# Loss-of-function variants in the CAPN1 activator CD99L2 cause X-linked spastic ataxia

## TL;DR

The study identifies CD99L2 as a gene linked to X-linked spastic ataxia and shows how genome analysis improves diagnosis in rare movement disorders.

## Contribution

Discovers CD99L2 as a novel X-linked gene causing spastic ataxia and reveals its role in CAPN1 signaling.

## Key findings

- Genome analysis beyond exomes increases diagnostic yield by 7.5% in rare movement disorders.
- Loss-of-function variants in CD99L2 cause X-linked spastic ataxia through disrupted CAPN1 signaling.
- CD99L2 interacts with CAPN1, and its dysfunction leads to neurodegeneration and synaptic disturbances.

## Abstract

Most patients with a rare movement disorder (MD) do not receive a molecular diagnosis, and the underlying genetic variants and mediating genes remain elusive. Here, we evaluate the diagnostic accuracy of conventional and next-generation sequencing-based genetic testing strategies in a cohort of 2,811 individuals with ataxia, spastic paraplegia and dystonia. Exome sequencing establishes genetic diagnoses in 19.3% of cases, and specificity of phenotypic features and age at testing are positive predictors. Genome analysis ‘beyond the exome’ increases the diagnostic yield by 7.5%, mostly due to the improved detection of structural variants and repeat expansions. Unsolved cases are included in the Solve-RD cohort and subjected to gene-burden analysis, providing evidence for loss-of-function variants in X-chromosomal CD99L2 causing spastic ataxia. Cellular studies show that the transmembrane protein CD99L2 occurs mainly in a ubiquitinated form and serves as an activating interactor of the calcium-dependent protease CAPN1. Ablation of cytoplasmic or extracellular domains of CD99L2 leads to its intracellular mislocalization and abrogation of its interplay with CAPN1. Transcriptome analysis in CD99L2 patient-derived fibroblasts reveals synaptic function-specific disturbances. Impaired CAPN1 activation and dysregulation of downstream neuronal pathways constitute the likely molecular cause for neurodegeneration.

Here the authors compare genetic testing strategies in rare movement disorders, improve diagnostic yield with genome analysis, and establish CD99L2 as an X-linked spastic ataxia gene, showing that CD99L2–CAPN1 signaling disruption likely drives neurodegeneration.