Non-coding genome in nail-patella syndrome: Genetic diagnosis as a guide for personalized follow-up

Limb malformations are paradigmatic of altered gene regulation in human disease. Nail-Patella Syndrome (NPS) is a rare condition characterized mainly by skeletal defects, glomerulonephritis and glaucoma, with variable expressivity. NPS is caused by the haploinsufficiency or loss-of-function of LMX1B, which encodes a transcription factor involved in limb dorsalization, in the renal glomerular filtration barrier and the anterior segment of the eye. The dorsal expression of LMX1B in the developing limbs is under the control of LMX1B autoregulatory modules (LARMs), which are non-coding cis-regulatory elements (CREs) with a limb-specific enhancer activity. Here, we describe the regulatory landscape and report regulatory anomalies at the LMX1B locus in four families, including the deletion of a CRE, two structural variations disrupting the CRE-promoter interaction, and a 5'UTR variant causing an upstream open reading frame (ORF). Molecular mechanisms involving the non-coding genome can have a tissue-specific impact on gene expression, resulting in incomplete forms of the syndrome, and sometimes modifying its classical mode of inheritance. While approximately 95% of individuals with NPS carry pathogenic variants in the coding regions of LMX1B, non-coding alterations explain the remaining cases. This work highlights the importance of genomic diagnosis (gene ORF versus CRE alteration) for precision medicine and genetic counselling in rare diseases.