Four Loss of Function Pathogenic Variants in ARHGAP29 in Non-Syndromic Cleft Lip and Palate

Abstract The pathophysiological basis of non-syndromic cleft lip and/or palate (NsCL/P) is still largely unclear. However, exome sequencing (ES) has allowed to associate several genes with NsCL/P, often with reduced penetrance. Among these genes, the Rho GTPase activating protein 29 (ARHGAP29) has been previously implicated in 7 families with NsCL/P. We investigated a cohort of 224 NsCLPs for which no genetic mutation had been identified by diagnostic testing. We used ES and bioinformatic variant filtering and identified four novel likely pathogenic/pathologic variants in ARHGAP29 in four multiplex families. One was a missense variant leading to the substitution of the first methionine with threonine, two were heterozygous frameshift variants leading to a premature termination codon, and the last one was a nonsense variant. All variants were predicted to result in loss of function, either through NMD-mediated mRNA decay, or by truncated ARHGAP29, or by non-translation or abnormal N-terminal initiation of translation of ARHGAP29. The truncated ARHGAP29 proteins would lack the important RhoGAP domain. The variants were not present in the control population databases, and the loss of intolerance score (pLI) of ARHGAP29 is 1.0, suggesting that ARHGAP29 haploinsufficiency is not tolerated. Phenotypes ranged from microform CL to complete bilateral CLP, with one unaffected mutation carriers. These results extend the mutational spectrum of ARHGAP29 and show that it is an important gene underlying variable NsCL/P phenotypes. ARHGAP29 should be included in diagnostic genetic testing for NsCL/P, especially familial cases, as it may be mutated in ⁓2% of patients with high penetrance (88%).