Submission Details

Primary Ciliary Dyskinesia (PCD) is a genetically heterogeneous group of disorders, usually beginning in early childhood, characterized by chronic cough, recurrent infections of the upper and lower respiratory tract, randomization of left/right body asymmetry, and subfertility (PMID: 32943623). A subset of PCD cases have complex congenital heart defects (PMID: 17515466). The PCD phenotype results from structural and/or functional abnormalities of motile cilia and flagella. The axonemes of most motile cilia have a 9+2 microtubule structure with nine peripheral doublet microtubules surrounding a central pair apparatus (CPA). Sperm flagella also have a 9+2 axonemal structure that is required for sperm motility. Motile 9+0 cilia lack a central pair and are found in the embryonic node where they play a role in establishing left–right asymmetry. The CPA is a complex structure that regulates ciliary motility and waveform (PMID: 35578022). The CPA comprises at least ten protein complexes, or projections, that associate with two central microtubules (PMID: 35578023). The Cilia-and Flagella-Associated Protein 54 (CFAP54) is a subunit of one of these projections, the C1d projection.

CFAP54 was first reported in relation to PCD patients by Zhao et al. in 2023 (PMID: 37725231). Zhao et al. describe two independent patients (and a sibling) with biallelic CFAP54 mutations and chronic respiratory symptoms including chronic rhinitis and sinusitis, bronchiectasis, and a productive/wet cough. One of these patients (male) presented with abnormal sperm morphology that included short or absent flagella. In 2024, Wohlgemuth et al. (PMID: 39362668) reported an additional four independent probands with biallelic CFAP54 mutations and PCD phenotypes: chronic upper and lower respiratory symptoms including chronic rhinitis and sinusitis, bronchiectasis, and a productive/wet cough. Wohlgemuth et al. noted that a subset of their CFAP54 patients, subjected to more detailed studies, had normal nasal nitric oxide production rates (182.3 nL/min and 176.4 nL/min), normal ciliary beating by high-speed video microscopy, and normal ciliary ultrastructure by transmission electron microscopy (TEM). In neither of these studies did patients present with situs abnormalities. Of note, one unpublished patient with biallelic pathogenic CFAP54 variations was reported to present with a central pair sheath defect in TEM studies (M. Lejendre, personal communication, May 30, 2024).

Primary Ciliary Dyskinesia associated with CFAP54 is an autosomal recessive disorder caused by homozygous or compound heterozygous variations in the CFAP54 gene. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found the molecular mechanism and autosomal recessive mode of inheritance to be consistent among unrelated patients, while the phenotypic variability among them appeared to represent a spectrum of disease rather than separate disease entities. Therefore, cases caused by inherited CFAP54 variants have been lumped into a single disease entity, Primary Ciliary Dyskinesia 54 (MONDO:0100607, OMIM:621125).

Genetic evidence from seven probands carrying biallelic CFAP54 mutations from three publications was evaluated in this curation (PMIDs: 37725231, 393626680, 39462806). Eleven unique variants from six probands were scored (four nonsense, three splice site, two missense, one frameshift, and one in-frame 18 bp insertion). Of note, two published male infertility studies report patients with spermatogenic failure, multiple morphological abnormalities of the sperm flagella, azoospermia, and biallelic CFAP54 mutations (PMIDs: 39267058, 36593121). One of these studies reports on a patient that underwent careful examination, including CT scanning and had no obvious PCD symptoms such as sinusitis, bronchitis, pneumonia or otitis media (PMID: 36593121). The second study did not incorporate comprehensive pulmonary assessments of their two patients (PMID: 39267058). Neither study investigated respiratory ciliary structure/function in their patients. It remains unclear if these patients might have subtle respiratory phenotypes or if spermatogenic failure alone may be part of the spectrum of disease seen in CFAP54 patients.

The gene-disease association between CFAP54 and PCD 54 is supported by gene expression data that show CFAP54 expression in ciliated tissues. GTEx RNA-seq expression studies in reference human tissues show strong expression of CFAP54 in lung, testis, brain, and Fallopian tube (PMID: 23715323). This pattern is consistent with CFAP54 as a subunit of the C1d projection in the CPA of motile cilia and flagella (sperm). CFAP54 together with CFAP46, CFAP74, and CFAP221 are among the subunits that form the C1d projection. Coimmunoprecipitation studies using Chlamydomonas reinhardtii axonemal extracts confirm the interaction of these four proteins (PMID: 20421426). Immunofluorescence microscopy analyses of respiratory epithelial cells show that CFAP46 localizes along the entire ciliary axoneme in healthy individuals. Loss of normal CFAP46 localization is seen in the respiratory cells of PCD patients with loss-of-function CFAP54 variants (PMID:39362668). This loss suggests the disruption of the C1d projection complex in these patients. In vitro ciliary transport assays analyzing the ciliary transport of fluorescent nanoparticles on cultured respiratory epithelium from PCD patients and healthy controls show that in vitro ciliary transport is impaired in CFAP54-variant individuals (PMID:39362668).

Two mouse models have been used to support the gene-disease relationship between CFAP54 and PCD. Knock-in of a human pathogenic CFAP54 variant (Cfap54:c.7316_7317insGGCTGAATTCTTGGCGCA) into mice resulted in respiratory and infertility phenotypes commonly seen in human CFAP54-PCD (PMID: 37725231). These mice had mucus accumulation in the sinus cavity suggestive of abnormal ciliary motility in respiratory cells. These mice also showed abnormalities in sperm flagella (absent or shortened flagella with abnormal TEM ultrastructure). Hydrocephalus, a phenotype repeatedly seen in mouse models for PCD, was also reported. As in humans, these mice show no situs inversus or other laterality defects, which are typically associated with dysfunction of motile cilia of the embryonic node. Nodal cilia lack a central pair apparatus, so mouse models as well as humans with CFAP54-PCD would not be expected to develop the laterality defects often associated with PCD. A second Cfap54 knockout mouse model also resulted in PCD phenotypes (PMID: 20421426). The respiratory cilia of these mice appear to lack the C1d projection and beat with reduced rate. Ex vivo experiments show a reduction in ciliary clearance in tracheal epithelial cilia and brain ependymal cells, results consistent with the accumulation of mucus in the sinus cavity and hydrocephalus. A second strain of this mouse PCD model with relatively mild hydrocephalus and without signs of early mortality had male infertility due to sperm cell malformations (PMID: 20421426).

In summary, there is Strong evidence supporting a gene-disease relationship between variants in CFAP54 and Primary Ciliary Dyskinesia 54. This classification was approved by the ClinGen Motile Ciliopathy GCEP on June 12, 2025 (SOP Version 11).

Primary Ciliary Dyskinesia (PCD) is a genetically heterogeneous group of disorders, usually beginning in early childhood, characterized by chronic cough, recurrent infections of the upper and lower respiratory tract, randomization of left/right body asymmetry, and subfertility (PMID: 32943623). A subset of PCD cases have complex congenital heart defects (PMID: 17515466). The PCD phenotype results from structural and/or functional abnormalities of motile cilia and flagella. The axonemes of most motile cilia have a 9+2 microtubule structure with nine peripheral doublet microtubules surrounding a central pair apparatus (CPA). Sperm flagella also have a 9+2 axonemal structure that is required for sperm motility. Motile 9+0 cilia lack a central pair and are found in the embryonic node where they play a role in establishing left–right asymmetry. The CPA is a complex structure that regulates ciliary motility and waveform (PMID: 35578022). The CPA comprises at least ten protein complexes, or projections, that associate with two central microtubules (PMID: 35578023). The Cilia-and Flagella-Associated Protein 54 (CFAP54) is a subunit of one of these projections, the C1d projection.

CFAP54 was first reported in relation to PCD patients by Zhao et al. in 2023 (PMID: 37725231). Zhao et al. describe two independent patients (and a sibling) with biallelic CFAP54 mutations and chronic respiratory symptoms including chronic rhinitis and sinusitis, bronchiectasis, and a productive/wet cough. One of these patients (male) presented with abnormal sperm morphology that included short or absent flagella. In 2024, Wohlgemuth et al. (PMID: 39362668) reported an additional four independent probands with biallelic CFAP54 mutations and PCD phenotypes: chronic upper and lower respiratory symptoms including chronic rhinitis and sinusitis, bronchiectasis, and a productive/wet cough. Wohlgemuth et al. noted that a subset of their CFAP54 patients, subjected to more detailed studies, had normal nasal nitric oxide production rates (182.3 nL/min and 176.4 nL/min), normal ciliary beating by high-speed video microscopy, and normal ciliary ultrastructure by transmission electron microscopy (TEM). In neither of these studies did patients present with situs abnormalities. Of note, one unpublished patient with biallelic pathogenic CFAP54 variations was reported to present with a central pair sheath defect in TEM studies (M. Lejendre, personal communication, May 30, 2024).

Primary Ciliary Dyskinesia associated with CFAP54 is an autosomal recessive disorder caused by homozygous or compound heterozygous variations in the CFAP54 gene. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found the molecular mechanism and autosomal recessive mode of inheritance to be consistent among unrelated patients, while the phenotypic variability among them appeared to represent a spectrum of disease rather than separate disease entities. Therefore, cases caused by inherited CFAP54 variants have been lumped into a single disease entity, Primary Ciliary Dyskinesia 54 (MONDO:0100607, OMIM:621125).

Genetic evidence from seven probands carrying biallelic CFAP54 mutations from three publications was evaluated in this curation (PMIDs: 37725231, 393626680, 39462806). Eleven unique variants from six probands were scored (four nonsense, three splice site, two missense, one frameshift, and one in-frame 18 bp insertion). Of note, two published male infertility studies report patients with spermatogenic failure, multiple morphological abnormalities of the sperm flagella, azoospermia, and biallelic CFAP54 mutations (PMIDs: 39267058, 36593121). These studies did not incorporate comprehensive pulmonary assessments or investigate respiratory ciliary structure or function in these patients. It remains unclear if these patients also had respiratory phenotypes. Spermatogenic failure is part of the spectrum of disease seen in CFAP54-PCD.

The gene-disease association between CFAP54 and PCD 54 is supported by gene expression data that show CFAP54 expression in ciliated tissues. GTEx RNA-seq expression studies in reference human tissues show strong expression of CFAP54 in lung, testis, brain, and Fallopian tube (PMID: 23715323). This pattern is consistent with CFAP54 as a subunit of the C1d projection in the CPA of motile cilia and flagella (sperm). CFAP54 together with CFAP46, CFAP74, and CFAP221 are among the subunits that form the C1d projection. Coimmunoprecipitation studies using Chlamydomonas reinhardtii axonemal extracts confirm the interaction of these four proteins (PMID: 20421426). Immunofluorescence microscopy analyses of respiratory epithelial cells show that CFAP46 localizes along the entire ciliary axoneme in healthy individuals. Loss of normal CFAP46 localization is seen in the respiratory cells of PCD patients with loss-of-function CFAP54 variants (PMID:39362668). This loss suggests the disruption of the C1d projection complex in these patients. In vitro ciliary transport assays analyzing the ciliary transport of fluorescent nanoparticles on cultured respiratory epithelium from PCD patients and healthy controls show that in vitro ciliary transport is impaired in CFAP54-variant individuals (PMID:39362668).

Two mouse models have been used to support the gene-disease relationship between CFAP54 and PCD. Knock-in of a human pathogenic CFAP54 variant (Cfap54:c.7316_7317insGGCTGAATTCTTGGCGCA) into mice resulted in respiratory and infertility phenotypes commonly seen in human CFAP54-PCD (PMID: 37725231). These mice had mucus accumulation in the sinus cavity suggestive of abnormal ciliary motility in respiratory cells. These mice also showed abnormalities in sperm flagella (absent or shortened flagella with abnormal TEM ultrastructure). Hydrocephalus, a phenotype repeatedly seen in mouse models for PCD, was also reported. As in humans, these mice show no situs inversus or other laterality defects, which are typically associated with dysfunction of motile cilia of the embryonic node. Nodal cilia lack a central pair apparatus, so mouse models as well as humans with CFAP54-PCD would not be expected to develop the laterality defects often associated with PCD. A second Cfap54 knockout mouse model also resulted in PCD phenotypes (PMID: 20421426). The respiratory cilia of these mice appear to lack the C1d projection and beat with reduced rate. Ex vivo experiments show a reduction in ciliary clearance in tracheal epithelial cilia and brain ependymal cells, results consistent with the accumulation of mucus in the sinus cavity and hydrocephalus. A second strain of this mouse PCD model with relatively mild hydrocephalus and without signs of early mortality had male infertility due to sperm cell malformations (PMID: 20421426).

In summary, there is Strong evidence supporting a gene-disease relationship between variants in CFAP54 and Primary Ciliary Dyskinesia 54. This classification was approved by the ClinGen Motile Ciliopathy GCEP on June 12, 2025 (SOP Version 11).