CFAP43

Inheritance Pattern: AR

Disease ID:MONDO:0054723

Submitter: Ambry Genetics

Inheritance Pattern: AR

Disease ID:MONDO:0017173

Submitter: Orphanet

Inheritance Pattern: AR

Disease ID:MONDO:0054723

Submitter: ClinGen

Spermatogenic Failure 19 is a form of male infertility caused by multiple morphologic abnormalities of the sperm flagella (MMAF) that impair sperm motility (PMID: 28552195). Individuals with Spermatogenic Failure 19 present with a combination of sperm flagellar malformations (absent, short, coiled, bent, and/or irregular-caliber flagella), unassembled sperm fibrous sheaths, and defects in axoneme structure (a lack of or misalignment of the central pair microtubules, disorganized double microtubules) (PMIDs: 31781811, 31210147). Mutations were first reported in the *CFAP43* (*Cilia-and Flagella-Associated Protein 43*) gene in association with Spermatogenic Failure 19 in 2017 by Tang et al. (PMID: 28552195). Whole exome sequencing was used to identify biallelic *CFAP43* mutations in men with MMAF. The specific disease entity, Spermatogenic Failure 19, is an autosomal recessive disorder caused by homozygous or compound heterozygous mutation in the *CFAP43* 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 of primary male infertility caused by inherited *CFAP43* variants have been lumped into a single disease entity, Spermatogenic Failure 19 (MONDO: 0054723, OMIM: 617592). Evidence from 15 probands in 3 publications has been included in this curation representing 16 unique *CFAP43* variants (3 missense, 5 nonsense, 6 frameshift, 2 splice site, and 1 large deletion). The mechanism of pathogenicity in *CFAP43* mutations appears to be biallelic loss of function. There is additional case-level evidence available in the literature, but its inclusion in this curation was not necessary to reach the maximum score for genetic evidence (12 points). The gene-disease association between *CFAP43* and Spermatogenic Failure 19 is supported by gene expression and protein localization studies. RNAseq studies in humans (PMID: 24309898) show a high level of *CFAP43* expression in testis. Murine RNAseq studies during sperm development show a pattern of increasing *CFAP43* expression during the progression of spermatogenesis (PMID: 31781811). Immunoelectron and stimulated-emission-depletion microscopy performed on TbCFAP43 and TbCFAP44 in the flagellated protozoan *Trypanosoma brucei* show that both proteins are located between the doublet microtubules 5 and 6 (DMT 5-6) and the paraflagellar rod (PMID: 3319078). The paraflagellar rod runs parallel to the axoneme along most of its length and is connected to axoneme doublet microtubules 4-7. The DMT 5-6 bridge limits inter-doublet sliding, offering a firm plane that is vertical to the bending plane of the flagella. Were CFAP43 to also be localized to the DMT 5-6 bridge in humans (as has been shown in *T. brucei*), the absence of CFAP43 in human patients could destabilize this complex, producing both peri-axonemal and axonemal defects that are consistent with the defective sperm phenotypes seen in patients with Spermatogenic Failure 19. Two animal models have been used to support the gene-disease relationship between *CFAP43* and Spermatogenic Failure 19. Frameshift mutations in the mouse *CFAP43* ortholog, *Cfap43*, were induced by CRISPR/Cas9 technology. *Cfap43*-deficient male mice, like human male patients with biallelic mutation in *CFAP43*, exhibited male infertility and reduced or no sperm motility (PMID: 28552195). Almost all spermatozoa of *Cfap43*-deficient male mice had flagellar abnormalities. These flagella had short, coiled, or other distorted shapes, consistent with the clinical phenotypes seen in human patients with MMAF. In addition, these mice showed ultrastructural defects consistent with those seen in human patients: disorganized axoneme, no central pair complex (CPC), disarranged outer dense fibers and peripheral microtubules. *Trypanosoma brucei* was used as a model organism to characterize the role of TbCFAP43 in the structure and beating of the trypanosome flagellum (PMID: 29449551). Inducible RNA interference knockdown of *TbCFAP43* in *T. brucei* produced cells with abnormal flagellar beating, multi-flagellated cells, a reduction in cell proliferation, and severe ultrastructural defects: disorganized axoneme ultrastructure, 90° rotated CPC, displaced CPC and DMTs, and abnormally enlarged flagellar pocket with multiple flagella. The ultrastructural defects and abnormal flagellar beating seen in trypanosome *TbCFAP43* knockdown are consistent with the abnormal sperm motility, abnormal sperm axoneme morphology, and central pair defects seen in patients with *CFAP43* mutations and suggest that CFAP43 is required for axonemal organization in sperm flagella. *Cfap43*-deficient mice were used to demonstrate that Cfap43 plays an important role in intra-manchette transport (IMT) during spermeogenesis (PMID: 33046149). Intra-manchette transport (IMT) transfers structural and functional proteins via microtubule tracks and motor proteins to the basal body region. The manchette is essential for the shaping of the sperm head and formation of the sperm tail. A role for CFAP43 in intra-manchette transport is consistent with the defects seen in sperm morphology and motility in *CFAP43* patients. In summary, there is **definitive** evidence supporting a gene-disease relationship between variants in *CFAP43* and Spermatogenic Failure 19. This has been repeatedly demonstrated in both research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Motile Ciliopathy GCEP on October 13, 2022 (SOP Version 9).

Inheritance Pattern: AD

Disease ID:MONDO:0009366

Submitter: ClinGen

Normal Pressure Hydrocephalus (NPH) is a neurological disorder characterized by an abnormal accumulation of cerebrospinal fluid (CSF) in the brain’s ventricles and cavities. Normally, CSF is secreted by choroid cells into the lateral ventricles, flows to the third and fourth ventricles and then to the spinal cord. If the flow of CSF throughout the brain and spinal cord is in some way disrupted and CSF accumulates, the ventricles enlarge, resulting in hydrocephalus. The difference between NPH and other forms of hydrocephalus is that even though CT or MRI brain imaging of hydrocephalus patients shows enlarged ventricles, intracranial pressure remains within normal range (PMID: 30707192). NPH is a chronic, steadily progressing disease, frequently not diagnosed until patients are 65 years old or older (PMID: 32160166). In addition to the enlargement of ventricles, NPH patients develop gait and balance disturbances as the dominant symptom, often accompanied by cognitive decline and urinary incontinence. In humans, the synchronized beat of ependymal motile cilia helps drive circulation of the CSF within brain spaces. Loss or dysfunction of cilia in the brain ventricles is associated with restrained CSF circulation, causing CSF accumulation in the ventricles (PMIDs: 35903173, 34233705). A mutation was first reported in the *CFAP43* (*Cilia-and Flagella-Associated Protein 43*) gene in association with NPH1 in a Japanese family (PMID: 31004071). Whole exome sequencing of a 55-year-old woman and two unaffected siblings was used to identify a heterozygous nonsense *CFAP43* mutation (NM_025145.73:c.4506G>A, p.Trp1502Ter) present in both tested affected family members and absent in three unaffected siblings. The genotypes of the affected mother and a third affected sibling were not available. The specific disease entity, Normal Pressure Hydrocephalus 1, is an autosomal dominant disorder caused by monoallelic mutation in the *CFAP43* gene. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found the autosomal dominant mode of inheritance and the phenotypes seen in family members with NPH1 to be distinct from the molecular mechanism, autosomal recessive mode of inheritance, and phenotype of male patients with Spermatogenic Failure 19. We are treating Normal Pressure Hydrocephalus 1 (MONDO:0009366, OMIM:236690) and Spermatogenic Failure 19 (MONDO: 0054723, OMIM: 617592) as separate disease entities. Of note, in addition to the usual triad of symptoms associated with NPH (gait disturbance, cognitive impairment, and urinary incontinence) two of the three affected siblings were described as having recurrent respiratory tract infections and chronic sinusitis. While these patients carry a variant in a cilia and flagella associated gene (*CFAP43*), 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, no chronic ear infections, no nasal nitric oxide measurements, no studies of ciliary function, and fertility was not assessed. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found the autosomal dominant mode of inheritance, molecular mechanism, and phenotypes reported in these family members with NPH, 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. A second, more recent publication, reports a Japanese proband and her mother carrying the same monoallelic nonsense *CFAP43* mutation (NM_025145.73:c.4506G>A, p.Trp1502Ter) reported earlier (PMID: 39572557). This proband developed respiratory symptoms after treatment for an autoimmune condition but there is little if any evidence that these symptoms are caused by an emergent form of PCD caused by this *CFAP43* monoallelic variant. NPH1 is a late onset disease, but the authors report no family history of NPH and the proband and her mother show no hydrocephalus symptoms. Of note: this variant is present in gnomAD v.4.1.0 at a GrpMax allele frequency of 0.0005, with 31 alleles / 44766 total alleles in the East Asian population. Evidence from one proband with NPH1 described above (PMID: 31004071) has been included in this curation, representing one unique nonsense variant associated with NPH1. There are no additional cases of *CFAP43* related NPH1 in the literature, hence we scored only 0.1 out of 12 possible points for genetic evidence. The gene-disease association between *CFAP43* and NPH1 is supported by gene expression and protein localization studies. Human RNAseq expression studies show that *CFAP43* is expressed in ciliated tissues, including the brain (PMID:25970244). In mice, in situ expression studies show *Cfap43* transcripts in multiciliated tissues, including brain cells (ependymal epithelial cells), during embryogenesis as well as in adult mice (PMID: 31884020). 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 support a relationship between loss of *CFAP43* and ciliary dysfunction. CRISPR/Cas9 technology was used in mice to generate a frameshift *Cfap43* mutation similar to the nonsense *CFAP43* mutation seen in human NPH1 patients (PMID: 31004071), probably in the hopes of replicating the human phenotype and providing insight into the molecular mechanism of disease. *Cfap43-/-* mice developed hydrocephalus. Heterozygote *Cfap43+/-* mice, however, showed no differences from wild-type mice. The hydrocephalus seen in this mouse model is consistent with the phenotype seen in NPH1 patients, but the autosomal recessive inheritance pattern of the mouse model compared to the autosomal dominant inheritance reported in human cases is problematic and makes this, mechanistically, a weak animal model. A second mouse model using Cre/Lox technology also generated a *Cfap43* knockout (PMID: 31884020). This mouse model confirms a role for Cfap43 in airway epithelia mucus clearance, brain ventricle development and function, and sperm development and function, all processes requiring motile cilia 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. The autosomal recessive inheritance pattern of this mouse model compared to the autosomal dominant inheritance reported in human NPH1 cases is again, mechanistically, problematic and weakens the model. A Tetrahymena thermophila *FAP43* knockout showed signs of impaired ciliary motility and had a reduced cilia beat amplitude (PMID: 29687140). Together, all three of these animal models confirm the plausibility that autosomal recessive, loss of function mutations in human *CFAP43* could impair ciliary motility and affect cerebrospinal fluid movement by ependymal cilia, leading to hydrocephalus, but fail to support the autosomal dominant NPH1 disease assertion. 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 altering CSF flow in the brain. In summary, due to the limited genetic evidence supporting a *CFAP43*-NPH1 relationship and contradictory animal model experimental evidence, the relationship between *CFAP43* and Normal Pressure Hydrocephalus 1 has been disputed. This classification was approved by the ClinGen Motile Ciliopathy GCEP on February 12, 2026 (SOP Version 12).

Inheritance Pattern: AD

Disease ID:MONDO:0009366

Submitter: Ambry Genetics

Inheritance Pattern: AR

Disease ID:MONDO:0016575

Submitter: ClinGen

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. *CFAP43* (*Cilia-and Flagella-Associated Protein 43*) was first reported in relation to a PCD patient by Awad et al in 2025 (PMID: 41341611). The study reported two male siblings with chronic respiratory symptoms characterized by chronic sinusitis and a chronic wet cough since infancy, with a missense variant in *CFAP43* (NM_025145.7:c.421T>A (p.Trp141Arg) present in the homozygous state. The patients also presented with male infertility with multiple morphological abnormalities of the sperm flagella (MMAF) but no situs abnormalities. A localized area of bronchiectasis is reported in one of the siblings. The authors reported no ultrastructural studies or characterization of ciliary function. Previous studies have associated homozygous or compound heterozygous loss-of-function mutations in the *CFAP43* gene with Spermatogenic failure 19 (MONDO: 0054723, OMIM: 617592), an autosomal recessive form of male infertility caused by multiple morphologic abnormalities of the sperm flagella (MMAF) that impair sperm motility (PMID: 28552195). Impaired flagella have defects in axoneme structure (a lack of or misalignment of the central pair microtubules) (PMIDs: 31781811, 31210147). Previous studies have reported no respiratory phenotype with Spermatogenic Failure 19. Per criteria outlined by the ClinGen Lumping & Splitting Working Group, we found the combination of male infertility, MMAF, and chronic respiratory infection reported in Awad et al to be sufficiently distinct from the infertility phenotypes in the absence of respiratory symptoms reported in patients diagnosed with Spermatogenic Failure 19. For the purposes of this gene curation, *CFAP43* will be considered separately in relation to Primary Ciliary Dyskinesia (MONDO: 0016575), with male infertility as part of the spectrum of phenotypes associated with the disease. The gene-disease association between *CFAP43* and PCD is 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 Left-Right Organizer, 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 the ortholog Fap43p is exclusively targeted to cilia and is present along the length of the cilium (PMID: 29687140). Cre/Lox technology was used in mice to generate a *Cfap43* knockout (PMID: 31884020) that 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. 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, including elevated ciliary beat frequencies and reduced cilia generated flow (PMID: 31884020). 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, there is Limited evidence of association between variants in *CFAP43* and Primary Ciliary Dyskinesia, despite compelling experimental evidence of a role for CFAP43 in motile ciliary function. More genetic evidence is needed showing probands with PCD symptoms and biallelic *CFAP43* variants to support a stronger classification. This classification was approved by the ClinGen Motile Ciliopathy GCEP on February 12, 2026 (SOP Version 12).