Submission Details

Primary Ciliary Dyskinesia (PCD) is a genetically heterogeneous group of disorders, usually beginning in early childhood, characterized by recurrent infections of the upper and lower respiratory tract, randomization of left/right body asymmetry, and subfertility (PMID: 32943623). The PCD phenotype results from structural and/or functional abnormalities of motile cilia and flagella.

A mutation was first reported in the CFAP43 (Cilia-and Flagella-Associated Protein 43) gene in association with Normal Pressure Hydrocephalus 1 (NPH 1) in a Japanese family (PMID: 31004071). In addition to hydrocephalus, the diagnostic enlarged brain ventricles, and the usual triad of symptoms associated with NPH (gait disturbance, cognitive impairment, and urinary incontinence), two out of three affected family members were described as having recurrent respiratory tract infections and chronic sinusitis. The proband was a 55 year old woman who died of pneumonia at the age of 60 years. Whole exome sequencing of the proband and two unaffected siblings was used to identify a monoallelic nonsense CFAP43 mutation present in two affected siblings and absent in three unaffected siblings. The genotypes of the affected mother and a third affected sibling were not available. While these patients carried a variant in a cilia and flagella associated gene (CFAP43), were diagnosed with NPH, and two of the affected siblings had respiratory symptoms, they had none of the other hallmark features of Primary Ciliary Dyskinesia. There was no report of neonatal respiratory distress, no laterality defects, no bronchiectasis and no chronic ear infections. Authors made no mention of nasal nitric oxide measurements, studies of ciliary function, or assessment of fertility. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found the clinical phenotypes in these NPH 1 family members to be distinct from those of patients with Primary Ciliary Dyskinesia. We are treating Normal Pressure Hydrocephalus 1 (MONDO:0009366, OMIM:236690) and Primary Ciliary Dyskinesia (MONDO: 0016575) as separate disease entities.

Evidence from the CFAP43 variant described above has not been scored in this curation because the clinical features for Primary Ciliary Dyskinesia have not been met by the information available for members of the family presented by Morimoto et al., 2019 (PMID: 31004071). There are no other cases of CFAP43 related PCD in the literature, hence we scored 0 out of 12 possible points of genetic evidence.

The gene-disease association between CFAP43 and PCD is, however, supported by gene expression and protein localization studies. Human RNAseq expression studies show that CFAP43 is expressed in ciliated tissues (PMID:25970244), including trachea and lung, as well as brain and testis (PMID: 24309898). In mice, in situ expression studies show Cfap43 transcripts in multiciliated tissues, including the LRO, oviduct, nasal cavity, pharynx, lung, and brain (PMID: 31884020). Immunofluorescent studies in mice also show that CFAP43 protein localizes to the cilia of mouse tracheal epithelial cells and lung sections. Immunofluorescent studies in Tetrahymena thermophila show that Fap43p is exclusively targeted to cilia and is present along the length of the cilium (PMID: 29687140).

Three animal models have been used to support the gene-disease relationship between CFAP43 and Primary CIliary Dyskinesia. Cre/Lox technology was used in mice to generate a Cfap43 knockout (PMID: 31884020). This mouse model confirms a role for Cfap43 in airway epithelia mucus clearance, brain development and function, and male fertility, all processes requiring motile cilia or flagella function. A loss of normal Cfap43 function in mice increased tracheal ciliary beat frequency and reduced tracheal cilia generated flow. Knockout mice retained motile ependymal cilia but developed enlarged ventricles and hydrocephalus. These mice also had male infertility, immotile sperm, and abnormal sperm morphology. A Tetrahymena thermophila FAP43 knockout showed signs of impaired ciliary motility and had a reduced cilia beat amplitude (PMID: 29687140). Cfap43 knockdown leads to ciliary defects in Xenopus embryos (PMID: 31884020). Xenopus cfap43 morphants and crispants had elevated ciliary beat frequencies and reduced cilia generated flow. The multiciliated cells of Xenopus embryo skin serve as a model for the mammalian airway epithelium. Cfap43 knockdown confirmed changes in ciliary motility and a function for cfap43 in the mucociliary epithelium. All three of these animal models confirm the plausibility that a mutation in human CFAP43 could impair ciliary or flagellar motility or function, leading to a form of PCD.

Tetrahymena orthologs of human CFAP43 and CFAP44, Fap43p and Fap44p, were shown to be interacting proteins by two methods: Co-immunoprecipitation and a BirA* proximity labeling assay of Tetrahymena cell extracts, followed by mass spectrometry (PMID: 29687140). Authors of this study propose that a Fap43p-Fap44p complex might be involved in the regulation of ciliary beat. Genetic and biochemical approaches combined with cryo-electron tomography identified Tetrahymena orthologs of CFAP43 and CFAP44, FAP43 and FAP44 as dimerized components of the T/TH (Tether/Tether Head) complex (PMID: 29514928). The T/TH complex is structurally linked to the inner dynein arm motor domains as well as to other axonemal complexes that may be involved in regulating ciliary motility. A change in ciliary function is consistent with a defective CFAP43 causing a PCD phenotype

In summary, due to the absence of a CFAP43 variant clearly associated with PCD, despite strong experimental evidence for CFAP43 playing a role in motile ciliary function in other organisms, there is at this time a disputed relationship between variants in CFAP43 and Primary Ciliary Dyskinesia. This classification was approved by the ClinGen Motile Ciliopathy GCEP on December 8, 2022 (SOP Version 9).