Molecular Landscape in Limb Anomalies: Diagnostic Yield and New Candidate Genes

Congenital limb anomalies remain without an etiological diagnosis in up to 65% of patients. To help close this gap, we describe the genetic diagnostic outcomes of a large cohort. Patients whose primary indication for genetic consultation was a limb anomaly were included from 2014 to 2024. Demographic, investigation, and diagnostic information were extracted, described, and compared. One hundred and thirty-two patients were included in the final cohort, with an average molecular diagnostic yield of 36%. The most common conditions were polydactyly (24%) and radial anomalies (19%). Fifty percent had syndromic features. Seven (5%) patients underwent chromosomal microarray (CMA) only, 81 (63%) CMA and a gene panel, and 43 (32%) subsequently underwent exome sequencing. Exome yielded a diagnosis in 11 (25%). We identified 25 novel mutations in known disease-causing genes, including TBX3 (3 cases) and expanded the phenotype of several loci, including BMP4 and HNRNPH2. Finally, we identified two new limb anomalies candidate loci, for which previously published mouse studies from other groups suggested roles in limb development: HOXA11 and a 2q31.1 deletion involving HOXD10 and HOXD12. This represents the second largest described limb anomalies cohort. Exome-wide sequencing associated with literature and database searches for mouse data represents an opportunity to identify novel etiologies in this group of disorders, including two candidate loci we identified.