Ogiwara Yasuko, Kobori Yoshitomo, Suzuki Erina, Hattori Atsushi, Tanase-Nakao Kanako, Osaka Akiyoshi, Iwahata Toshiyuki, Okada Hiroshi, Kuroki Yoko, Fukami Maki
Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.
Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan.
Cytogenet Genome Res. 2024;164(3-4):133-138. doi: 10.1159/000540634. Epub 2024 Jul 29.
Isodicentric Y chromosomes are relatively common structural variants of the human genome. The underlying mechanism of isodicentric Y chromosomes with short arm breakpoints [idic(Yq)] remains to be clarified.
We encountered a Japanese man with azoospermia and mild short stature. G-banding and array-based comparative genomic hybridization indicated that his karyotype was 45,X/46,X,idic(Y)(qter→p11.32::p11.32→qter) with a ∼1.8 Mb terminal deletion. Whole-genome sequencing suggested that the Y chromosome had four breakpoints in a ∼7 kb region of the pseudoautosomal region 1 (PAR1).
This case was assumed to have an idic(Yq) resulting from multiple DNA double-strand breaks in PAR1. This rearrangement may have been facilitated by the PAR1-specific chromatin architecture. The clinical features of the patient can be ascribed to SHOX haploinsufficiency and the presence of a 45,X cell line, although copy-number gains of some Yq genes and the size reduction of PAR1 may also contribute to his spermatogenic failure.
