Cardiofacioneurodevelopmental Syndrome (CFNDS, CCDC32)

Autosomal recessive disorder of the CCDC32 gene, a chaperone for assembly of the AP2 adaptor complex, and its differential diagnosis with the RASopathies and other syndromes with clefting, heart disease and developmental delay

Literature and regulatory information update: 31 October 2026.

0. Initial Reference Table

1. Introduction

1.1 Definition and delimitation of the entity

Cardiofacioneurodevelopmental syndrome (CFNDS) is an autosomal recessive disorder caused by biallelic loss-of-function variants in the CCDC32 gene, located at 15q15.1, and characterised by craniofacial anomalies, with bilateral cleft lip and palate as the most constant finding, by congenital heart disease of variable type, and by global developmental delay that progresses to intellectual disability [1, 6]. OMIM describes it as a syndrome with microcephaly, facial midline defects, developmental delay and cerebellar hypoplasia, with variable cardiac defects, including atrioventricular canal defect and ventricular septal defect, and with reported heterotaxy [1]. The name is a formal OMIM designation (entry #619123) and not a generic clinical category: the verbal similarity with cardiofaciocutaneous (CFC) syndrome, a RASopathy caused by activating variants in BRAF, MAP2K1, MAP2K2 or KRAS, is purely terminological, because CFNDS does not result from activation of the RAS-MAPK pathway, has recessive inheritance, and the published reports do not describe the skin changes that accompany CFC in 95% of patients, such as keratosis pilaris, palmoplantar hyperkeratosis and sparse, curly hair [1, 2, 6, 14, 15].

This distinction has practical importance. Noonan syndrome, cardiofaciocutaneous syndrome, Costello syndrome and Noonan syndrome with multiple lentigines were grouped by the Oxford Desk Reference under the term "neuro-cardio-facio-cutaneous syndromes", a family of overlapping conditions caused by variants that activate Ras/MAPK signalling [16]. A child with congenital heart disease, hypertelorism, a short webbed neck, short stature and developmental delay may suggest a RASopathy; the presence of bilateral cleft lip and palate, parental consanguinity and nail and digital anomalies points to CFNDS and to other recessive syndromes outside the RAS pathway [6, 16]. The RASopathies and CDK13-related disorder, which shares heart disease, facial dysmorphism and ID, enter the differential diagnosis.

1.2 Discovery and milestones

CFNDS was described in 2020 by Harel, Griffin, Arbogast and colleagues, in an article in Human Molecular Genetics that brought together, through the GeneMatcher platform, two independent consanguineous families: an Arab Muslim family with a 6-year-old girl and an affected fetus, and an Iranian family from Isfahan with a 3-year-old boy [2]. In both probands, exome sequencing identified homozygous frameshift variants in CCDC32, then a gene with no associated disease, and CRISPR-Cas9 depletion of the zebrafish orthologue reproduced microcephaly, changes in facial cartilage, cerebellar hypoplasia and laterality defects [2]. As the patients had features in common with the ciliopathies, the authors showed that ccdc32 depletion reduced the number and length of cilia in Kupffer's vesicle and in cultured mouse kidney cells, and proposed a ciliary contribution to the mechanism [2]. OMIM created the entry in December 2020 [1].

In 2022, Abdalla and colleagues described a 9-year-old Egyptian girl with a homozygous deletion of 32,583 base pairs (bp) in CCDC32 and proposed, from the three living individuals then known, a core phenotype consisting of developmental delay and bilateral cleft lip and palate, with variable anomalies of the face, brain, heart, fingers and toes, and postnatal growth delay or microcephaly [6]. The same work drew attention to the functional link between CCDC32 and adaptor protein complex 2 (AP2), suggested by a genome-wide analysis of co-essential modules that had placed C15orf57 alongside AP2 and transferrin endocytosis [6, 17]. In the experimental validation of that work, CCDC32 interacted with the AP2 complex, localised to clathrin-coated pits and was required for efficient transferrin uptake [3, 17]. This link was later demonstrated: in 2024, Wan and colleagues identified CCDC32 as a chaperone required for AP2 assembly, in a hand-off mechanism from the chaperone AAGAB, and a commentary in the same journal placed CFNDS among the "coatopathies", diseases in which the coat subunits are normal but their assembly fails [18, 19]. The 2026 studies by Yang and by Sloan detailed the role of CCDC32 in stabilising clathrin-coated pits and the membrane control of AP2 assembly [20, 21]. CCDC32 had first been identified in 2011, in a yeast two-hybrid screen, as a protein that interacts with the C-terminal fragment of annexin A2 [22].

The fourth published patient is Portuguese, followed at the Genetics Department of the Centro Hospitalar Universitário de São João, Porto, presented at the 2022 annual meeting of the Portuguese Society of Human Genetics and described in 2024 in Clinical Dysmorphology [7, 23]. In February 2026, Albuainain and colleagues, from Erasmus MC in Rotterdam, added two siblings diagnosed by RNA sequencing after microarray and trio exome had been negative, and reviewed the literature, which until then included four living individuals and one fetus in four families [9].

1.3 Nomenclature

The designation CFNDS is that of OMIM; Orphanet has no dedicated entity and associates CCDC32 with the category of non-specific syndromic intellectual disability (ORPHA:528084) [1, 8]. The gene synonym C15orf57 appears in the functional literature and in expression databases [6, 18]. The numbering of the variants published in 2020 refers to an old version of a transcript that is not expressed in human tissues; the correct numbering uses the MANE Select transcript NM_001080792.4 (section 2.3) [4, 6].

2. Molecular Genetics and Pathophysiology

2.1 The CCDC32 gene and its transcripts

CCDC32 lies at 15q15.1, at the GRCh38 coordinates 15:40,520,993–40,565,042 given by NCBI (NCBI Gene 90416; Ensembl ENSG00000128891), and encodes a small protein with a coiled-coil domain, present in the cytosol and nucleus [3, 18]. The gene has eight reference transcripts in the NCBI and Ensembl databases; according to the Genotype-Tissue Expression (GTEx) project expression data analysed by Abdalla and colleagues, NM_001080792.4 is the main transcript and is expressed in all tissues, whereas NM_001080791.4 is not expressed in human tissues [6]. NM_001080792.4 is the MANE Select transcript, with protein NP_001074261.1, in both ClinVar and VariantValidator [4, 5]. The founding article described a 194-amino-acid protein, corresponding to the NM_001080791.2 transcript then used, whereas the 2026 functional studies worked with a 185-amino-acid isoform; the eLife reviewers noted that this isoform differs from the one used in the nomenclature of the patients' variants [2, 20]. Zebrafish have a single orthologue, with 46% identity and 64% similarity [2]. By in situ hybridisation, ccdc32 messenger RNA is detected in zebrafish from 1 hour post-fertilisation and, throughout embryogenesis, is concentrated in the developing head, the neural tube and Kupffer's vesicle [2, 3].

In the gnomAD database, CCDC32 shows no strong constraint against heterozygous loss of function: the pLI score is 0.16, the observed/expected ratio of loss-of-function variants is 0.45, with an upper bound of 0.78, and 9 loss-of-function variants were observed against 20.1 expected [24]. These values are compatible with a recessive disease in which heterozygous carriers have no phenotype, as shown by the heterozygous parents and siblings in the published families [1, 6].

2.2 Function: chaperone for assembly of the AP2 adaptor complex

Adaptor protein complex 2 (AP2) is the main cargo adaptor of clathrin-mediated endocytosis (CME): it links the transmembrane proteins to be internalised to the clathrin coat [6, 21]. It is a heterotetramer formed by the subunits α (encoded by AP2A1 or AP2A2, about 100 kDa), β2 (AP2B1, about 100 kDa), μ2 (AP2M1, 50 kDa) and σ2 (AP2S1, 17 kDa), which assemble from two hemicomplexes, α/σ2 and β2/μ2 [6, 21]. In eukaryotic cells, assembly of the adaptor complexes depends on dedicated chaperones, and subunits that fail to assemble are degraded [18].

Wan and colleagues showed in 2024 that the chaperone AAGAB initiates AP2 assembly by binding and stabilising the α and σ2 subunits, but that the AAGAB:α:σ2 complex cannot recruit the remaining subunits [18]. CCDC32 recognises this complex, displaces AAGAB and forms a ternary α:σ2:CCDC32 complex that acts as a template to recruit μ2 and β2 in succession; at the end, CCDC32 is released and AP2 is complete [18]. In HeLa cells lacking CCDC32, the AP2 subunits decrease, the transferrin receptor accumulates at the surface and transferrin endocytosis fails; in mouse adipocytes lacking Ccdc32, the glucose transporter GLUT4 also accumulates at the surface, showing that CCDC32 regulates CME in general and not a single cargo [18]. Among the five adaptor complexes (AP1 to AP5), only AP2 is depleted in the absence of CCDC32, whereas loss of AAGAB depletes AP1, AP2 and AP4; the COP-I coat is unaffected [18]. A truncated form of CCDC32 reproducing a patient variant does not perform this function [18, 19].

Yang and colleagues (eLife, 2026) described a second, later role: CCDC32 is recruited to nascent clathrin-coated pits, binds the appendage domain of the α subunit and, when reduced by RNA interference, allows flat, unstable clathrin structures to accumulate, without invagination [20]. Binding to AP2 depends on an α-helix encoded by residues 78 to 98; its deletion abolishes binding and the early function in CME, and a mutant truncated at residue 54, designed to mimic a patient variant, neither co-immunoprecipitates AP2 nor is recruited to the pits [20]. Sloan and colleagues (Science Advances, June 2026) showed that CCDC32 binds the α appendage with high affinity, at the canonical site of endocytic regulators and in a previously unknown conserved pocket, that it contains cargo-sorting motifs typical of transmembrane proteins, and that two amphipathic helices bind the α/σ2 hemicomplex and membranes containing phosphatidylinositol 4,5-bisphosphate (PIP2) [21]. In solution, CCDC32 prevents assembly and even disassembles AP2 tetramers; the presence of a PIP2-containing membrane stabilises the final stages, which led the authors to propose that the membrane acts as a switch that releases the inhibition and allows assembly to be completed [21]. The same authors report that deletion of CCDC32 causes loss of all AP2 subunits in vivo [21].

2.3 Pathogenic variants and nomenclature

Two types of alleles have been described: two small duplications that shift the reading frame, each in one family, and an intragenic deletion of about 32.6 kb that removes exons 3 and 4, found in several families with no known relationship [2, 4, 6]. The 2020 variants were published on NM_001080791.2; projection onto the MANE transcript NM_001080792.4, obtained in ClinVar and confirmed in VariantValidator, shifts the numbering by 27 nucleotides and 9 codons [2, 4, 5].

In family A, the c.54dupT duplication (old numbering) lay within a homozygous segment of about 9.06 Mb and was absent from gnomAD, TOPMed, Geno2MP and the Greater Middle East Variome; nine homozygous variants had survived exome filtering [2]. In family B, the c.189_190dupGG duplication (old numbering) lay within a 5.23 Mb homozygous segment and was the only homozygous variant to survive the filters; each allele came from one parent [2]. OMIM records these variants as alleles 618941.0001 (rs1890756020) and 618941.0002 (rs1890742129), and the Egyptian deletion as 618941.0003; dbSNP projects the two duplications onto NM_001080792.4:c.27dup and c.162_163dup, in agreement with ClinVar [1, 3, 25]. In the gene entry, OMIM describes the Egyptian deletion as 32,583 bp with GRCh38 coordinates chr15:40,529,942–40,562,524, the same values as in the original article [3, 6].

The Egyptian deletion was detected by CNV analysis of the trio exome data, was absent from structural variant databases (Database of Genomic Variants, Database of Genomic Structural Variation, gnomAD structural variant set) and was confirmed by quantitative polymerase chain reaction (PCR), junction PCR and breakpoint sequencing [6]. It leaves exons 1 and 2 of the eight transcripts intact and removes the rest of the coding region and the 3' untranslated region in seven of them, so it behaves as a null allele [6]. In December 2025, the Erasmus MC laboratory submitted to ClinVar the detection of the same 32 kb deletion, homozygous and of biparental origin, in the two Dutch siblings [4]. In 2023, a laboratory at the Hospital Israelita Albert Einstein, São Paulo, submitted a deletion with an overlapping interval, detected by genome sequencing in an affected individual of Brazilian origin, without stating the zygosity [4]. The Portuguese deletion also removes exons 3 and 4, but the published abstract does not define the breakpoints [7]. The sources consulted do not clarify whether the recurrence of this deletion in families from Egypt, the Netherlands and Brazil results from a shared ancestral allele or from independent events at a site of genomic instability.

2.4 Disease mechanism and genotype–phenotype correlation

All published variants are loss-of-function: the two duplications create premature stop codons early in the protein, and the deletion removes most of the coding region [2, 6]. According to Yang and colleagues, the truncated proteins that would result from the known variants end before the helix of residues 78 to 98 and would lose the ability to bind AP2; the authors acknowledge, however, that the transcripts may be degraded by nonsense-mediated decay [20]. The same authors consider the alleles hypomorphic, because complete loss of AP2 is lethal in Drosophila and zebrafish embryos, and Wan and colleagues suggest that other CME factors partly compensate for the absence of CCDC32 [18, 20]. Sloan and colleagues stress that the consequences of loss of AAGAB, CCDC32 and AP2 do not overlap: deletion of Ap2b1 in the mouse prevents embryonic development and causes cleft palate, loss of CCDC32 allows development but causes craniofacial malformations, and AAGAB variants cause a skin disease without craniofacial changes, punctate palmoplantar keratoderma type 1 [18, 21].

The link to AP2 helps explain the distribution of malformations. In mice, homozygous disruption of Ap2m1 or Ap2b1 and an in-frame deletion of Ap2s1 cause embryonic or perinatal lethality; 25% of late embryos lacking Ap2b1 have complete cleft of the secondary palate; mice homozygous for the Ap2b1 p.(Met448Lys) variant have double-outlet right ventricle, Taussig-Bing anomaly, atrioventricular septal defect or ventricular septal defect, aortic arch anomalies, cleft palate, micrognathia and thymic aplasia; and deletion of Ap2m1 in cochlear inner hair cells causes profound deafness [6]. AP2-dependent endocytosis regulates turnover of the ephrin-B1 receptor during palatal shelf growth, which led Abdalla and colleagues to propose a common pathway with craniofrontonasal syndrome, caused by EFNB1 variants, which shares hypertelorism and cleft lip and palate and was the first clinical diagnosis considered in the Egyptian patient [6]. In humans, an AP2B1 polymorphism has been associated with non-syndromic cleft lip and/or palate, and a recurrent de novo AP2M1 variant has been described in four patients with global delay and myoclonic-atonic epilepsy, according to the review by Abdalla and colleagues [6].

The ciliary hypothesis of the founding article rests on the zebrafish model: F0-edited embryos, with 85% and 70% mosaic altered alleles for the two guides, had smaller heads at 72 hours, an altered angle of the ceratohyal cartilages and a hypoplastic cerebellum, without global growth delay; cardiac looping was normal, midline or reversed; expression of the laterality gene southpaw was bilateral or right-sided; and the cilia of Kupffer's vesicle, the zebrafish left–right organiser, were fewer and shorter [2]. In cultured mouse kidney cells, reduction of Ccdc32 decreased the percentage of ciliated cells and cilium length [2]. The authors noted that hallmarks of the ciliopathies, such as cystic kidney disease and polydactyly, were missing, and left open non-ciliary functions, since demonstrated in CME [2, 18].

With six living patients, no genotype–phenotype correlation has been established. The two patients with duplications had normal or tall stature, whereas the Egyptian patient and the Portuguese patient, both with deletion of exons 3–4, had short stature; the number of cases does not allow this difference to be attributed to the allele type [6, 7]. Intrafamilial variability is known only in family A, in which the child had heart disease and the fetus had no detected heart disease [2].

2.5 Inheritance and penetrance

Transmission is autosomal recessive. In family A, the consanguineous parents and two unaffected siblings were heterozygous and the affected fetus was homozygous; in family B, the parents, first cousins, were heterozygous; in the Egyptian family, the parents and a brother were heterozygous; in the Portuguese family, the mother was heterozygous and the father was not tested [1, 2, 6, 7]. The heterozygous parents were healthy; the younger brother of the Egyptian patient, also heterozygous, had global delay, epilepsy, profound sensorineural deafness and cerebellar atrophy, a picture that the authors distinguished from CFNDS and did not explain by the heterozygous deletion [6]. All homozygotes described were affected, but the number of cases is too small to estimate penetrance.

3. Clinical Spectrum and Manifestations by System

3.1 Source of the data

Clinical knowledge of CFNDS rests on case reports: two probands and a fetus in the founding article, an Egyptian patient in 2022, a Portuguese patient described in a congress abstract and in a 2024 article, and two Dutch siblings in 2026, whose individual description was not accessible [2, 6, 7, 9, 23]. There are no cohorts, natural history studies or treated-disease data allowing reliable frequencies; the proportions below are counts across the four living individuals with a detailed description and serve only to guide clinical suspicion. The reports with known age describe children and adolescents aged 3 to 15 years at the last assessment.

3.2 Comparative overview of published patients

Table sources: Harel and colleagues for A-II-1, B-II-1 and the fetus; Abdalla and colleagues for the Egyptian patient; Quental and colleagues for the Portuguese patient [2, 6, 7].

3.3 Face and oral cavity

Bilateral cleft lip and palate is the most constant finding: it is present in the four living patients with a detailed description and in the fetus, which had bilateral cleft lip [2, 6, 7]. Abdalla and colleagues could not define a common face beyond the cleft, partly because the 2020 patients were published without photographs [6]. Hypertelorism is present in three of the four patients, and patient A-II-1 had, by contrast, hypotelorism [2, 6, 7]. A broad nasal root, large, prominent, malformed or low-set ears and upslanting palpebral fissures recur [2, 6, 7]. In the Egyptian patient, at 9 years, the face had sparse, laterally arched eyebrows, marked hypertelorism, strabismus, a short nose with a very broad bridge and depressed tip, a wide mouth with upturned corners, a thick lower vermilion, an accentuated Cupid's bow and low-set, posteriorly rotated ears, with a prominent antihelix and uplifted lobes [6]. The Portuguese patient had thick eyebrows [7]. Patient A-II-1 had a rigid upper lip, micrognathia and missing teeth attributed to the cleft, and the Egyptian patient had delayed tooth eruption and caries [2, 6].

3.4 Growth and head circumference

Microcephaly is common: Z −2.5 in patient B-II-1, −3.80 z in the Egyptian patient at 9 years and present in the Portuguese patient from birth, with borderline microcephaly in patient A-II-1 [2, 6, 7]. Stature is variable. The two 2020 patients had heights on the 80th and 97th centiles, whereas the Egyptian patient had proportionate short stature (116 cm, −3.16 z, and weight 18.5 kg, −3.37 z, at 9 years) and the Portuguese patient short stature at 15 years [2, 6, 7]. Birth weight was 3.1 kg in patient B-II-1 and 2900 g (−1.36 z), at term, in the Egyptian patient [2, 6]. In the Egyptian patient, a hand radiograph at 4.5 years showed markedly delayed bone maturation, with a carpal bone age of 18 months and a metacarpal and phalangeal bone age of 3.5 years [6].

3.5 Heart and vessels

The four living patients with a detailed description had a cardiac anomaly, but a different one in each: atrioventricular canal defect in patient A-II-1, ventricular septal defect with pulmonary valve stenosis in patient B-II-1, mitral valve prolapse in the Egyptian patient and atrial septal defect in the Portuguese patient [2, 6, 7]. The fetus in family A had no heart disease detected on ultrasound [2]. Hypertrophic cardiomyopathy, arrhythmias and progressive heart disease have not been described; the short published follow-up does not allow them to be excluded.

3.6 Laterality and spleen

Patient A-II-1 had abdominal situs inversus with asplenia associated with the atrioventricular canal defect, a combination typical of heterotaxy; Abdalla and colleagues refer to it as situs inversus totalis, but the original article and OMIM describe abdominal situs inversus [1, 2, 6]. Depletion of ccdc32 in zebrafish altered cardiac looping and the asymmetric expression of southpaw, which supports a role for CCDC32 in laterality [2]. The other patients have no described laterality anomalies; in the Egyptian patient, abdominal ultrasound was normal [6].

3.7 Neurodevelopment, behaviour and brain

Global developmental delay is present in all patients and progressed to ID in the two patients assessed at 9 and 15 years [2, 6, 7]. The Egyptian patient sat unsupported at 2 years, walked after 3 years and, at 9 years, spoke in two- to three-word phrases, with a friendly temperament [6]. Patient B-II-1 had moderate motor and language delay and hyperactivity at 3 years [2]. Epilepsy has not been described in any homozygote; the electroencephalogram of patient B-II-1 was normal [2].

Structural brain changes are variable: hypoplastic cerebellar tonsils in patient A-II-1, hypoplasia of the corpus callosum in the Egyptian patient, normal magnetic resonance imaging in the Portuguese patient and hypoplasia of the vermis and pons with an abnormal cisterna magna in the fetus of family A [2, 6, 7]. OMIM includes cerebellar hypoplasia in the description of the entity, and the 2026 review lists microcephaly, facial malformations, developmental delay, cerebellar hypoplasia and cardiac anomalies as possible components of the phenotype [1, 9].

3.8 Hands, feet, nails and skeleton

All living patients with a detailed description have mild anomalies of the fingers: clinodactyly, camptodactyly or brachydactyly [2, 6, 7]. The nails are often affected, with digital clubbing in three patients, nail aplasia of the thumbs and toes in patient B-II-1 and hypoplastic toenails in the Portuguese patient [2, 6, 7]. The Egyptian patient had small hands, short fingers, moderate, passively reducible flexion of the distal interphalangeal joints of the 2nd to 5th fingers with absent or faint creases, short 5th fingers with a single crease and radial clinodactyly, partial cutaneous syndactyly of the 2nd to 5th fingers and brachymesophalangy of the 5th finger with cone-shaped epiphyses on radiography; the feet were small, with a broad forefoot, a short, tapering hallux and short 5th toes [6]. The Portuguese patient had large halluces [7]. There was mild kyphosis in patient A-II-1, and a short neck with mild webbing, a sacral dimple and a prominent coccyx in the Egyptian patient [2, 6].

3.9 Hearing, eyes and airways

The Egyptian patient had moderate bilateral conductive hearing loss on brainstem auditory evoked potentials, strabismus and operated bilateral lacrimal duct obstruction, with a normal fundus [6]. The Portuguese patient had recurrent otitis and respiratory infections [7]. Ophthalmological and audiological assessment was normal in the 2020 patients [2]. The Egyptian patient spent about one month in a neonatal intensive care unit for respiratory distress [6].

3.10 Blood and other systems

The Egyptian patient had repeated thrombocytopenia with no identified cause; bone marrow biopsy showed a slightly hypocellular marrow [6]. There are no haematological data for the other patients in the accessible sources. Patient B-II-1 had cryptorchidism, and the Portuguese patient a bicornuate uterus on abdominal ultrasound [2, 7]. The Egyptian patient had hypoplastic areolae [6]. Renal assessment was normal in the 2020 patients [2].

3.11 Core phenotype and spectrum

The core phenotype proposed in 2022 combines developmental delay and bilateral cleft lip and palate, with variable findings of the face, brain, heart, fingers and nails, and postnatal growth delay or microcephaly [6]. The Portuguese patient, described later, fits this core and adds atrial septal defect, bicornuate uterus and recurrent respiratory infections [7]. Heart disease, although it gives the syndrome its name, has no characteristic type [6]. Attenuated forms without clefting have not been described, nor have adult phenotypes.

4. Clinical Recognition and Warning Signs

4.1 When to suspect

CFNDS should be included in the diagnostic hypothesis when a child with cleft lip and palate, especially bilateral, also has congenital heart disease, microcephaly or developmental delay, particularly if the parents are consanguineous or there are affected siblings [2, 6]. The combination of hypertelorism, a broad nasal root, large or malformed ears, small hands with brachydactyly or clinodactyly, and hypoplastic, aplastic or watch-glass nails strengthens the suspicion [2, 6, 7]. The presence of heterotaxy with asplenia in a child with clefting and heart disease is another context for suspicion [2].

The guidelines of the American Cleft Palate-Craniofacial Association (ACPA) recommend referral for a full genetic evaluation in a child with a cleft who has a positive family history, unexplained prenatal or postnatal growth deficiency, developmental delay or ID, associated major or minor malformations, or a recognised genetic diagnosis [11]. All published patients with CFNDS meet at least three of these criteria [2, 6, 7]. The ACPA notes that complex craniofacial syndromes may not express all their manifestations in the first years of life and that periodic genetic reassessment, with updated testing, is part of follow-up [11].

4.2 By age

In the prenatal period, ultrasound may detect bilateral cleft lip and posterior fossa anomalies, such as hypoplasia of the vermis and pons, which led to the ultrasound diagnosis in the fetus of family A [2]. In the newborn, bilateral cleft lip and palate, respiratory distress and severe feeding difficulties, which required a nasogastric tube for two months in the Egyptian patient, are the described forms of presentation [6]. In the infant and young child, motor delay, with walking after 3 years in the Egyptian patient, and language delay become evident; microcephaly may be present from birth [6, 7]. At school age and in adolescence, ID, short stature and microcephaly define the picture [6, 7].

4.3 Warning and emergency signs

In children with asplenia, fever above 38.5 °C requires immediate medical assessment because of the risk of sepsis, and signs of intestinal volvulus, such as feeding intolerance, bilious vomiting or abdominal pain, require urgent evaluation, according to the multidisciplinary approach to heterotaxy [26]. In a child with a cleft, upper airway obstruction may present in the newborn as poor weight gain and feeding problems, and in the older child as noisy breathing and obstructive sleep apnoea [11]. Repeated thrombocytopenia, such as that of the Egyptian patient, should be evaluated before surgery [6].

4.4 Newborn screening

There is no newborn screening for CFNDS. Universal newborn hearing screening is relevant, because children with cleft palate have an increased risk of middle ear disease and one of the patients had conductive hearing loss [6, 11].

5. Diagnosis: Criteria, Tests and Algorithms

5.1 Criteria

There are no formal clinical criteria. The diagnosis is molecular and is established by identifying biallelic pathogenic or likely pathogenic variants in CCDC32, homozygous in the published families, in a patient with a compatible phenotype [1, 6]. The core phenotype of developmental delay and bilateral cleft lip and palate guides suspicion, but is not specific [6].

5.2 First-line test

The 2021 guideline of the American College of Medical Genetics and Genomics (ACMG), developed with the GRADE method, strongly recommends that exome or genome sequencing be considered a first- or second-tier test in patients with congenital anomalies with onset before 1 year or with developmental delay or ID with onset before 18 years, because of the higher diagnostic yield compared with conventional tests and the possible cost advantage when ordered early [10]. CFNDS meets both criteria. All published diagnoses were made by exome, genome or RNA-seq; none would have been made by chromosomal microarray alone [2, 4, 6, 7, 9].

5.3 Limitations of the tests

The known mutational spectrum of CCDC32 has two types of alleles with different technical requirements. The small duplications are detected by exome or genome sequencing with conventional analysis of single-nucleotide variants and small insertions and deletions; in family A, the microarray of the proband and the fetus was normal [2]. The intragenic deletion of about 32.6 kb, which removes exons 3 and 4, is the most recurrent allele in the known families and requires copy number variant analysis with intragenic resolution [4, 6]. In the Egyptian family, it was detected by CNV analysis of the trio exome data and confirmed by quantitative PCR and junction PCR [6]; in the Portuguese patient, by clinical exome [7]; in the Brazilian record, by genome sequencing with read-pair mapping [4]. In the Dutch siblings, the single-nucleotide polymorphism array (SNP array) and the trio exome, analysed for ID and congenital malformation genes, did not detect it; the diagnosis came from clinical RNA sequencing, which showed skipping of two exons in the CCDC32 transcript [9]. A negative exome, particularly without CNV analysis or with analysis restricted to a virtual panel that does not include CCDC32, does not exclude the diagnosis.

RNA sequencing of cultured fibroblasts, with and without inhibition of nonsense-mediated decay by cycloheximide, increased the diagnostic yield by 13% in a series of 96 individuals from Erasmus MC, 67 of them with undiagnosed neurodevelopmental disorders, by detecting intragenic deletions, monoallelic expression, pseudoexon insertions and variants affecting transcription [27]. The Dutch siblings with CFNDS were diagnosed with this approach [9].

In consanguineous disease, analysis of regions of homozygosity is useful: the variants in families A and B lay in homozygous segments of 9.06 Mb and 5.23 Mb, and the analysis of family B prioritised variants in regions of homozygosity of at least 1.5 Mb [2]. The use of old transcript versions can generate discordant nomenclatures for the same variant, as happens with the 2020 variants (section 2.3) [4].

5.4 Report content

The report should state the gene, the MANE transcript NM_001080792.4 and its version, the Human Genome Variation Society (HGVS) nomenclature of the variants at DNA and protein level (for example, NM_001080792.4:c.27dup, p.(Thr10TyrfsTer12)), the zygosity, the classification according to the criteria of the ACMG and the Association for Molecular Pathology (ACMG/AMP), and, for deletions, the genomic coordinates with the reference assembly and the confirmation method [4–6]. The ClinVar submissions of the CCDC32 deletions used the 2015 ACMG criteria [4]. Parental testing confirms that the variants are in trans; when one parent is unavailable, as in the Portuguese family, in which only the mother was tested, confirmation of the trans configuration remains incomplete [7].

5.5 Variants of uncertain significance and segregation

Missense or splicing variants in CCDC32 have not been described as a cause of CFNDS in the sources consulted. Faced with a variant of uncertain significance, segregation in the family, assessment of the transcript by RNA-seq and the functional analysis of AP2 described in the cellular studies are the routes to reclassification [9, 18, 20].

5.6 Evaluation at diagnosis

There is no published protocol for CFNDS. The initial evaluation follows from the described manifestations and from the recommendations for children with clefts and with heterotaxy: assessment by the cleft team in the first weeks of life; paediatric assessment of growth, feeding and development; audiological assessment; cardiological assessment with echocardiography, because the four living patients with a detailed description had a cardiac anomaly; abdominal ultrasound to assess situs, spleen, kidneys and pelvic anatomy; ophthalmological assessment; brain magnetic resonance imaging when clinically justified; and full blood count, given the described thrombocytopenia [2, 6, 7, 11, 26]. Extending these recommendations to CFNDS is an inference from the cases and from the manifestation-based guidelines, not a published specific recommendation.

5.7 Algorithm

5.8 Prenatal and preimplantation diagnosis

When the family variants are known, prenatal diagnosis by chorionic villus sampling or amniocentesis is possible, as in other monogenic syndromes with a defined familial variant [16]; the sources consulted do not describe its use, nor that of preimplantation genetic testing, in families with CFNDS. Without a molecular diagnosis, fetal ultrasound may show bilateral cleft lip and posterior fossa anomalies, as in the fetus of family A [2]. The ACPA recommends prenatal counselling with a craniofacial orthodontist when the cleft is diagnosed in pregnancy [11].

6. Differential Diagnosis

6.1 Principles

In the table, AD denotes autosomal dominant inheritance and AR autosomal recessive inheritance. The differential diagnosis of CFNDS is organised into three groups: the RASopathies, which share heart disease, hypertelorism, short stature, short neck and developmental delay and which justify the label "RASopathy-like" sometimes applied to CFNDS; syndromes with orofacial clefting, heart disease and ID outside the RAS pathway, which are the closest clinical differentials; and the ciliopathies and other laterality disorders, considered when there is heterotaxy [2, 6, 16]. Because the CFNDS face is not recognisable and the number of patients is small, diagnosis depends on broad molecular testing and not on morphological comparison [6, 10].

6.2 Comparative table

Table sources: NS, CFC, Costello and NS with multiple lentigines [14–16, 28–30]; CDK13 [31]; craniofrontonasal [32]; Opitz G/BBB [33]; 22q11.2 [34]; CHARGE [35]; Kabuki [36]; OFD1 [37]; heterotaxy and primary ciliary dyskinesia [26]. The RASopathies, CDK13-related disorder, craniofrontonasal syndrome, Opitz G/BBB syndrome, the 22q11.2 deletion, CHARGE syndrome, Kabuki syndrome and heterotaxy enter the differential diagnosis.

6.3 RASopathies

Noonan syndrome is the most common of the RASopathies, affecting about 1 in 2500 people according to the Oxford Desk Reference and 1 in 2000 according to Smith's, which estimates the RASopathies as a whole at more than 1 in 1000 people, and its face, with a high forehead, hypertelorism, low-set, rotated ears, a short nose and a marked philtrum, partly overlaps that of CFNDS [16, 28]. The heart disease of Noonan syndrome is, however, characteristic: 50 to 80% of patients have congenital heart disease, pulmonary valve stenosis with dysplasia occurs in 25 to 71% and hypertrophic cardiomyopathy in 20 to 29% [14]. More than ten genes are associated with Noonan syndrome, including PTPN11, SOS1, RIT1 and RAF1, and a parent is affected in 30 to 75% of families; LZTR1 variants may be transmitted in a dominant or recessive manner [14]. Cardiofaciocutaneous syndrome shares with CFNDS heart disease (77%) and moderate to severe ID (more than 95%), but has relative macrocephaly (88%), a prominent forehead and bitemporal narrowing (100%), sparse curly hair (100%) and skin changes in 95% [15]. Costello syndrome is defined by a heterozygous HRAS variant and combines a coarse face, lax skin with deep palmar creases, papillomas, hypertrophic cardiomyopathy and chaotic atrial tachycardia with a lifetime risk of malignant tumours of about 15%, which Smith's places at 10 to 15% by 20 years, mainly rhabdomyosarcoma [14, 16, 29].

Bilateral cleft lip and palate, microcephaly, nail anomalies and parental consanguinity set CFNDS apart from the RASopathies, which are dominant and in whose consulted descriptions cleft lip does not feature, cleft palate appearing only as an occasional finding in CFC and Noonan syndrome with multiple lentigines [6, 14, 15, 30]. The Oxford Desk Reference recommends, in the Noonan-like phenotype, microarray in all sporadic girls, to exclude monosomy X, and in all patients with developmental delay, followed by a panel, exome or genome with full clinical information provided to the laboratory [16]. Information on clefting and consanguinity steers the laboratory towards an analysis that includes recessive genes such as CCDC32.

6.4 Syndromes with clefting, heart disease and ID outside the RAS pathway

Craniofrontonasal syndrome was the first diagnosis considered in the Egyptian patient and is the differential with the greatest overlap: hypertelorism, cleft lip and/or palate, short neck, syndactyly, agenesis of the corpus callosum and, occasionally, heart disease, bicornuate uterus, hearing loss and ID [6, 32]. It is distinguished by craniosynostosis and a bifid nasal tip in females, nails with longitudinal splitting, dry curly hair and X-linked inheritance, with females more severely affected because of X-inactivation mosaicism [32]. Abdalla and colleagues proposed a mechanistic link between the two entities, through regulation of ephrin-B1 receptor turnover by AP2-dependent endocytosis [6].

CDK13-related disorder combines ID, septal and pulmonary valve defects, pulmonary artery hypoplasia, congenital glaucoma, posterior embryotoxon, metopic craniosynostosis and changes of the corpus callosum or vermis, but it is dominant and almost always de novo [31]. Opitz G/BBB syndrome combines hypertelorism, cleft lip with or without cleft palate in 50%, conotruncal heart disease and ID in about half of males, and is distinguished by hypospadias and laryngotracheo-oesophageal defects, which cause dysphagia with aspiration and stridor [33]. The 22q11.2 deletion syndrome causes cleft palate or velopharyngeal insufficiency (67%) and heart disease in 85%, mainly ventricular septal defect, right aortic arch and tetralogy of Fallot, and microcephaly in 24 to 30% in childhood, but rarely cleft lip [34]. CHARGE syndrome has cleft lip and/or palate in 15 to 20% and heart disease in 75 to 80%, but is distinguished by colobomas, choanal atresia and anomalies of the ears and cranial nerves [35]. Kabuki syndrome has heart disease in about half of patients and cleft palate, but the face, with long palpebral fissures and eversion of the lateral third of the lower eyelid, and persistent fetal fingertip pads (96%) set it apart from CFNDS [36].

6.5 Ciliopathies and laterality disorders

The heterotaxy of patient A-II-1 and the zebrafish ciliary model led Harel and colleagues to consider the ciliopathies [2]. Oral-facial-digital syndrome type I, an X-linked dominant ciliopathy, combines hypertelorism or telecanthus (50%), median pseudocleft of the upper lip (32 to 58%), cleft palate and ID or neurological impairment in about 60%, but is distinguished by multiple oral frenula, a lobulated tongue with nodules and asymmetric shortening of the digits [37]. Heterotaxy, isolated or associated with primary ciliary dyskinesia, has numerous monogenic causes, including CCDC genes such as CCDC39, CCDC40, CCDC103 and CCDC114, and presents with chronic oto-sino-pulmonary infections, but without cleft lip and palate or ID in most patients [2, 26]. The recommendation to test for CNVs and sequence variants in all patients with heterotaxy, and to consider genome sequencing when panels do not explain the phenotype, also applies to suspected CFNDS [26].

6.6 Other disorders of the AP2 complex

Disorders of the AP2 subunits and chaperones form a closely related mechanistic group, but with distinct phenotypes: the recurrent de novo AP2M1 variant causes global delay with myoclonic-atonic epilepsy, and heterozygous AAGAB variants cause punctate palmoplantar keratoderma type 1, a skin disease without craniofacial changes [6, 18, 21]. The clinical overlap with CFNDS is small; the relationship matters mainly for interpreting the mechanism.

7. Treatments and Risk Management Strategies

7.1 Principles and sources of the recommendations

There is no targeted treatment for CFNDS, nor any specific guideline or consensus; a search of PubMed, Europe PMC and ClinicalTrials.gov in October 2026 identified no guidance document and no registered clinical trial [38]. Management is symptomatic and follows the manifestation-based guidelines: the ACPA parameters for the evaluation and treatment of patients with cleft lip/palate and other craniofacial differences (2018 revision), the multidisciplinary approach to heterotaxy of Saba and colleagues (2022) for the patient with asplenia or abnormal situs, and the 2021 ACMG guideline for diagnosis [10, 11, 26]. Applying these recommendations to CFNDS is an extrapolation, declared as such, from diseases that share the same manifestations.

The ACPA bases its guidance on general principles: management by an interdisciplinary team that sees a sufficient number of patients per year; the first evaluation within the first weeks of life and, if possible, the first days; treatment plans defined by the team and communicated in writing to the family; care coordinated by the team but delivered locally whenever possible, with complex procedures reserved for experienced centres; and longitudinal follow-up with recording of outcomes [11]. The team may include anaesthesiology, audiology, imaging, genetic counselling, clinical genetics, neurology, nursing, paediatric dentistry, orthodontics, otorhinolaryngology, paediatrics, psychology, plastic and maxillofacial surgery and speech and language therapy [11].

7.2 Feeding and growth

Feeding difficulties are present in all published patients and were severe in two: the Egyptian patient needed nasogastric tube feeding for two months and patient B-II-1 had severe feeding difficulties [2, 6]. The ACPA recommends that a team member, usually the nurse or another feeding specialist, contact the family soon after referral, assess feeding, teach special techniques and devices and monitor nutrition and growth; the mother's choice of feeding method should be supported provided that oral feeding has been assessed as safe [11]. In the newborn with a cleft, poor weight gain and feeding problems are often related to the airway and require coordination between otorhinolaryngology, surgery and speech and language therapy [11]. Growth should be monitored with weight, height and head circumference charts, because two of the four patients had short stature and three had microcephaly [2, 6, 7]. There are no data on the use of growth hormone in CFNDS, and the sources consulted did not assess somatotropic function in these patients.

7.3 Cleft lip and palate

Surgical repair of cleft lip is usually started in the first 12 months of life and may be performed as early as is safe; presurgical maxillary orthopaedics and primary rhinoplasty may be indicated in some patients [11]. In a child with typical development, cleft palate should be closed by 18 months and preferably earlier, with muscular reconstruction of the soft palate; the aim is normal speech and swallowing function [11]. Secondary velopharyngeal surgery should be performed only after imaging assessment of the velopharyngeal mechanism during speech; alveolar bone grafting is scheduled with the orthodontist, before eruption of the permanent teeth in the cleft region; and orthognathic surgery is deferred, whenever possible, until physical maturation is complete [11]. Procedures should be coordinated to reduce the number of anaesthetics and hospital admissions, and an experienced paediatric anaesthetist should be present at all operations on children [11]. The published patients had their clefts repaired "at the appropriate time", without description of ages or techniques [6].

7.4 Hearing, middle ear and airways

Children with cleft palate have an increased risk of middle ear disease, and the Egyptian patient had moderate bilateral conductive hearing loss, while the Portuguese patient had recurrent otitis [6, 7, 11]. The ACPA recommends recording the result of newborn hearing screening and, if it is failed, performing a full diagnostic audiological evaluation by 3 months; starting behavioural audiological assessments at about 9 months and repeating them at least every 6 to 12 months until 5 years; and, after 5 years, if hearing is consistently normal, performing them annually until adolescence [11]. Each assessment includes pure-tone and, when possible, speech audiometry, tympanometry, stapedial reflexes and otoacoustic emissions; children with ventilation tubes are assessed regularly; persistent hearing loss leads to consideration of amplification (hearing aid, bone-anchored hearing aid, cochlear implant or FM system) and immediate referral to the school [11]. Treatment of otitis media may include systemic or topical antibiotics, tympanostomy tube placement, tympanoplasty and cholesteatoma surgery; Eustachian tube function should be reassessed over time [11]. Upper airway obstruction may result from the facial skeleton, soft tissues, nasal septum, choanae or larynx and trachea, and obstructive sleep apnoea should be sought in the older child [11].

7.5 Dentition and orthodontics

The ACPA recommends early paediatric dental consultation, dental care within 6 months of eruption of the first tooth and no later than 12 months of age, and regular lifelong follow-up, with surveillance for caries, periodontal disease and eruption abnormalities [11]. Craniofacial orthodontics may begin in the prenatal period when the cleft is diagnosed in pregnancy and continues into adulthood, with active treatment in phases rather than continuously from the mixed to the permanent dentition [11]. The Egyptian patient had delayed tooth eruption and caries, and patient A-II-1 missing teeth attributed to the cleft [2, 6].

7.6 Heart

The four living patients with a detailed description had a cardiac anomaly, ranging from structural defects with potential surgical indication, such as atrioventricular canal defect, to mitral valve prolapse [2, 6, 7]. Cardiological assessment with echocardiography at diagnosis and follow-up dictated by the lesion found follow from this frequency; the sources do not describe the cardiac course or treatment of the patients. In patients with heterotaxy, the multidisciplinary approach recommends paediatric cardiology assessment of anatomy, function and electrophysiology, with cardiac magnetic resonance imaging, computed tomography, catheterisation and prolonged electrocardiographic recording (Holter) when necessary [26].

7.7 Asplenia, laterality and gut

The asplenia of patient A-II-1 calls for the infection prevention measures of the asplenic patient [2]. Saba and colleagues recommend, in all patients with heterotaxy, abdominal ultrasound to assess the presence and anatomy of the spleen and assessment by an immunology or infectious diseases specialist, who guides the evaluation of splenic function, vaccines and antimicrobial prophylaxis [26]. Patients with asplenia or functional hyposplenism should seek immediate medical care for fever above 38.5 °C and receive all routine vaccines plus the 23-valent pneumococcal polysaccharide vaccine and meningococcal vaccines, according to local standards [26]. Antimicrobial prophylaxis in functional hyposplenism can usually be stopped at 5 years, but may be prolonged in high-risk patients [26]. Families should seek immediate care for signs of volvulus (feeding intolerance, bilious vomiting, vague abdominal pain); an upper gastrointestinal contrast study is performed only for symptoms, screening for malrotation in asymptomatic patients not being recommended; and patients with chronic wet cough, chronic nasal congestion or recurrent oto-sino-pulmonary infections should be assessed for primary ciliary dyskinesia [26]. The recurrent respiratory infections of the Portuguese patient justify this assessment, although she had no described laterality anomaly [7, 26].

7.8 Neurodevelopment, education and behaviour

Global developmental delay and ID require early intervention, speech and language therapy, special educational support and behavioural assessment; patient B-II-1 had hyperactivity [2, 6]. The ACPA recommends that the team monitor motor, cognitive and social development, speech and language in the first year, and that it provide parents with information on normal speech development and the disorders for which the child is at risk, with assessment of prelinguistic communication [11]. The approach to heterotaxy recommends annual screening for developmental and psychological disorders [26]. The sources consulted do not describe epilepsy in homozygotes or the use of psychotropic drugs; hyperactivity and behavioural disorders are treated according to general paediatric standards.

7.9 Haematology, eyes and other manifestations

The repeated thrombocytopenia of the Egyptian patient led to bone marrow biopsy, which showed a slightly hypocellular marrow, with no additional diagnosis [6]. A full blood count before surgery and in the event of bleeding is prudent; the frequency of thrombocytopenia in CFNDS is unknown. Ophthalmological assessment should look for strabismus and lacrimal duct obstruction, both present in the Egyptian patient, who underwent surgery for the lacrimal obstruction [6]. Cryptorchidism, present in patient B-II-1, and the bicornuate uterus of the Portuguese patient are managed according to usual standards [2, 7].

7.10 Drugs, regulatory status and trials

No drug has an approved indication for CFNDS from the United States Food and Drug Administration (FDA), the European Medicines Agency (EMA), the Portuguese National Authority of Medicines and Health Products (INFARMED) or the Brazilian Health Regulatory Agency (ANVISA), and there are no registered clinical trials; the literature consulted describes no medicine in development for CFNDS [9, 38]. The medication used is that of the manifestations (antibiotics for otitis media and for prophylaxis in the asplenic patient, vaccines, perioperative analgesia and anaesthesia), with no particularities described in CFNDS [11, 26].

7.11 Recent research and level of evidence

The studies of the last 12 months (Albuainain, February 2026; Yang, version of record January 2026; Sloan, June 2026) add one family and mechanistic knowledge, but none evaluated a therapeutic intervention [9, 20, 21]. The cellular studies do not allow the clinical effect of any AP2-directed approach to be predicted, and there are no press releases, regulatory submissions, opinions or authorisations related to CFNDS. The absence of results in the searches does not prove that no early-stage projects exist.

7.12 Perioperative care, pregnancy and transition

Children with CFNDS undergo several operations (cleft, heart disease, ear, lacrimal ducts), which makes relevant the coordination of interventions to reduce the number of anaesthetics, the presence of an experienced paediatric anaesthetist and the availability of intensive care when the airway may be compromised [11]. Chronic respiratory disease or previous postoperative pulmonary complications justify preoperative pulmonary optimisation with antibiotics and airway clearance [26]. Thrombocytopenia, when present, should be known before surgery [6]. There are no data on pregnancy in women with CFNDS; the oldest patient described was 15 years old and had a bicornuate uterus, a malformation to be considered in any future pregnancy [7]. The ACPA recommends that the team offer continuing care to adults and that transition to adult providers be planned by the team paediatrician [11].

7.13 Agents to avoid

The sources consulted do not identify drugs contraindicated in CFNDS. In patients with asplenia, the precautions for the asplenic patient apply, with the vaccination and prophylaxis plan defined by the immunology or infectious diseases specialist [26].

8. Reproductive Options and Family Counselling

8.1 Recurrence risks

CFNDS is transmitted in an autosomal recessive manner [1, 2]. When both parents are heterozygous, as was shown in families A, B and the Egyptian family, each pregnancy has a 25% probability of an affected child, 50% of a heterozygous carrier child and 25% of a child without the variant; the carriers described were healthy [1, 2, 6]. Intrafamilial recurrence is documented in three families: the fetus in family A, the older brother of the Egyptian patient, with cleft lip and palate and early neonatal death, who was not tested, and the two Dutch siblings [2, 6, 9]. A healthy sibling of a patient has a two-thirds probability of being a carrier.

8.2 Consanguinity and cascade testing

All families with an accessible description were consanguineous: first cousins once removed in family A, first cousins in family B, and reported consanguinity in the Egyptian and Portuguese families [2, 6, 7]. Family B was identified in a cohort of 60 children with suspected genetic disease and consanguineous parents [1]. In consanguineous families, testing for the familial variant can be offered to adult siblings and to consanguineous partners of known carriers, to estimate the risk to their pregnancies; when the partner is not from the family and the variant has not been described in the population, the risk of having an affected child is very low, but not zero, because the gene has rare loss-of-function variants in gnomAD [24]. The exon 3–4 deletion, found in families with no known relationship, requires that partner testing include CNV analysis of CCDC32 [4, 6].

8.3 Prenatal and preimplantation diagnosis

With the familial variants identified, molecular prenatal diagnosis by chorionic villus sampling or amniocentesis is possible [16]. The anomaly scan may show bilateral cleft lip and posterior fossa anomalies, as in the fetus of family A, whose pregnancy was terminated by parental decision; the absence of fetal heart disease does not exclude the disease, because that fetus had no detected heart disease [2]. The sources consulted do not describe preimplantation genetic testing in this disease. The ACPA recommends prenatal counselling with a craniofacial orthodontist and information on infant orthopaedics when the cleft is diagnosed in pregnancy [11].

8.4 Counselling of minors and other situations

The sources consulted do not specifically address carrier testing in minor siblings. The ACPA includes counselling on recurrence risk and prognosis in the full genetic evaluation of the child with a cleft and recommends genetic reassessments throughout follow-up [11]. Germline mosaicism, which the Oxford Desk Reference considers a small theoretical risk in de novo dominant variants, carries little weight in a recessive disease with confirmed heterozygous parents [16].

9. Special Considerations: Population Diversity and Epidemiology

9.1 Frequency

There are no estimates of the prevalence or incidence of CFNDS. The available information is a case count: six living individuals and one fetus in five families published up to October 2026, to which are added one Brazilian individual recorded in ClinVar without publication and one deceased, untested Egyptian sibling [2, 4, 6, 7, 9]. This count measures the number of published diagnoses, not the frequency of the disease, and the probability of underdiagnosis is high, because the most frequent deletion escapes some routine methods [9].

9.2 Geographical distribution and populations

The published families come from the Middle East (an Arab Muslim family and an Iranian family from Isfahan), North Africa (Egypt) and Europe (Portugal and the Netherlands), and there is one record from Brazil [2, 4, 6, 7, 9]. Parental consanguinity is present in all families with an accessible description, which is expected in a rare recessive disease [2, 6, 7]. The two small duplications were each found in a single family; the deletion of about 32.6 kb was found in the Egyptian and Dutch families and has an overlapping interval in the Brazilian record, and the Portuguese deletion removes the same exons [4, 7]. The sources consulted do not establish whether this is a shared founder allele or recurrent events; there are no carrier frequency data in any population.

9.3 Portugal and Brazil

The Portuguese patient was the fourth patient published worldwide, described by a team from the Genetics Department of the Centro Hospitalar Universitário de São João and the Faculty of Medicine of the University of Porto [7, 23]. In Brazil, the Genetics and Molecular Diagnosis Laboratory of the Hospital Israelita Albert Einstein submitted to ClinVar, in 2023, a pathogenic CCDC32 deletion detected by genome sequencing in an affected individual, without an associated clinical publication [4].

9.4 Reference networks and patient associations

In the European Union, patients fall within ERN ITHACA, the European reference network for rare congenital malformations and rare intellectual disability, and ERN CRANIO, the network for rare craniofacial anomalies and ear, nose and throat disorders, which includes orofacial clefts [12, 13]. Orphanet classifies the gene in the category of non-specific syndromic intellectual disability (ORPHA:528084), which makes it difficult to identify the disease in registries using Orphanet codes [8]. No patient associations specific to CFNDS were found; families can turn to cleft lip and palate patient associations and to those listed by the ERNs.

10. Illustrative Clinical Case

10.1 Egyptian girl with a homozygous 32.6 kb deletion in CCDC32 (Abdalla et al., 2022)

Abdalla and colleagues, from the Institute of Human Genetics of the University Medical Center Hamburg-Eppendorf and Alexandria University, described in 2022 a girl, the third child of healthy consanguineous Egyptian parents [6]. The couple's second child, a boy with similar cleft lip and palate, had died in the early neonatal period without genetic study. The patient was born at term, weighing 2900 g (−1.36 z), with bilateral cleft lip and palate; she spent about one month in a neonatal intensive care unit for respiratory distress and was fed by nasogastric tube for two months [6]. During childhood, global developmental delay, growth delay and repeated thrombocytopenia with no identified cause emerged; she sat unsupported at 2 years and walked after 3 years, and surgery for the malformations was performed at the appropriate time [6].

At the last assessment, at 9 years, she had ID with speech limited to two- to three-word phrases, a friendly temperament, a weight of 18.5 kg (−3.37 z), a height of 116 cm (−3.16 z) and a head circumference of 48 cm (−3.80 z) [6]. The face had sparse, laterally arched eyebrows, marked hypertelorism, upslanting palpebral fissures, strabismus, a short nose with a very broad bridge and depressed tip, a wide mouth, a thick lower vermilion and low-set, posteriorly rotated ears; there was a short neck with mild webbing, hypoplastic areolae, a sacral dimple, small hands with flexion of the distal interphalangeal joints and short 5th fingers, and small feet with a short hallux [6]. A hand radiograph at 4.5 years showed a carpal bone age of 18 months and brachymesophalangy of the 5th finger [6]. Brain magnetic resonance imaging revealed hypoplasia of the corpus callosum; echocardiography, mitral valve prolapse; auditory evoked potentials, moderate bilateral conductive hearing loss; abdominal ultrasound and fundoscopy were normal; and bone marrow biopsy, requested because of the thrombocytopenia, showed a slightly hypocellular marrow [6]. Craniofrontonasal syndrome was the first clinical diagnosis considered [6].

Trio exome found no relevant point variants, but CNV analysis of the same data suggested a deletion of more than 25 kb in CCDC32, homozygous in the patient and heterozygous in the parents [6]. Quantitative PCR showed zero copies of exons 3 and 4.1 in the patient and one copy in the parents, and junction PCR and breakpoint sequencing defined a deletion of 32,583 bp, NC_000015.10:g.40529942_40562524del, which removes exon 3 and the downstream exons, leaving exons 1 and 2 intact [6]. The younger brother, with global delay, epilepsy, profound sensorineural deafness, ataxia and cerebellar atrophy, was heterozygous, and his condition was not attributed to CFNDS [6]. Figure 1 of the article shows the pedigree, the face, the hands and the hand radiograph, and Figure 2 the diagram of the eight CCDC32 transcripts with the deletion, the quantitative PCR, the junction PCR gel and the breakpoint electropherogram (full text open access: https://onlinelibrary.wiley.com/doi/full/10.1002/ajmg.a.62762) [6].

10.2 Lessons from the case

The case illustrates three practical points. First, CFNDS may be mistaken for another syndrome with clefting and hypertelorism, such as craniofrontonasal syndrome [6, 32]. Second, the most recurrent allele is an intragenic deletion that is seen only with CNV analysis, which in this case was performed on the exome data, and which in the Dutch siblings went unnoticed until RNA sequencing [6, 9]. Third, not all affected members of a consanguineous family share the same diagnosis: the heterozygous brother with epilepsy and sensorineural deafness had a different condition, which requires its own investigation [6]. The management described in the article is limited to diagnosis and surgery for the malformations; there is no specific treatment to compare with guidelines.

11. Prognosis and Long-Term Follow-up

11.1 Prognosis

There are no data on survival or long-term course: the oldest patient described was 15 years old, and all reports are cross-sectional [2, 6, 7]. The sources describe an early neonatal death in a sibling with cleft lip and palate, presumably affected but not tested, and a termination of pregnancy [2, 6]. In surviving patients, ID and language delay persist: at 9 years, the Egyptian patient spoke in two- to three-word phrases, and the Portuguese patient had ID at 15 years [6, 7]. The prognosis of each patient depends mainly on the type of heart disease, the presence of asplenia and the severity of ID; in heterotaxy in general, estimated survival after cardiac surgery is about 60% at 15 years, a figure that does not apply directly to CFNDS without heterotaxy [26].

11.2 Surveillance table

The following recommendations are not specific to CFNDS: they apply the guidelines for its manifestations to the disease, and their extension to CFNDS is based on the findings of the published cases.

11.3 Transition to adulthood

The ACPA recommends that adults continue to have access to team care and that the team paediatrician follow the patient until transfer to adult providers [11]. End-of-growth procedures, such as orthognathic surgery and definitive rhinoplasty, fall within this phase [11]. There are no descriptions of adults with CFNDS.

12. Summary and Final Considerations

Cardiofacioneurodevelopmental syndrome is an autosomal recessive disease of CCDC32, described in 2020 and known in six living patients and one fetus from five families, all with reported consanguinity when the information is available, plus one Brazilian ClinVar record [2, 4, 6, 7, 9]. The clinical core is the association of bilateral cleft lip and palate and global developmental delay with ID, accompanied by feeding difficulties, a cardiac anomaly of variable type, microcephaly, hypertelorism and anomalies of the hands and nails; heterotaxy with asplenia, conductive hearing loss, thrombocytopenia and cerebral hypoplasias occur in isolated patients [2, 6, 7]. Despite its name, it is not a RASopathy: the differential with the RASopathies rests on the cleft, recessive inheritance and the absence of the skin changes of cardiofaciocutaneous syndrome, and the closest differential is that of syndromes with clefting, heart disease and ID, especially craniofrontonasal syndrome [6, 14, 32].

CCDC32 is a chaperone for assembly of the AP2 adaptor complex of clathrin-mediated endocytosis, which receives the α/σ2 hemicomplex from AAGAB and serves as a template for incorporation of μ2 and β2, and which also stabilises clathrin-coated pits; loss of this function explains the overlap with the cleft palate and heart disease phenotypes of mice with AP2 defects [6, 18, 20, 21]. The most recurrent allele is an intragenic deletion of about 32.6 kb of exons 3 and 4, which requires CNV analysis and may escape microarray and restricted exome analyses, having in one case been detected only by RNA sequencing [4, 6, 9]. The reference transcript for nomenclature is NM_001080792.4 [4].

There is no targeted treatment and there are no trials. Management follows the cleft team guidelines (lip surgery in the first year and palate surgery by 18 months, audiological surveillance every 6 to 12 months until 5 years and annually thereafter, paediatric dentistry by 12 months), cardiological and abdominal assessment at diagnosis, the measures for the asplenic patient when there is heterotaxy, and neurodevelopmental support [11, 26]. Genetic counselling rests on the 25% recurrence risk for heterozygous parents and on the need to test for CNVs in relatives and partners [1, 6].

13. References

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