Exome sequencing of 1190 non-syndromic clubfoot cases reveals <i>HOXD12</i> as a novel disease gene.

Abstract

Clubfoot, presenting as a rigid inward and downward turning of the foot, is one of the most common congenital musculoskeletal anomalies. The aetiology of clubfoot is poorly understood and variants in known clubfoot disease genes account for only a small portion of the heritability. Exome sequence data were generated from 1190 non-syndromic clubfoot cases and their family members from multiple ethnicities. Ultra-rare variant burden analysis was performed comparing 857 unrelated clubfoot cases with European ancestry with two independent ethnicity-matched control groups (1043 in-house and 56 885 gnomAD controls). Additional variants in prioritised genes were identified in a larger cohort, including probands with non-European ancestry. Segregation analysis was performed in multiplex families when available. Rare variants in 29 genes were enriched in clubfoot cases, including <i>PITX1</i> (a known clubfoot disease gene), <i>HOXD12</i>, <i>COL12A1</i>, <i>COL9A3</i> and <i>LMX1B</i>. In addition, rare variants in posterior <i>HOX</i> genes (<i>HOX9-13</i>) were enriched overall in clubfoot cases. In total, variants in these genes were present in 8.4% (100/1190) of clubfoot cases with both European and non-European ancestry. Among these, 3 are <i>de novo</i> and 22 show variable penetrance, including 4 <i>HOXD12</i> variants that segregate with clubfoot. We report <i>HOXD12</i> as a novel clubfoot disease gene and demonstrate a phenotypic expansion of known disease genes (myopathy gene <i>COL12A1</i>, Ehlers-Danlos syndrome gene <i>COL9A3</i> and nail-patella syndrome gene <i>LMX1B</i>) to include isolated clubfoot.