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This work describes an automatic methodology to discriminate between individuals with the genetic disorder Pitt-Hopkins syndrome (PTHS), and healthy individuals. As input data, the methodology accepts unconstrained frontal facial photographs, from which faces are located with Histograms of Oriented Gradients features descriptors. Pre-processing steps of the methodology consist of colour normalisation, scaling down, rotation, and cropping in order to produce a series of images of faces with consistent dimensions. Sixty eight facial landmarks are automatically located on each face through a cascade of regression functions learnt via gradient boosting to estimate the shape from an initial approximation. The intensities of a sparse set of pixels indexed relative to this initial estimate are used to determine the landmarks. A set of carefully selected geometric features, for example, relative width of the mouth, or angle of the nose, are extracted from the landmarks. The features are used to investigate the statistical differences between the two populations of PTHS and healthy controls. The methodology was tested on 71 individuals with PTHS and 55 healthy controls. Two geometric features related to the nose and mouth showed statistical difference between the two populations.