ABSTRACT: Background: Biallelic variants in TDRD9, a component of the germline piRNA pathway, have been associated with male infertility, but the stage-specific consequences of partial TDRD9 dysfunction in humans remain unclear. Methods: We studied a 22-year-old man with idiopathic non-obstructive azoospermia and his unaffected parents. Exome sequencing and segregation analysis were integrated with minigene splicing and protein-stability assays, testicular histology, acrosomal staining, meiotic chromosome spreads, exploratory bulk RNA sequencing, transposable-element profiling, and LINE-1 open reading frame 1 protein immunofluorescence. Obstructive azoospermia samples with preserved spermatogenesis served as controls where indicated. Results: The proband carried a paternal splice-acceptor variant, c.1714-1G>C, and a maternal missense variant, c.2402A>C (p.Gln801Pro), in TDRD9. The splice variant caused exon 16 skipping and was predicted to generate p.Val572ArgfsTer5; p.Gln801Pro accelerated protein decay and was associated with reduced testicular TDRD9 abundance. Histology and acrosomal staining showed round-spermatid arrest, abnormal acrosome formation, and rare late spermatids. In the spermatocytes examined, chromosome-axis formation, synapsis, and sex-body formation showed no overt abnormalities. Exploratory transcriptomic findings were concordant with depletion of late spermiogenic programs. Evolutionarily young LINE-1 features were enriched among upregulated transposable-element features, and LINE-1 open reading frame 1 protein accumulated in spermatids. Conclusions: This deeply phenotyped case supports an association between compound heterozygous TDRD9 variants, postmeiotic spermatogenic failure, and impaired LINE-1 suppression. The data are compatible with residual TDRD9 activity permitting meiotic progression in the cells examined, but larger genotype-phenotype cohorts and direct piRNA analyses are required to test this model and assess clinical utility.
