Expanding the genotype and phenotype spectrum of SYT1-associated neurodevelopmental disorder

Genet Med. 2022 Apr;24(4):880-893. doi: 10.1016/j.gim.2021.12.002. Epub 2022 Jan 29.


Purpose: Synaptotagmin-1 (SYT1) is a critical mediator of neurotransmitter release in the central nervous system. Previously reported missense SYT1 variants in the C2B domain are associated with severe intellectual disability, movement disorders, behavioral disturbances, and electroencephalogram abnormalities. In this study, we expand the genotypes and phenotypes and identify discriminating features of this disorder.

Methods: We describe 22 individuals with 15 de novo missense SYT1 variants. The evidence for pathogenicity is discussed, including the American College of Medical Genetics and Genomics/Association for Molecular Pathology criteria, known structure-function relationships, and molecular dynamics simulations. Quantitative behavioral data for 14 cases were compared with other monogenic neurodevelopmental disorders.

Results: Four variants were located in the C2A domain with the remainder in the C2B domain. We classified 6 variants as pathogenic, 4 as likely pathogenic, and 5 as variants of uncertain significance. Prevalent clinical phenotypes included delayed developmental milestones, abnormal eye physiology, movement disorders, and sleep disturbances. Discriminating behavioral characteristics were severity of motor and communication impairment, presence of motor stereotypies, and mood instability.

Conclusion: Neurodevelopmental disorder-associated SYT1 variants extend beyond previously reported regions, and the phenotypic spectrum encompasses a broader range of severities than initially reported. This study guides the diagnosis and molecular understanding of this rare neurodevelopmental disorder and highlights a key role for SYT1 function in emotional regulation, motor control, and emergent cognitive function.

Keywords: Intellectual disability; Neurotransmission; Synapse; Synaptic vesicle; Synaptotagmin.

MeSH terms

  • Calcium / metabolism
  • Genotype
  • Humans
  • Intellectual Disability* / genetics
  • Movement Disorders* / genetics
  • Neurodevelopmental Disorders* / genetics
  • Phenotype
  • Synaptotagmin I* / genetics


  • SYT1 protein, human
  • Synaptotagmin I
  • Calcium