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So far, few genetic factors have been described as contributors to spermatogenic failure. Here, we report the first re-sequencing study of the Y-chromosomal\n                    <jats:italic>Azoospermia Factor c<\/jats:italic>\n                    (\n                    <jats:italic>AZFc<\/jats:italic>\n                    ) region, combined with gene dosage analysis of the multicopy\n                    <jats:italic>DAZ, BPY2<\/jats:italic>\n                    , and\n                    <jats:italic>CDY<\/jats:italic>\n                    genes and Y-haplogroup determination. In analysing 2324 Estonian men, we uncovered a novel structural variant as a high-penetrance risk factor for male infertility. The Y lineage R1a1-M458, reported at &gt;20% frequency in several European populations, carries a fixed ~1.6 Mb\n                    <jats:italic>r2\/r3<\/jats:italic>\n                    inversion, destabilizing the\n                    <jats:italic>AZFc<\/jats:italic>\n                    region and predisposing to large recurrent microdeletions. Such complex rearrangements were significantly enriched among severe oligozoospermia cases. The carrier vs non-carrier risk for spermatogenic failure was increased 8.6-fold (p=6.0\u00d710\n                    <jats:sup>\u22124<\/jats:sup>\n                    ). This finding contributes to improved molecular diagnostics and clinical management of infertility. Carrier identification at young age will facilitate timely counselling and reproductive decision-making.\n                  <\/jats:p>","DOI":"10.7554\/elife.65420","type":"journal-article","created":{"date-parts":[[2021,3,29]],"date-time":"2021-03-29T20:00:44Z","timestamp":1617048044000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.65420","source":"Crossref","is-referenced-by-count":20,"title":["A common 1.6 mb Y-chromosomal inversion predisposes to subsequent deletions and severe spermatogenic failure in humans"],"prefix":"10.7554","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0588-3987","authenticated-orcid":true,"given":"Pille","family":"Hallast","sequence":"first","affiliation":[{"name":"Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia"},{"name":"Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge, United 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Estonia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marina","family":"Grigorova","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rodrigo","family":"Flores","sequence":"additional","affiliation":[{"name":"Institute of Genomics, Estonian Biocentre, University of Tartu, Tartu, Estonia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark A","family":"Jobling","sequence":"additional","affiliation":[{"name":"Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olev","family":"Poolamets","sequence":"additional","affiliation":[{"name":"Andrology Unit, Tartu University Hospital, Tartu, 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