The genetics of isolated orofacial clefts: from genotypes to subphenotypes


  • A Jugessur,

    1. Musculoskeletal Disorders Theme, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Vic.
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  • PG Farlie,

    1. Musculoskeletal Disorders Theme, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Vic.
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  • N Kilpatrick

    1. Musculoskeletal Disorders Theme, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Vic.
    2. Department of Dentistry, Royal Children’s Hospital, Parkville, Vic., Australia
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Dr A Jugessur, Musculoskeletal Disorders Theme, Murdoch Childrens Research Institute, Royal Children’s Hospital, Flemington Road, 3052 Parkville, Vic., Australia. Tel: +613 9345 4109, Fax: +613 8341 6429, E-mail:


Orofacial clefts are the most common craniofacial birth defects and one of the most common congenital malformations in humans. They require complex multidisciplinary treatment and are associated with elevated infant mortality and significant lifelong morbidity. The development of craniofacial structures is an exquisitely orchestrated process involving the coordinated growth of multiple, independently derived primordia. Perturbations impacting on the genesis or growth of these primordia may interfere with the proper morphogenesis of facial structures, resulting in clefting of the lip, the primary or secondary palate, or a combination of these sites. A variety of genetic approaches involving both human populations and animal models have greatly facilitated the search for genes involved in human clefting. In this article, we review the most prominent genes for orofacial clefts in the context of developmental pathways that shape the craniofacial complex. We highlight several Mendelian clefting syndromes that have provided valuable clues in identifying genes for the more common, isolated forms of clefting. Finally, we elaborate on a number of potential subclinical features (subphenotypes) associated with what have previously been diagnosed as ‘isolated’ clefts that may serve as additional markers for identifying individuals or families in whom there may be a greater risk of inheriting a cleft.

Epidemiology of orofacial clefts

Orofacial clefts are the most common craniofacial birth defects in humans, with an average worldwide prevalence at birth of 1.2/1000 (Mossey and Little, 2002). They represent a significant public health burden in terms of the immediate and long-term medical costs as well as the social impact on patients and their families (Berk and Marazita, 2002). In the United States, for example, the lifetime cost for treating orofacial clefts has been estimated to be approximately $100 000 (Centers for Disease Control and Prevention, Clinically, patients experience feeding difficulties in infancy; speech, hearing and dental problems as they grow older, and potentially life-long social and psychological sequelae from the facial deformity itself. Clefts also appear to be associated with a higher risk of cancer in later life (Zhu et al, 2002) and increased overall mortality well into adulthood (Christensen et al, 2004).

Orofacial clefts can be broadly divided into those that affect the lip only (CL), both the lip and palate (CLP), or the palate alone (CP) (Figure 1). Although CL and CLP are traditionally collapsed to form the single group of cleft lip with or without cleft palate (CL/P), recent data suggest that these two categories may have different genetic causes and should, when feasible, be analysed separately (Harville et al, 2005; Rahimov et al, 2008). Epidemiological data across different populations have shown that the prevalence of CP is generally lower than that of CL/P and families at high risk for one type of cleft are not at increased risk for the other type, reflecting the distinct developmental origins of each form of cleft (Jugessur and Murray, 2005). Occasionally, however, both CL/P and CP can occur within the same pedigree, suggesting at least some overlap in the aetiology of these two broader categories of clefts. Such instances of ‘mixed clefting’ are more commonly observed in clefting syndromes, such as Van der Woude syndrome (VWS) caused by mutations in the interferon regulatory factor 6 gene (IRF6) (Kondo et al, 2002) and CL/P with hypodontia caused by mutations in the muscle segment homeobox 1 gene (MSX1) (van den Boogaard et al, 2000).

Figure 1.

 Common forms of orofacial clefts. (a) left-sided cleft lip (CL); (b) left-sided cleft lip and palate (CLP); and (c) cleft palate only (CP). The first two panels are usually collapsed to form the single group of cleft lip with or without cleft palate (CL/P)

A further subdivision of orofacial clefts into ‘syndromic’vs‘isolated’ forms depends on whether additional structural and/or developmental anomalies occur with the cleft. Whilst over 400 Mendelian disorders have been reported in OMIM ( in which clefting occurs as part of the overall clinical presentation, most studies suggest that around 70% of CL/P cases and half of all CP cases arise in the absence of other abnormalities and are thus collectively termed isolated defects (Jugessur and Murray, 2005). A finer subdivision of isolated clefts has recently been proposed based on the presence/absence of subtle subclinical features associated with the overt cleft, with the potential to improve the power of genetic analyses and the accuracy of risk estimates for genetic counselling (Weinberg et al, 2006b; Marazita, 2007).

Compared with other birth defects, orofacial clefts have a high rate of familial recurrence (Lie et al, 1994). In one study, the risk of cleft recurrence in first degree relatives was 32 for cleft lip and 56 for cleft palate alone compared to the reference populations, suggesting a stronger genetic basis for cleft palate compared with cleft lip (Sivertsen et al, 2008). In twin studies, the observed concordance rate of 40–60% in monozygotic (MZ) twins is much higher than the 3–5% concordance rate in dizygotic (DZ) twins. Although this weakens the case for either a purely genetic or purely environmental cause, the high concordance rate in MZ twins nevertheless provides compelling evidence for a strong genetic component to orofacial clefting.

The identification of genetic and environmental risk factors for clefting has been the subject of intensive research for several decades (Jugessur and Murray, 2005; Lidral and Moreno, 2005). The past few years in particular have witnessed major strides in the mapping of orofacial cleft loci, with the list of candidate genes rapidly expanding from the first reported association of transforming growth factor alpha (TGFA) gene variants with isolated CL/P in 1989 (Ardinger et al, 1989) to now include IRF6, MSX1, TGFB3, FOXE1, FGFR1, FGFR2, FGF8, PDGFC, CRISPLD2, PVRL1, GABRB3, MSX2, SATB2, TBX10, TBX22, GLI2, JAG2, MTHFR, RARA, LHX8, SKI and SPRY2, among the most prominent candidate genes for clefts (Ding et al, 2004; Lidral and Murray, 2004; Marazita et al, 2004; Jugessur and Murray, 2005; Lidral and Moreno, 2005; Vieira et al, 2005; Chiquet et al, 2007; Riley and Murray, 2007; Riley et al, 2007). Many of these genes are summarized in Table 1 and will be reviewed in detail in the sections below.

Table 1.   Candidate genes for orofacial clefting
Gene name Gene IDaChromosomeGene description Molecular function | Biological process | Pathwayb
  1. N/A, not available.

  2. aGene ID from NCBI Entrez Gene (

  3. bData collated from the PANTHER database (

BMP465214q22.2Bone morphogenetic protein 4Other signalling molecule | Skeletal development | TGF-beta signalling pathway→Transforming growth factor beta
FGF122465q31Fibroblast growth factor 1Growth factor | Cell surface receptor mediated signal transduction; MAPKKK cascade; Ligand-mediated signalling; Angiogenesis; Cell cycle control; Cell proliferation and differentiation | FGF signalling athway→fibroblast growth factor; Angiogenesis→Fibroblast Growth Factor
FGF1022555p12Fibroblast growth factor 10 precursorGrowth factor | Receptor protein tyrosine kinase signalling pathway | FGF signalling pathway→fibroblast growth factor
FGF1222573q28Fibroblast growth factor 12Growth factor | Receptor protein tyrosine kinase signalling pathway | FGF signalling pathway→fibroblast growth factor
FGF222474q26-q27Fibroblast growth factor 2Growth factor | Cell surface receptor mediated signal transduction; MAPKKK cascade; Ligand-mediated signalling; Angiogenesis; Cell cycle control; Cell proliferation and differentiation | FGF signalling pathway→fibroblast growth factor; Angiogenesis→Fibroblast Growth Factor
FGF4224911q13.3Fibroblast growth factor 4Growth factor | Receptor protein tyrosine kinase signalling pathway; Developmental processes | FGF signalling pathway→fibroblast growth factor
FGF522504q21Fibroblast growth factor 5Growth factor | Receptor protein tyrosine kinase signalling pathway; MAPKKK cascade; Ligand-mediated signalling; Neurogenesis; Cell cycle control; Cell proliferation and differentiation; Oncogene | FGF signalling pathway→fibroblast growth factor
FGF7225215q15-q21.1Fibroblast growth factor 7Growth factor | Cell surface receptor mediated signal transduction; MAPKKK cascade; Ligand-mediated signalling; Ectoderm development; Cell cycle control; Cell proliferation and differentiation; Oncogene | FGF signalling pathway→fibroblast growth factor
FGF8225310q24.32Fibroblast growth factor 8Growth factor | Cell surface receptor mediated signal transduction | FGF signalling pathway→fibroblast growth factor
FGF9225413q11-q12Fibroblast growth factor 9Growth factor | Receptor protein tyrosine kinase signalling pathway | FGF signalling pathway→fibroblast growth factor
FGFR122608p12Fibroblast growth factor receptor 1Tyrosine protein kinase receptor; Protein kinase | Protein phosphorylation; Receptor protein tyrosine kinase signalling pathway; Neurogenesis; Cell proliferation and differentiation; Other oncogenesis | FGF signalling pathway→FGFR1-4; Angiogenesis→Fibroblast Growth Factor Receptor-1
FGFR2226310q26.13Fibroblast growth factor receptor 2Tyrosine protein kinase receptor; Protein kinase | Protein phosphorylation; Receptor protein tyrosine kinase signalling pathway; Neurogenesis; Cell proliferation and differentiation; Other oncogenesis | FGF signalling pathway→FGFR1-4; Angiogenesis→Fibroblast Growth Factor Receptor-1
FGFR322614p16.3Fibroblast growth factor receptor 3Tyrosine protein kinase receptor; Protein kinase | Protein phosphorylation; Receptor protein tyrosine kinase signalling pathway; Neurogenesis; Cell proliferation and differentiation; Other oncogenesis | FGF signalling pathway→FGFR1-4; Angiogenesis→Fibroblast Growth Factor Receptor-1
FGFR422645q35.1-qterFibroblast growth factor receptor 4Tyrosine protein kinase receptor; Protein kinase | Protein phosphorylation; Receptor protein tyrosine kinase signalling pathway; Neurogenesis; Cell proliferation and differentiation; Other oncogenesis | FGF signalling pathway→FGFR1-4; Angiogenesis→Fibroblast Growth Factor Receptor-1
FOXE123049q22Forkhead box E1Other transcription factor; Nucleic acid binding | Carbohydrate metabolism; mRNA transcription regulation; Other receptor mediated signalling pathway; Cell communication; Vision; Embryogenesis; Anterior/posterior patterning; Segment specification; Neurogenesis; Mesoderm development; Cell cycle control; Cell proliferation and differentiation; Cell structure | Insulin/IGF pathway-protein kinase B signalling cascade→Forkhead transcription factor; PI3 kinase pathway→FOXO; Interleukin signalling pathway→Forkhead in Rhabdomyosarcoma-like 1; TGF-beta signalling pathway→Co-activators or corepressors
GLI227362q14.2GLI-Kruppel family member GLI2Zinc finger transcription factor | mRNA transcription regulation; Embryogenesis | Hedgehog signalling pathway→Cubitus interruptus | Hedgehog signalling pathway→Cubitus interruptus repressor
IRF636641q32.2Interferon regulatory factor 6Other transcription factor; Nucleic acid binding | mRNA transcription regulation; Interferon-mediated immunity; Oncogenesis | N/A
MSX144874p16.3-p16.1msh homeobox 1Homeobox transcription factor; Other DNA-binding protein | mRNA transcription regulation; Skeletal development | N/A
MSX244885q34-35msh homeobox 2Homeobox transcription factor; Other DNA-binding protein | mRNA transcription regulation; Skeletal development | N/A
PDGFC560344q32Platelet derived growth factor CGrowth factor | Ligand-mediated signalling; Other developmental process; Cell proliferation and differentiation | Angiogenesis→Platelet-Derived Growth Factor
PDGFRA51564q12Platelet-derived growth factor receptor, alpha polypeptideTyrosine protein kinase receptor; Protein kinase | Protein phosphorylation; Receptor protein tyrosine kinase signalling pathway; Stress response; Gametogenesis; Embryogenesis; Cell proliferation and differentiation; Oncogenesis; Cell motility | Angiogenesis→Platelet-Derived Growth Factor Receptor
PTCH157279q22.3Patched homolog 1Molecular function unclassified | Biological process unclassified | Hedgehog signalling pathway→Patched
PVRL1581811q23Poliovirus receptor-related 1Other receptor; Other defense and immunity protein | Cell adhesion-mediated signalling; Immunity and defense | Alzheimer disease-presenilin pathway
RARA591417q21Retinoic acid receptor, alphaNuclear hormone receptor; Transcription factor; Nucleic acid binding | mRNA transcription regulation; Cell communication; Developmental processes; Oncogenesis | Vitamin D metabolism and pathway→Retinoid X Receptor, Alpha
RUNX28606p21Runt-related transcription factor 2Other transcription factor | Skeletal development; Oncogenesis | N/A
SMAD140864q31SMAD family member 1Other transcription factor | mRNA transcription regulation; Receptor protein serine/threonine kinase signalling pathway; Other intracellular signalling cascade; Ligand-mediated signalling; Developmental processes; Oncogenesis | Wnt signalling pathway→Mothers against decapentaplegic homolog 4; TGF-beta signalling pathway→RSmads
SUMO173412q33SMT3 suppressor of mif two 3 homolog 1 Other miscellaneous function protein | Protein modification; Inhibition of apoptosis; Chromosome segregation; Miscellaneous | p53 pathway→Small ubiquitin-like modifier 1
TBX1689922q11T-box 1Other transcription factor; Nucleic acid binding | mRNA transcription regulation; Developmental processes | N/A
TBX1034785311q13.1T-box 10Other transcription factor; Nucleic acid binding | mRNA transcription regulation; Developmental processes | N/A
TBX2250945Xq21.1T-box 22Other transcription factor; Nucleic acid binding | mRNA transcription regulation; T-cell mediated immunity; Cell proliferation and differentiation | N/A
TCOF169495q33.1Treacher Collins-Franceschetti syndrome 1Transporter | Apoptosis; Hearing; Neurogenesis | N/A
TFAP2A70206p24Transcription factor AP-2 alphaOther transcription factor | mRNA transcription regulation; Ectoderm development; Oncogenesis | N/A
TGFA70392p13Transforming growth factor, alphaOther cytokine | Cytokine and chemokine mediated signalling pathway; Ligand-mediated signalling; Cell cycle control; Cell proliferation and differentiation | EGF receptor signalling pathway→Epidermal growth factor
TGFB1704019q13.2Transforming growth factor, beta 1Growth factor | Other receptor mediated signalling pathway; Developmental processes; Cell proliferation and differentiation | TGF-beta signalling pathway→Transforming growth factor beta
TGFB270421q41Transforming growth factor, beta 2Growth factor | Other receptor mediated signalling pathway; Developmental processes; Cell proliferation and differentiation | TGF-beta signalling pathway→Transforming growth factor beta
TGFB3704314q24Transforming growth factor, beta 3Growth factor | Other receptor mediated signalling pathway; Developmental processes; Cell proliferation and differentiation | TGF-beta signalling pathway→Transforming growth factor beta
TGFBR170469q22.33Transforming growth factor, beta receptor I Molecular function unclassified | Biological process unclassified | N/A
TGFBR270483p24.1Transforming growth factor, beta receptor II Other cytokine receptor; Serine/threonine protein kinase receptor; Protein kinase | Protein phosphorylation; Cytokine and chemokine mediated signalling pathway; Receptor protein serine/threonine kinase signalling pathway; Other developmental process | TGF-beta signalling pathway
TGFBR370491p33-p32Transforming growth factor, beta receptor IIITGF-beta receptor | Cytokine and chemokine mediated signalling pathway; Receptor protein serine/threonine kinase signalling pathway | N/A
WNT3A897801q42Wingless-type MMTV integration site family, member 3AOther signalling molecule | Ligand-mediated signalling; Developmental processes | Cadherin signalling pathway; Wnt signalling pathway
WNT9B748417q21Wingless-type MMTV integration site family, member 9BOther signalling molecule; Extracellular matrix structural protein | Ligand-mediated signalling | Cadherin signalling pathway; Wnt signalling pathway

Lip and palate development

Facial clefting results from a failure of normal developmental processes. Understanding the developmental sequence leading to the formation of craniofacial structures clarifies why clefts occur in certain patterns and how disparate genetic influences can yield similar phenotypes. The details of human craniofacial development have been summarized in a number of reference texts [e.g. (Moore and Persaud, 2007)]. The maxillo-mandibular complex is derived from five facial primordia: the paired mandibular and maxillary prominences and the frontonasal prominence. The creation of a seamless, symmetrical facial structure depends on the coordinated growth of each of these independently generated prominences. Each facial prominence initially consists of an epithelial outgrowth populated by mesoderm and neural crest cells derived from the midbrain and hindbrain (O’Rahilly and Muller, 2007). The mandibular prominences are derived from the caudal domain of the first branchial arch and fuse directly with each other around the 4th week of gestation when the foetus is typically 3–5 mm in length. The extreme rarity of mandibular clefts indicates that this early fusion event is very robust, a fact that may be explained by the small size of the embryo at the stage when fusion occurs. The generation of the midfacial structures, including the maxilla, primary palate and secondary palate, involves a more complex series of fusion events between the lateral aspects of the frontonasal process and each of the maxillary processes (Figure 2). This three-way fusion occurs both later in development, starting during the 5th week of gestation and proceeds over an extended period of time, completing around the 7th week. The fusion events required for normal development of the secondary palate begin in the 8th week and are complete by the 10th, making formation of the secondary palate the latest fusion event when the foetus is typically 4 cm in length. Failure of fusion between these prominences or their derivatives is the cause of the majority of facial clefts. However, the factors that result in the failure of fusion are complex and varied, impacting on many different developmental events. While these developmental events are complex, a brief summary of the key stages illustrates why such a diverse array of genetic insults culminates in different types of orofacial clefts with broadly overlapping characteristics.

Figure 2.

 Diagrams representing a 4.5-week gestation human embryo and 14-week gestation human foetus illustrating the embryonic origins of the facial structures. The midfacial region is created by fusion of the frontonasal process at the top (yellow) and the paired maxillary processes in the middle portion of the developing face (green). The border between the lateral nasal process and the maxillary process is a common site of clefting. Failure of fusion at this site results in cleft of the lip and/or primary palate, which forms from the intermaxillary segment. The mandible is created by fusion of the paired maxillary processes (blue) at around 3.5 weeks of gestation. IMS, intermaxillary segment; LNP, lateral nasal prominence; MNP, medial nasal prominence; NP, nasal pit

The maxillary prominence is derived from the rostral aspect of the first branchial arch and is populated by neural crest from the same axial level as those that populate the mandibular prominence. The entire facial skeleton is derived from the neural crest and any influence that impedes the growth or differentiation of this population will have a marked impact on orofacial development. The severity of malformation resulting from a deficiency in the neural crest population can be seen in Treacher Collins syndrome, where mutations in TCOF1 result in death of neural crest cells prior to leaving the neural tube (Dixon et al, 2000). The derivatives of the maxillary prominence include the zygomatic complex, the lateral maxilla and the secondary palate, which forms as an outgrowth of the maxillary prominence. The frontonasal prominence is populated by midbrain neural crest cells that migrate laterally over the developing brain to coalesce over the medial forebrain. The frontonasal prominence subsequently extends in a caudal direction to produce the midfacial structures including the medial part of the nose, the philtrum, the intermaxillary segment and the primary palate. The left and right maxillary prominences fuse with the intermaxillary segment to form a continuous upper jaw including the primary palate. The palatal shelves (precursors of the secondary palate) initially grow vertically from the oral aspect of the maxillary prominence, but as the tongue flattens with increasing muscular development and the oral volume increases with overall growth, the palatal shelves elevate to eventually oppose each other as they become horizontal [for in-depth reviews of these processes, see (Dudas et al, 2007; Gritli-Linde, 2007; Meng et al, 2009)]. The ensuing growth of the palatal shelves eventually results in contact and fusion to form the secondary palate. In addition, the independently generated primary and secondary palates must fuse at their sites of contact, a process requiring a number of differentially expressed transcription factors, growth factors, and cell-signalling molecules (Gritli-Linde, 2008; Gu et al, 2008).

The fusion event itself is a multi-step process involving the initial adhesion of opposing epithelia via cell and extracellular matrix adhesion processes, consolidation of the epithelial junction through intercalation of epithelial cells, extension of the site of fusion and removal of the bi-epithelial seam through apoptosis and migration (Figure 3) (Tudela et al, 2002; Martinez-Sanz et al, 2008; Murillo et al, 2009). Facial clefts result from a failure of complete fusion between any of the facial primordia; hence, knowledge of the embryological sites of fusion is important for understanding how a particular cleft type arises. For example, failure of palatal shelf elevation results in cleft palate but does not affect lip and primary palate fusion, whereas a failure of fusion between a maxillary prominence and one side of the intermaxillary segment results in unilateral cleft lip and palate.

Figure 3.

 Diagrammatic representation of the steps of fusion in a theoretical pair of facial prominences. The facial prominences initially consist of a layer of epithelium (a). The facial prominences are populated through the migration of mesenchymal cells (b) and early growth of the prominences is driven by proliferation of the mesenchyme (c). Initial contact is made through opposing epithelia as the prominences grow towards each other (d) and this initial adhesion is consolidated through intercalation of epithelial cells (e). The intervening epithelium is removed through a combination of apoptosis and migration (f), resulting in complete fusion of the facial prominences (g). Failure of any of these stages of the fusion process can result in an orofacial cleft

Genes and pathways implicated in orofacial clefting

A variety of genetic approaches have been used to identify multiple genes and genetic pathways critical for craniofacial development. These include informative mouse models for orofacial clefting (Juriloff, 2002; Juriloff and Harris, 2008), linkage and association scans (Marazita and Neiswanger, 2002; Marazita et al, 2004; Birnbaum et al, 2009), cytogenetics (Brewer et al, 1998, 1999; Higgins et al, 2008), studying rare Mendelian cleft syndromes that phenocopy isolated clefts (Kondo et al, 2002; Zucchero et al, 2004), and gene expression analyses in human and mouse embryonic tissues (Brown et al, 2003; Mukhopadhyay et al, 2004; Cai et al, 2005; Gong et al, 2005). The diversity of embryological events that contribute to the formation of the facial structures is reflected in the large number of genes known or suspected to be involved in clefting (Jugessur et al, 2009). While a complete discussion of each of these genes is beyond the scope of this review, we provide here a brief summary of some of the key candidate genes for clefts and their respective roles in genetic pathways known to shape the craniofacial complex.

Extracellular signalling factors

The transforming growth factor beta (TGF-β) superfamily.  The TGF-β superfamily of growth factors regulate many aspects of skeletal development, including cartilage and bone formation, mesoderm patterning, and craniofacial and limb development (Wan and Cao, 2005). This group of structurally related growth and differentiation factors include TGF-βs, bone morphogenetic proteins (BMPs), and activins (Meng et al, 2009). One member of this superfamily, transforming growth factor alpha (TGF-α), binds to epidermal growth factor receptor (EGFR) and elicits responses similar to but more potent than EGF. The expression pattern of TGF-α in palatal tissues, especially in the midline seam and subjacent mesenchyme of the palatal shelves at the time of shelf fusion, supports a role for TGFA in clefting. A recent review of the accumulated evidence for TGFA concluded that this gene is a risk factor for orofacial clefts, possibly as a modifier gene rather than directly causing clefting (Vieira, 2006).

Although other members of the Tgf-β family are temporally and spatially expressed in the developing palate, only the Tgfb3 knockout inhibits normal palatal shelf fusion in mice (Nawshad et al, 2004). The medial edge epithelium (MEE) in Tgfb3−/− mice exhibits a number of defects, including excess proliferation (Cui et al, 2003), less apoptosis (Martinez-Alvarez et al, 2000), morphological and adhesion deficiencies (Tudela et al, 2002), and a failure to degrade the basement membrane and undergo epithelial-mesenchymal transformation (Kang and Svoboda, 2002). Furthermore, in chickens, where the secondary palate is normally cleft, exogenous TGF-β3 can induce palatal fusion through a process that requires physical contact of the MEE and formation of the midline seam (Nawshad et al, 2004). Thus, Tgf-β3 signalling is unequivocally a key pathway in palate development in the mouse and chicken. In humans, significant linkage to the TGFB3 region was reported in a recent genome scan meta-analysis for isolated CL/P (Marazita et al, 2004), despite a lack of association with this gene in previous studies (Marazita and Neiswanger, 2002).

Like other TGF-β superfamily members, BMPs exert their effects by binding to two types (Type-I and -II) of membrane-bound receptor serine/threonine kinases (Nohe et al, 2004). After binding of a BMP, the Type-II receptor phosphorylates the Type I receptor, resulting in recruitment of a group of transcriptional co-activators called Smads into the complex, followed by translocation of the complex into the nucleus and transcriptional activation of specific target genes (Greene and Pisano, 2004; Nohe et al, 2004).

Interactions between BMPs and MSX1 are important in orofacial development, as demonstrated in a study by Zhang et al, in which Msx1 was required for the expression of Bmp4 and Bmp2 in the palatal mesenchyme and Shh in the MEE (Zhang et al, 2002). More importantly, transgenic expression of Bmp4 in the palatal mesenchyme of Msx1−/− mutant mice rescued the cleft palate phenotype. The link between Bmp4 and Msx1 is particularly noteworthy in that mice lacking Msx1 exhibit cleft palate and abnormalities of craniofacial and tooth development (Satokata and Maas, 1994). In humans, a nonsense mutation in MSX1 was responsible for tooth agenesis and mixed clefting (van den Boogaard et al, 2000). MSX1 is also deleted in patients with Wolf–Hirschhorn syndrome (WHS), caused by deletions in the 4p16.3 region (Nieminen et al, 2003). Among a range of clinical features, patients with WHS present with closure defects such as cleft lip and palate, coloboma of the eye, and cardiac septal defects. Finally, complete sequencing of MSX1 revealed that 2% of patients with isolated CL/P carried mutations in this gene (Jezewski et al, 2003).

Bmp4 appears to be particularly important in lip and palate fusion. In a Bmp4 conditional knockout mouse model, all embryos had bilateral cleft lip at 12-day post-conception, but by 14.5 days, only 22% still exhibited cleft lip (Liu et al, 2005a,b). Many of the initial clefts thus appeared to have been rescued or healed in utero, possibly through complementation or cross-regulation of other Bmp genes (Jiang et al, 2006). A mutation search in individuals with subepithelial oris orbicularis (OO) muscle defects found potentially deleterious BMP4 mutations in a small proportion of cases (Marazita, 2007; Suzuki et al, 2009), indicating that these subtle defects may be part of a broader phenotypic spectrum of CL/P (Weinberg et al, 2006b).

Platelet-derived growth factor signalling.  The gene for platelet-derived growth factor C (PDGFC) has a well-substantiated role in palatogenesis. Genetic linkage, association and cytogenetic deletions support the existence of a human CL/P locus in the 4q31-ter region containing the PDGFC locus [see (Choi et al, 2008) and references therein]. Mice in which the gene is knocked out die in the perinatal period, presumably due to feeding and respiratory difficulties from having a complete cleft of the secondary palate (Ding et al, 2004). In these mice, the palatal bones fail to extend across the roof of the oral–nasal cavity, suggesting that hypoplasia of palatal tissues combined with fusion defects of the MEE may contribute to the cleft palate seen in the Pdgfc−/− mice. Evidence from Zebrafish suggests that the Pdgf signalling system is important for chemoattraction of neural crest cells into the palatal shelves (Eberhart et al, 2008), suggesting that the hypoplasia in Pdgfc−/− mice could result from a neural crest migration deficiency.

In vitro PDGFC is downregulated by retinoic acid in mouse embryonic palatal mesenchymal cells (Han et al, 2006). A reduction in PDGFC activity by retinoic acid may inhibit proliferation in palatal shelves, thus resulting in cleft palate. More recently, Choi and colleagues performed sequence analysis and SNP genotyping on 1048 multiplex CL/P families and 1000 case–control samples from multiple geographic origins (Choi et al, 2008). Although no mutations were found in coding regions, one SNP in particular (rs28999109) was associated with CL/P in some but not all populations. The T-allele of this SNP disrupted potential transcription regulatory motifs and was associated with a significant decrease in PDGFC gene promoter activity (Choi et al, 2008).

Fibroblast growth factor signalling.  The fibroblast growth factor (FGF) signalling pathway is highly conserved evolutionarily and plays an important role in several aspects of craniofacial development, including neural crest induction, skeletogenesis and epithelial-mesenchymal interactions (Nie et al, 2006). Multiple members of the FGF family are expressed in overlapping domains during development of the nasal and midfacial region (Bachler and Neubuser, 2001). Convincing evidence linking orofacial clefting to members of the FGF family and their receptors has been obtained from studies in transgenic mice. Fgf8, for example, is expressed within the developing pharyngeal arch ectoderm and endoderm during neural crest cell migration through the pharyngeal arches (Abu-Issa et al, 2002). Fgf8 mouse mutants exhibit a range of defects involving the palate, mandible, middle ear bones, thyroid and external ear (Abu-Issa et al, 2002). Furthermore, mice homozygous for a hypomorphic allele of Fgfr1– resulting in reduced but not completely ablated Fgfr1 function – have craniofacial defects, including cleft palate (Trokovic et al, 2003). The rescue of these defects by reverting the hypomorphic Fgfr1 allele back to wild type in neural crest cells demonstrates that Fgf signalling is essential for distribution and patterning of the neural crest within the facial primordia.

In humans, mutations in FGFR1, 2, and 3 are associated with craniosynostosis and other facio-skeletal malformations (Pauws and Stanier, 2007). A good example is Apert syndrome, caused by mutations in FGFR2, where ∼75% of patients present with CP or bifid uvula (Kreiborg and Cohen, 1992). Loss-of-function mutations in FGFR1 on the other hand underlie KAL2, an autosomal dominant form of Kallmann syndrome associated with hypogonadism and anosmia, and clefting in around 5–10% of patients (Dode et al, 2003). As with VWS, some individuals with KAL2 may present with clefts as the only component of the phenotype, which further underscores the need for careful phenotypic assessments in gene-mapping efforts (Murray and Schutte, 2004).

More recently, diagnostic sequencing of 12 FGF-related genes in 184 individuals with isolated CL/P identified seven potential disease-causing mutations, including a nonsense mutation in FGFR1, a de novo missense mutation in FGF8, and other missense variants in FGFR1, FGFR2, and FGFR3 (Riley et al, 2007). Interestingly, the nonsense mutation was identified both in a patient with Kallmann syndrome and her father with isolated CLP only, again highlighting non-penetrance issues in identifying mutations in isolated CL/P (Riley et al, 2007).

Sonic Hedgehog signalling.  Sonic Hedgehog (SHH) is a member of the hedgehog family of secreted proteins regulating key developmental events during embryogenesis (Cohen, 2004). Shh signalling is essential for normal patterning and growth of the face, and analysis of Shh–Fox gene regulatory interactions indicate that Fox genes at least partially mediate the action of Shh in facial development (Jeong et al, 2004). In humans, loss of one SHH allele is sufficient to cause holoprosencephaly (abnormal forebrain and facial development), whereas both alleles need to be lost in the mouse knockout to produce a similar phenotype (Chiang et al, 1996; Roessler et al, 1996). In chick embryos, transient loss of SHH signalling in the embryonic face results in defects analogous to bilateral cleft lip and palate seen in humans and other characteristics reminiscent of the mild forms of holoprosencephaly (Hu and Helms, 1999).

Cell signalling is initiated through the binding of Shh to its cell surface receptor Ptch1 to relieve its basal repression of Smoothened (Smo) (Mullor et al, 2002). Smo then activates the GLI family of zinc-finger transcription factors to transduce the Shh signal to the nucleus. Human PTCH is a tumour suppressor gene that maps to chromosome 9q22.3, in the vicinity of a region highly likely to contain a strong candidate gene for orofacial clefts (Marazita et al, 2004). Mutations in various members of the SHH pathway (e.g. SHH, PTCH, PTCH2, GLI2, GLI3, SMO, and CBP) can lead to strikingly different diseases, including holoprocencephaly, Gorlin Syndrome (a.k.a nevoid basal cell carcinoma syndrome), Pallister–Hall syndrome, Rubinstein–Taybi syndrome and cancer (Cohen, 2004). Gorlin syndrome for example is caused by mutations in PTCH and is associated with cleft palate in 5% of cases (Evans et al, 1993). Because of this association with clefts, PTCH was examined for mutations in cases of isolated CL/P (Mansilla et al, 2006). Two missense mutations were found in the extracellular loops of PTCH, predicted to interfere with SHH binding. Missense mutations in PTCH may thus represent rare causes of isolated CL/P.

Shh and Bmp signalling has recently been linked to the function of transcription factor Hand2 in murine palatogenesis. Mice lacking Hand2 expression have cleft palate due to a severely hypoplastic mandible (Yanagisawa et al, 2003). Furthermore, Hand2 controls cell proliferation via Shh and Bmp2 in the anterior palate (Xiong et al, 2009). Using a conditional inactivation approach, the authors further showed that Hand2 function is indispensable in the palatal epithelium, but not in the palatal mesenchyme during palatogenesis.

The Fgf-Shh signalling network may also play an important role in coordinating epithelial-mesenchymal interactions during the initial stages of palate development (Rice et al, 2004; Alappat et al, 2005). The Fgfr2b/Fgf10 signalling system has been demonstrated to be critical for normal development of the secondary palate (Rice et al, 2004). Fgfr2b is expressed in the oral epithelium, while Fgf10 is expressed in the underlying mesenchyme facilitating signalling between the tissue layers. Mice deficient in either Fgfr2b or Fgf10 exhibit cleft palate associated with a reduction in proliferation of epithelial and mesenchymal cell types and elevated cell death in the epithelium. Importantly, deletion of either the receptor or ligand results in loss of Shh and Ptc expression, indicating that Fgf and Shh signalling are components of the same pathway in palatogenesis.

WNT signalling.  Several recent reports have drawn attention to the role of Wnt signalling in orofacial clefting. The Wnt signalling pathway consists of a large family of secreted molecules that play major roles in a range of developmental processes (Sheldahl and Moon, 2004). Many of the Wnt signalling components are shared by other signalling pathways. Signal transduction is initiated when Wnt proteins bind to Frizzled (Fz) cell surface receptors, resulting in the activation of the cytoplasmic protein Dishevelled (Dv) (Clevers, 2006). WNT3 in particular appears to be a key signalling molecule in human limb development. Mutations in this gene are associated with the rare recessive disorder Tetra-amelia, characterized by complete limb agenesis and other anomalies including clefts (Niemann et al, 2004). Mutations in WNT7A have been associated with Fuhrmann syndrome which also involves a range of limb anomalies and cleft lip and palate (Woods et al, 2006). Another Wnt family member, Wnt9b, while not yet implicated in clefting in humans, leads to an incompletely penetrant cleft lip and palate as well as defects in kidney morphogenesis when disrupted in mice (Carroll et al, 2005). Juriloff et al (2006) later confirmed Wnt9b as the mutated gene responsible for the CL/P seen in A/WySn mice, and proposed that WNT9B and the 3′ conserved non-coding region should be examined for a role in human isolated CL/P.

Transcription factors

IRF6.  Of the large number of candidate genes thought to contribute to orofacial clefting, interferon regulatory factor 6 (IRF6) is among the few that have shown a convincing degree of consistency across studies (Jugessur et al, 2008; Rahimov et al, 2008). Mutations in this gene are known to cause two allelic autosomal-dominant clefting disorders: VWS and popliteal pterygium syndrome (PPS) (Kondo et al, 2002; de Lima et al, 2009). VWS is one of the best models for isolated CL/P in that ∼15% of affected individuals are clinically indistinguishable from isolated clefts. This observation rapidly led to the hypothesis that genetic variants in IRF6 might also be involved in the etiology of isolated clefts, which was subsequently confirmed in a large dataset of nearly 2000 families made up of 10 populations of diverse ancestry (Zucchero et al, 2004) and independently replicated in multiple studies [reviewed in (Jugessur et al, 2008)].

IRF6 belongs to a family of nine transcription factors that share a highly conserved winged-helix DNA-binding domain and a less conserved protein-binding domain (Kondo et al, 2002). It is strongly expressed in the leading edge ectoderm of the palatal shelves prior to and during formation of the secondary palate (Ben et al, 2005; Knight et al, 2006; Washbourne and Cox, 2006). IRF family members are known to regulate a variety of host defence mechanisms. Mice deficient in Irf1, 2, 3, 4, 5, 7, 8 or 9 have an impaired immune response (Ingraham et al, 2006). These mice, however, do not manifest any embryological abnormalities. In contrast, Irf6-null mice have abnormal skin, limb and craniofacial development (Kondo et al, 2002), consistent with the phenotypic distribution in VWS and PPS patients. A significant role for Irf6 in epidermal development was subsequently reported in two independent studies (Ingraham et al, 2006; Richardson et al, 2006), where Irf6-null mice were found to lack a normally stratified epidermis due to a defect in the keratinocyte proliferation-differentiation switch. More recently, mutations in the IRF6 transcriptional activation domain were shown to inhibit transcriptional activation (Little et al, 2008).

A breakthrough in our understanding of how IRF6 affects the risk of isolated CL/P was the recent identification of a common SNP that disrupted the binding site for transcription factor AP-2α within a highly conserved IRF6 enhancer element (Rahimov et al, 2008). The link between IRF6 and AP-2α is particularly noteworthy given the fact that previous data had demonstrated an essential role for AP-2α in cranial closure and craniofacial development (Schorle et al, 1996). Furthermore, mice carrying both wild-type and AP-2α-null cells have CLP and pronounced mandibular and maxillary dysmorphology, consistent with aberrant development of the facial prominences (Nottoli et al, 1998). Mutations in TFAP2A (the gene encoding AP-2α) cause Branchio-oculo-facial syndrome, characterized by some of the same features observed in VWS (occasional lip pits and orofacial clefts) (Milunsky et al, 2008). Lastly, TFAP2A maps to chromosome 6p24 where chromosomal anomalies have been associated with orofacial clefting (Lidral and Moreno, 2005). Taken together, these findings place IRF6 and AP-2α in a common developmental pathway in which disruptions may contribute to the pathogenesis of CL/P.

FOXE1.  Forkhead box E1 (FOXE1) is a member of the forkhead/winged-helix domain transcription factor family the members of which are key regulators of embryogenesis. The palatal shelves in Foxe1-null mutant mice fail to fuse and result in an extensive cleft of the secondary palate (De Felice et al, 1998). In humans, a loss-of-function mutation in FOXE1 is associated with Bamforth-Lazarus syndrome which includes thyroid agenesis, hair follicle defects, choanal atresia, and cleft palate among the clinical features (Clifton-Bligh et al, 1998; Castanet et al, 2002; Brancaccio et al, 2004). Three recent studies support a role for FOXE1 in isolated clefting. First, direct sequencing of 184 isolated CL/P patients detected missense mutations in FOXE1 in two unrelated patients, with none of the mutations detected in 186 matched controls (Vieira et al, 2005). Second, a meta-analysis of 13 genome-wide linkage studies produced the highest linkage signal on chromosome 9q21 (Marazita et al, 2004), which is near FOXE1 (9q22) and patched (PTCH; 9q22.3). In addition, these genes map to the region homologous to the clf2 locus in the mouse (Juriloff et al, 2006). A genome-wide screen for cleft loci in the cleft-susceptible A/WySn mouse strain had previously identified two epistatically interacting loci, clf1 and clf2, that contribute to a cleft lip phenotype (Juriloff et al, 2004). Third, a recent genome-wide linkage scan of 820 multiplex CL/P families showed that the FOXE1 region results were most significant in families in which some or all of the affected individuals have CL/P (Marazita et al, 2009). In the same paper, a follow-up fine-mapping SNP panel identified two genome-wide significant associations with SNPs in or near FOXE1 and IRF6.

GLI2.  The GLI family of zinc-finger transcription factors regulate the expression of downstream target genes in the SHH pathway. Loss-of-function mutations in GLI2 are associated with holoprosencephaly-like features, pituitary anomalies, polydactyly, and clefting of the lip and palate (Roessler et al, 2003). Among a wide array of genes known to contribute to holoprosencephaly, GLI2 has been specifically implicated in isolated clefting (Cohen, 2006). In a study of 104 cleft candidate genes spanning the length of chromosome 2, variants in GLI2 were associated with CL/P (Beaty et al, 2006). Furthermore, potentially deleterious missense mutations in conserved amino acids were identified upon sequencing of DNA from individuals with isolated CL/P (Vieira et al, 2005).

T-box transcription factors

The T-box transcription factor gene TBX22 was among the first genes to be identified for a major CP syndrome. Specifically, mutations in TBX22 were found to cause X-linked cleft palate (CPX), usually associated with ankyloglossia in which the lingual fraenulum is too short and limits the normal mobility of the tongue (Braybrook et al, 2001). Subsequently, TBX22 mutations were also found to account for a significant proportion of isolated CP cases (Marcano et al, 2004; Suphapeetiporn et al, 2007). TBX22 functions as a transcriptional repressor and the small ubiquitin-like modifier SUMO-1 is required for repressing its activity (see further below for SUMO) (Andreou et al, 2007). In mice, Tbx22 expression is localized to the developing palatal shelves and the base of the tongue where the ankyloglossia is observed (Braybrook et al, 2002; Bush et al, 2002). Expression of Tbx22 in the palatal shelves is at least partially regulated by the Meningioma gene (Mn1) and Mn1 knockout mice also develop a cleft palate, suggesting that Mn1 may also be a good candidate for cleft palate in humans (Liu et al, 2008).

Two additional members of the T-Box family, TBX1 and TBX10, have been implicated in CL/P pathogenesis. The genetics of 22q11.2 deletion syndrome are complex, but mutations in TBX1 have been identified in a small number of patients with a 22q11.2 deletion syndrome phenotype (Yagi et al, 2003; Paylor et al, 2006; Zweier et al, 2007). A significant proportion of patients with 22q11.2 deletion syndrome have palatal anomalies, including cleft palate in 9–11% of cases (Kobrynski and Sullivan, 2007). Deletion of Tbx1 in mice phenocopies a number of the features of the 22q11.2 deletion syndrome, including cleft palate (Jerome and Papaioannou, 2001). Tbx1 is strongly expressed in the pharyngeal endoderm and mice deficient for Tbx1 have pharyngeal hypoplasia, and as a consequence, disrupted neural crest cell migration (Vitelli et al, 2002), supporting the hypothesis that the common developmental issue with 22q deletion syndrome patients is a defect in neural crest cell development. Additionally, ectopic expression of TBX10 results in cleft lip and palate in transgenic mice (Bush et al, 2004) and mutations in this gene were also reported to be rare causes of CL/P in humans (Vieira et al, 2005).

TP63.  Mutations in the tumour protein p63 (TP63) gene are implicated in five distinct human developmental disorders, characterized by various degrees of limb abnormalities, ectodermal dysplasia, and orofacial clefts (van Bokhoven and Brunner, 2002). Whilst the phenotypes of these conditions are complex, cleft lip and/or palate is a feature in four of the five p63 syndromes. In addition, TP63 mutations have also been identified in isolated cleft lip and palate (Leoyklang et al, 2006). Interestingly, the distribution of mutations over the different p63 protein domains shows a clear pattern of genotype-phenotype correlation (Rinne et al, 2007), suggesting that specific mutations alter the function of p63 in subtly different ways. The TP63 gene is expressed in the branchial arch ectoderm in mice, is required for induction of factors involved in epithelial-mesenchymal signalling and has been demonstrated to be essential for limb and craniofacial development (Yang et al, 1999).

Cell adhesion

PVRL1.  Poliovirus receptor-related 1 (PVRL1) encodes nectin-1, an immunoglobulin-related transmembrane cell-cell adhesion molecule, which, in the mouse embryo, is expressed primarily in the MEE of the palatal shelves, the ectodermal component of tooth buds, the olfactory epithelium and the skin surface epithelium (Suzuki et al, 2000). Homozygosity for a common nonsense mutation in this gene (W185X) results in an autosomal recessive clefting disorder known as CL/P-ectodermal dysplasia syndrome (CLPED1) (Suzuki et al, 2000). The indigenous population of Margarita Island is remarkable in that it has a high incidence of CLPED1 (1/2000) and a high prevalence of isolated CL/P (5.4/1000). As a large enough sample of isolated CL/P could not be accrued from the limited indigenous population of the island, Sozen et al used a larger sample from neighbouring Venezuela to assess whether heterozygosity for the W185X mutation might also be a risk factor for isolated CL/P (Sozen et al, 2001). The results showed a highly significant association between heterozygosity for this mutation and isolated CL/P. Significant associations between variants in PVRL1 and isolated CL/P were subsequently confirmed (Avila et al, 2006; Neiswanger et al, 2006). Taken together, these findings suggest that both rare and common mutations within PVRL1 make minor contributions to the pathogenesis of isolated CL/P.

Protein modification

SUMO.  Small ubiquitin-like modifier (SUMO) proteins posttranslationally modify numerous cellular proteins and participate in a number of cellular processes such as nuclear transport, transcriptional regulation, apoptosis and protein stability (Su and Li, 2002). This gene was interrupted by a balanced reciprocal translocation between chromosome 2q and 8q in a patient born with unilateral CLP, and further mapping of the breakpoint on chromosome 2 confirmed SUMO1 haploinsufficiency (Alkuraya et al, 2006). In the same paper, strong Sumo1 expression was observed in the upper lip, primary palate, and MEE of the secondary palate at embryonic day 13.5. Furthermore, deletions involving SUMO1 were recently identified in a search for microdeletions among a large number of candidate genes for orofacial clefts (Shi et al, 2009).

It has newly been proposed that synergistic interactions may exist between the FGF signalling pathway, SUMO modification, and environmental risk factors in the causation of CL/P (Pauws and Stanier, 2007). Given protein sumoylation is influenced by environmental stress (Bossis and Melchior, 2006), external stress stimuli on the SUMO pathway might affect development of the lip and palate. Interestingly, several genes previously found to be strongly associated with orofacial clefting are also targets of SUMO modification (e.g. TBX22, MSX1, SATB2, TP63, PAX9, TRPS1, and EYA1) (Pauws and Stanier, 2007). Thus, aberrant SUMO modification of these genes during early pregnancy is likely to provide a high-risk environment for the pathogenesis of both Mendelian and idiopathic forms of orofacial clefts (Andreou et al, 2007).

Phenotypic aspects of isolated orofacial clefting

In many of the examples of clefting syndromes cited above, there is often a clear correlation between genetic mutation and cleft phenotype. However, as a consequence of genetic and allelic heterogeneity, incomplete penetrance, and the spectrum of phenotypic severity resulting from identical mutations, there is often no such clear-cut correlation for isolated clefts. Although multi-centre collaborations should enhance the capacity to identify such correlations through an increase in sample size, there remains the more fundamental question of when is an unaffected individual truly unaffected? The answer may not be as clear as previously thought with contemporary research focusing on refining the clinical descriptors of the cleft phenotype.

Until recently, understanding the genetic aetiology for orofacial clefts has been based upon the notion that an individual either has or does not have a cleft. However, whilst severe clefting is unmistakable (Figure 1), milder expressions such as a submucous cleft palate, a bifid uvula or forme fruste lip (also known as microform cleft) are harder to detect. Traditional definitions of ‘affected/unaffected’ relying solely on the basis of ‘no overt cleft = unaffected’ may be too simplistic in a way that might have hampered gene identification (Weinberg et al, 2006b). Currently, all unaffected family members are treated as though their genetic risks are equivalent. However, the range of phenotypic variation may extend beyond the externally visible, with increasing evidence that even without an overt CL/P an individual may have other features that fall under the ‘spectrum’ of clefting. Such ‘unaffected’ individuals may represent gene-carriers that are currently overlooked. The identification of unaffected individuals within cleft families who may be harbouring susceptibility factors is important and could lead to significant progress not only in improved recurrence risk estimations, genetic counselling and overall cleft management, but also in more targeted gene-mapping efforts.

Whilst there are a large number of potential clinical/subclinical features associated with the so-called ‘expanded cleft phenotype’ (Weinberg et al, 2006b), the strength of evidence for each varies. Three features in particular, namely subepithelial defects of the superior orbicularis oris (OO) muscle (Marazita, 2007), dental anomalies (specifically hypodontia) (Letra et al, 2007), and craniofacial morphology (Weinberg et al, 2008b) have received the greatest attention. Although additional features such as dermatoglyphic patterns, non-right-handedness and directional asymmetry have also been discussed in the context of clefting (Weinberg et al, 2006b), they appear to lack the strong theoretical basis that is associated with other features such as structural brain anomalies and neuropsychological deficits, and speech anomalies.

OO muscle defects

It has been hypothesized that subepithelial defects of the superior OO muscle result from the incomplete development of the OO sphincter, and as such may represent the mildest phenotypic expression of the clefting spectrum (Martin et al, 1993; Suzuki et al, 2009). Such defects have been identified (using high-resolution ultrasound) significantly more frequently in apparently ‘unaffected’ relatives of individuals with isolated CL/P than in unrelated controls with no family history of clefting (Martinez-Alvarez et al, 2000; Neiswanger et al, 2007). Furthermore, despite the traditional view that CL/P is etiologically distinct from CP, defects of the OO muscle have recently been reported in individuals previously diagnosed with isolated CP (Weinberg et al, 2008a). This in itself suggests that, in some cases at least, the diagnosis of isolated CP may also not be entirely accurate and further supports the hypothesis of ‘mixed clefting’ discussed earlier.

Dental anomalies

Dental anomalies, particularly hypodontia, microdontia and supernumerary teeth, occur more frequently in individuals with CL/P. Indeed, it has been suggested that, as with subepithelial defects of the OO muscle, the presence or absence of dental anomalies should be included in an overall assessment of the cleft phenotype (Letra et al, 2007). Given the close temporal and spatial development of the lip, palate and teeth, the most commonly reported anomaly—and one that warrants closer evaluation—is the congenitally absent lateral incisor. It is well recognized that in individuals with CL/P, the lateral incisor in the line of the cleft is often missing (Figure 4a) (Ribeiro et al, 2003). Likewise, in those same individuals there is an increased incidence of missing teeth outside the cleft area, particularly premolars and the contralateral lateral incisor (Figure 4b) (Menezes and Vieira, 2008). However, there is also some evidence that hypodontia is more common in the ‘unaffected’ siblings of individuals with a cleft (11.1%) than in unrelated controls (3.4%) (Eerens et al, 2001).

Figure 4.

 Examples of dental agenesis in two patients diagnosed with cleft lip and palate. (a) An orthopantogram (OPG) radiograph of a 10-year-old individual with a left-sided unilateral cleft of the lip and palate just prior to secondary alveolar bone grafting. Note the agenesis of the permanent upper left lateral incisor (tooth 22). (b) OPG of an 8-year-old individual with a right-sided unilateral cleft of the lip and palate prior to secondary alveolar bone grafting. Note the agenesis of both permanent upper lateral incisors (teeth 12 and 22) and the upper right second premolar (tooth 15)

Given the fact that there are a number of genes associated with both clefting and tooth agenesis [e.g. MSX1, TGFA, PAX9, TGFB3, FGFR1 and IRF6 (Slayton et al, 2003; Vieira et al, 2004, 2007)], pursuing the hypothesis that dental anomalies contribute to the cleft phenotype has the potential to make a significant contribution to contemporary understanding. However, validating the aetiology of a missing tooth can be challenging. Most studies use retrospective review of dental radiographs which, when screening for hypodontia, does not allow confirmation of the reason for a tooth to be missing (for example, whether the missing tooth is due to extraction or is congenitally missing). Furthermore, it is possible that the primary cleft-repair surgery itself may disrupt the developing tooth germs, resulting in agenesis or at least in some degree of tooth malformation. Therefore, detailed long-term clinical as well as radiological data on tooth development and dental intervention should be collected prospectively from affected families to facilitate more accurate subphenotyping.

Craniofacial morphology

It is widely recognized that craniofacial features of individuals with clefts are distinctive compared to those of unaffected people. Consequently, craniofacial shape and form of first-degree relatives of cleft patients might be expected to differ from that of the general population. Meta-analysis of cephalometric studies involving ‘unaffected’ parents of individuals with CL/P suggests that these adults ‘are characterized by a suite of consistent, yet subtle, craniofacial differences, which could indicate an underlying genetic liability’ (Weinberg et al, 2006a). The introduction of 3-dimensional photogrammetry has further refined and confirmed these differences (Weinberg et al, 2008b). Whilst potential embryological mechanisms exist that might explain why aberrations in specific craniofacial features may represent a risk marker for clefting, these mechanisms are complex and are yet to be fully explored. In addition, the accuracy, reproducibility and validity of these measures also require further investigation.

Neuropsychological deficits and brain anomalies

Given the close inter-relationship between the development of craniofacial structures and the brain, it is not surprising that neurological deficits have been reported in otherwise healthy individuals with isolated CL/P (Conrad et al, 2008). The aetiology of these deficits in isolated CL/P remains poorly understood. They were historically considered secondary to other factors, such as hearing or speech deficits. More recently, however, it has been suggested that these deficits could be a primary problem related to abnormal brain structure (Boes et al, 2007; Nopoulos et al, 2007a). Several candidate genes associated with CL/P (e.g. PVRL1, MSX1, and IRF6) are also associated with brain abnormalities and mental impairment (Nopoulos et al, 2007b). Therefore, it is feasible that these genes may have a more direct role in abnormal brain development and associated cognitive impairment in individuals with CL/P. The identification of milder neuropsychological deficits and brain anomalies in ‘unaffected’ relatives is yet to be reported, but given the close inter-relationship between face and brain development, this area requires further investigation. Such studies are likely to be hampered by the availability of large enough samples, low participation rates, the time-consuming nature of neuropsychological testing, access to and ethical considerations surrounding magnetic brain imaging of large numbers of ‘unaffected’ relatives of cleft patients and unrelated controls.

Speech pathology

Normal speech requires that the muscles that make up the velopharyngeal sphincter work in a coordinated fashion. Defects in any aspect of the nasopharyngeal anatomy and/or physiology may lead to velopharyngeal incompetence (VPI), which is characterized principally by aberrations in nasality (hyper- or hypo-nasality and nasal air emission). Whilst VPI is not uncommon in individuals with overt clefts of the palate, it can also occur in the absence of an overt cleft although its population prevalence is unknown. In addition to a variety of neuromuscular deficits, there are several potential causes of this VPI that may represent a subclinical feature or a risk marker for clefting. These include the presence of a submucous defect, occult anatomical defects of the levator palatini or musculus uvulae and an anatomic disproportion between the size of the nasopharynx and the length of the palate. Whilst there is a lack of strong evidence, anecdotal clinical experience suggests that these milder forms of deficit may be present, but often pass unnoticed in ‘unaffected’ siblings. It is possible that these deficits remain undiagnosed because clinical assessment of VPI (particularly relatively mild VPI) can be very subjective even to trained, experienced clinicians and definitive diagnosis often requires relatively invasive diagnostic testing such as nasendoscopy.


Every 2½ min, somewhere in the world, a child is born with an orofacial cleft. Not surprisingly, this birth defect is the single most commonly treated craniofacial malformation in a paediatric hospital setting. Although surgery can correct most of the structural defects, patients still face a lifetime of functional, social, and aesthetic challenges. Developmental studies in various animal models have been particularly insightful in unravelling the complex processes and mechanisms involved in clefting. The past few years have witnessed great advances in gene-identification for this complex birth defect, providing an unprecedented opportunity to identify genetically susceptible subgroups in the population. Whether through variant growth patterns or through variant metabolic pathways, genetically susceptible subgroups offer a rich opportunity for research by providing a more sensitive means of identifying substances that are teratogenic in humans. Ultimately, a clearer identification of genetic risk factors and subgroups of the population who are at risk will allow the generation of plausible new biological mechanisms for cleft causation, and new insights into the developmental biology of the face will help nurture the translation of scientific findings into clinical care.

To facilitate ongoing gene-identification efforts, more attention needs to focus on refining the isolated cleft phenotype. There is a growing body of evidence to suggest that the spectrum of isolated orofacial cleft phenotypes may be far more complex than traditionally considered. Detailed evaluation has revealed a range of subclinical features such as defects in the OO muscle, differences in craniofacial morphology, dental and brain anomalies, and neurological deficits in individuals with so-called ‘isolated’ clefts. Furthermore, by broadening the scope of clinical screening to include non-cleft first degree relatives, these and indeed other anomalies (e.g. speech) may well be confirmed as risk markers for isolated clefting. Revealing the full spectrum of affected individuals within cleft families through such detailed subphenotyping holds the promise of providing a useful benchmark for discriminating at-risk relatives and identifying specific risk genes. To achieve this, standardized protocols and data-sharing between cleft centres worldwide should be encouraged.


We thank Brian Schutte and Fedik Rahimov for many insightful comments on an earlier draft of the manuscript. We are especially grateful to the many families who have contributed to our cleft research over the years, and to our colleagues Jeff Murray, Rolv Terje Lie, Allen Wilcox, Håkon Gjessing, Min Shi, Clarice Weinberg, Mary Marazita, Kaare Christensen, Camilla Bille, Abee Boyles, Truc Trung Nguyen, Roy Nilsen, Sandra Daack-Hirsch, Michael Dixon, David Fitzpatrick, Andrew Lidral, Satoshi Suzuki, and Temis Felix for many helpful discussions.

Author contributions

All three authors were involved in the literature search, analysis of available evidence and the writing and editing of the manuscript.