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 46 (CFAP46) is a subunit of one of these projections, the C1d projection.

CFAP46 was first reported in relation to a PCD patient by Wohlgemuth et al. in 2024 (PMID: 39362668). Wohlgemuth et al. report a proband with biallelic CFAP46 likely pathogenic variations and chronic respiratory symptoms including chronic rhinitis and sinusitis, bronchiectasis, and chronic ear and hearing symptoms. This patient had a normal nasal nitric oxide production rate (235.6 nL/min), normal ciliary beating by high-speed video microscopy, and normal ciliary ultrastructure by transmission electron microscopy (TEM). This patient did not present with situs abnormalities, which are typically associated with dysfunction of motile cilia of the embryonic node. Nodal cilia lack a central pair apparatus, so patients with CFAP46-PCD would not be expected to develop the laterality defects often associated with PCD (PMID: 33279404).

Genetic evidence from a single proband carrying compound heterozygous CFAP46 variations from one publication was evaluated in this curation (PMID: 39362668). Two unique variants were scored: NM_001200049.3(CFAP46):c.19C>T(p.Gln7Ter), a nonsense mutation, and c.7286-2A>G(p.(Glu2429Gly_Met2430insfsTer9), a splice site variation shown by cDNA sequence analysis to lead to the activation of a cryptic splice site, causing a frameshift and premature stop. Of note, one additional unpublished PCD patient with heterozygous likely pathogenic CFAP46* variations and a central pair sheath defect in TEM studies was discussed by the Motile Ciliopathy GCEP but not included in this curation (M. Lejendre, personal communication, May 30, 2024).

Per criteria outlined by the ClinGen Lumping and Splitting Working Group we are asserting that CFAP46-Related Primary Ciliary Dyskinesia (MONDO:1010146) is a single autosomal recessive disease entity caused by inherited biallelic mutation in the CFAP46 gene. Please note that there remains a need for publication of additional probands to add support to this gene-disease association and to better establish the spectrum of phenotypes associated with CFAP46-related disease.

The gene-disease association between CFAP46 and PCD is supported by gene expression data that show CFAP46 expression in multiciliated tissues. GTEx RNA-seq expression studies in reference human tissues show strong expression of CFAP46 in lung, testis, brain, and Fallopian tube (PMID: 23715323). This pattern is consistent with CFAP46 as a subunit of the C1d projection in the CPA of motile cilia and flagella (sperm). CFAP46 together with CFAP54, 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). The analysis of high-resolution structures of the C. reinhardtii central apparatus by cryo-electron microscopy confirms a physical interaction between FAP46 and FAP54 within the C1d projection (PMID: 35578022). Immunofluorescence microscopy analyses of respiratory epithelial cells show that CFAP46 localizes along the entire ciliary axoneme in healthy individuals but is lost in the respiratory cells of a CFAP46-PCD patient (PMID:39362668). This loss suggests the disruption of the C1d projection. In vitro ciliary transport assays analyzing the ciliary transport of fluorescent nanoparticles on cultured respiratory epithelium from this CFAP46-PCD patient and healthy controls show that in vitro ciliary transport is impaired in the patient (PMID:39362668).

One non-human model-organism was used to support the gene-disease relationship between CFAP46 and PCD. Chlamydomonas reinhardtii cells carrying a null mutant for FAP46 have full length flagella but lack the C1d projection, resulting in impaired motility (PMID: 22573824). Rescue of the null mutant cells with wild-type FAP46 restores cell motility and normal flagellar movement. This same study shows that loss of FAP46 in Chlamydomonas results in a significant reduction in microtubule-sliding velocity, providing insight into the possible mechanism behind CFAP46 flagellar/ciliary motility defects (PMID: 22573824).

In summary, while this curation has technically scored as a Moderate classification, the Motile Ciliopathy GCEP has decided that in light of only one proband providing genetic evidence and this proband carrying possibly low penetrance CFAP46 variants with high allele frequencies, there is still Limited evidence supporting a gene-disease relationship between variants in CFAP46 and CFAP46-Related Primary Ciliary Dyskinesia. This classification was approved by the ClinGen Motile Ciliopathy GCEP on July 10, 2025 (SOP Version 11).