java plug-in for your browser. If you do not already have this , it can be downloaded from www.java.com.
  • In order to see side chains within the models use an indepth mutation view from your search results or use a new mutation analysis
  • Accessibility scores are given that represent the relative side chain surface accessibility to a probe the size of a water molecule. Scores are given from 0-9 where 0 denotes 0-9% accessibility, 1 denotes 10-19% accessibility, and so on up to 9. Residues with accessibilities up to 19% are considered to be buried.
  • DSSP analysis classifies secondary structure as a letter corresponding to the following values: turn (T), 310-helix (G), α-helix (H), π-helix (I), β-bridge (B), extended β-strands (E), bends (S) and unclassified regions are termed coil (C).