Candidate Genes for Nonsyndromic Cleft Palate Detected by Exome Sequencing

Abstract

Nonsyndromic cleft palate only (nsCPO) is a facial malformation that has a livebirth prevalence of 1 in 2,500. Research suggests that the etiology of nsCPO is multifactorial, with a clear genetic component. To date, genome-wide association studies have identified only 1 conclusive common variant for nsCPO, that is, a missense variant in the gene grainyhead-like-3 ( GRHL3). Thus, the underlying genetic causes of nsCPO remain largely unknown. The present study aimed at identifying rare variants that might contribute to nsCPO risk, via whole-exome sequencing (WES), in multiply affected Central European nsCPO pedigrees. WES was performed in 2 affected first-degree relatives from each family. Variants shared between both individuals were analyzed for their potential deleterious nature and a low frequency in the general population. Genes carrying promising variants were annotated for 1) reported associations with facial development, 2) multiple occurrence of variants, and 3) expression in mouse embryonic palatal shelves. This strategy resulted in the identification of a set of 26 candidate genes that were resequenced in 132 independent nsCPO cases and 623 independent controls of 2 different ethnicities, using molecular inversion probes. No rare loss-of-function mutation was identified in either WES or resequencing step. However, we identified 2 or more missense variants predicted to be deleterious in each of 3 genes ( ACACB, PTPRS, MIB1) in individuals from independent families. In addition, the analyses identified a novel variant in GRHL3 in 1 patient and a variant in CREBBP in 2 siblings. Both genes underlie different syndromic forms of CPO. A plausible hypothesis is that the apparently nonsyndromic clefts in these 3 patients might represent hypomorphic forms of the respective syndromes. In summary, the present study identified rare variants that might contribute to nsCPO risk and suggests candidate genes for further investigation.

Whole‐genome sequencing in a pair of monozygotic twins with discordant cleft lip and palate subtypes

“…Along with IRF6 , GRHL3 is essential to a functional oral periderm, and a failure of this process contributes to Van der Woude syndrome (Peyrard‐Janvid et al., ). The GRHL3 mutation (NM_198173:c.‐187G>A) identified in our study was also reported in a previous study in a patient with only nonsyndromic CP (Hoebel et al., ). Multiple study designs and statistical approaches could be used to address the rare variant hypothesis for NSCLP (Leslie et al., ).…”

Microphthalmia, Linear Skin Defects, Callosal Agenesis, and Cleft Palate in a Patient with Deletion at Xp22.3p22.2

“…13,17 The cleft palate present in our patient is a very unusual finding within the MLS spectrum, having been reported only once in a patient with lower limb linear skin defects and no identifiable abnormalities in karyotype or microarray. 7 There is no known candidate gene for nonsyndromic cleft palate in the Xp22.3p22.2 region, 24,25 however, pathogenic variants and deletions in some genes in this region, such as ANOS1 and MID1, result in syndromic orofacial cleft. ANOS1, also called KAL1, is the first gene found to be responsible for Kallmann syndrome, 26 a heterogeneous genetic condition characterized by hypogonadotropic hypogonadism with anosmia.…”

Novel rare variations in IRF6 in subjects with non‐syndromic cleft lip and palate and dental agenesis

“…This definition of the associated dental phenotype is also important because several authors have previously emphasized the importance of a correct clinical diagnosis of volunteers for genetic studies involving clefts, particularly with regard to VWS, characterized by the presence of orofacial clefts, lower lip pits, and dental agenesis (in 25% of cases) (Chen et al, ; Hoebel et al, ; Rutledge et al, ; Zucchero et al, ). For this reason, in the present study, oral photographs and familial history were reviewed in all cases where novel or rare variations were identified in order to confirm no alterations in the lower lip and no familial history for cleft or other alterations.…”

“…Cleft lip and palate (CLP) is the most common orofacial malformation and is classified as either non‐syndromic or syndromic according to whether they form part of a broader disorder or phenotype associated with other morphological anomalies (Gowans et al, ; Rahimov, Jugessur, & Murray, ). Approximately 70% of the orofacial cleft cases are non‐syndromic (NS) with multifactorial etiology including both genetic and environmental factors (Hoebel et al, ). These factors confound attempts to identify specific genes for the anomaly (Leslie et al, ).…”