SNVdistro

SNVdistro

SNVdistro visualises the frequency and distribution of SNVs on 3D protein structures. It combines data from gnomAD, dbSNP, and ClinVar to generate a customised pymol heatmap.

More detailed version

SNVdistro is a program designed to visualise the distribution, frequency, and clinical significance of single nucleotide variants (SNVs) on the three-dimensional structure of proteins. It integrates variant data from population and clinical databases such as gnomAD, dbSNP, and ClinVar to enable users to generate customisable 3D heatmaps using PyMOL, highlighting where variants cluster in protein structures. The tool uses UniProt ID as an input to identify the gene of interest and retrieves its reference sequence. The reference sequence is then used to search through Protein Data Base (PDB) for matching structural entries. It then searches through the database for SNVs in the coding sequence of the protein and applies user-defined filters (e.g. clinical significance, allele frequency etc).

The amino acid residues are then assigned a colour based on SNV frequency: red for residues with high frequency for SNVs, blue for low-frequency, and white where no variants are found. This allows the user to identify hotspots of pathogenicity or functionally significant regions, supporting the interpretation of variants of uncertain significance (VUS).