Background Lamb–Shaffer syndrome (LAMSHF) is a rare neurodevelopmental disorder caused by heterozygous mutation or microdeletion involving the SOX5 gene. LAMSHF is characterize by developmental delay, intellectual disability, poor expressive speech, mild dysmorphic facial features and skeletal abnormalities. Case presentation We presented a case of a child with delayed psychomotor development in all areas, scoliosis, peculiar facies, and suspicion of intermittent endotropia, alteration in the alignment of one foot and difficulty in standing. These clinical features lead to genetics studies, in which a novel pathogenic variant in the SOX5 gene was detected in association with LAMSHF. Conclusions LAMSHF should be suspected in patients with developmental delay, speech delay, intellectual disability, behavioural disturbances, ophthalmological alterations and skeletal abnormalities. A novel pathogenic mutation in the SOX5 gene c.1627del p.(Tyr543IlefsTer14) was identified in this patient as responsible of Lamb–Shaffer syndrome. This case contributes to understanding the genetic characteristics, clinical features, and diagnosis of LAMSHF.