Submission Details

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).