DYNC1H1 encodes the heavy chain of dynein 1, a protein that plays a critical role in intracellular transport and is also involved in neurogenesis, bipolar spindle apparatus formation, and interaction with certain regulatory proteins. Many variants of the gene are described in various neuromuscular, psychoneurological, congenital abnormalities, and malignancies. In this clinical case, the correlation of clinical manifestations with molecular genetic changes of the DYNC1H1 gene was evaluated. A variant was identified and presented de novo in the linker domain of the protein in a patient with abnormalities of brain development (pachygyria of the temporal and frontal lobes, polymicrogyria of the occipital lobes, cerebellar agenesis), polydactylitis, mental development disorder, and involvement of the neuromuscular system, as well as congenital cataracts. In this case, a new feature is described — polydactyly — not previously described in the variant c.4868G>A (p.Arg1623Gln), which expands the range of clinical manifestations and can contribute to the understanding of the mechanisms of phenotypic heterogeneity, as well as the development of optimal diagnostic algorithms.