Duplication of Yq- and proximal Yp-arms with deletion of almost all PAR1 (including SHOX) in a young man with non-obstructive azoospermia, short stature and skeletal defects


Duplications of Yq arm (and AZF) seems to be tolerated by fertile males, while mutations, deletions, duplications or haploinsufficiency of SHOX can originate a wide range of phenotypes, including short stature and skeletal abnormalities. We report a case of non-obstructive azoospermia in a young man with short stature, skeletal anomalies, normal intelligence and hormonal parameters. This male showed a very singular Y-chromosome aberration, consisting of a duplication of Yq and proximal regions of Yp, with a deletion of almost all PAR1 in Yptel, including SHOX. CBA- and RBA-banding and FISH-mapping with telomeric, centromeric, AZF and SHOX probes were used. These results were confirmed by array CGH, which revealed the following karyotype constitution: arr [hg19] Xp22.33 or Yp11.32p11.31 (310,932–2,646,815 or 260,932–2,596,815) ×1, Yp11.2q12 (8,641,183–59,335,913) ×2. We conclude that the haploinsufficience of SHOX may be the cause of short stature and skeletal defects in the patient, while the non-obstructive azoospermia could be related to the lack of X–Y pairing during meiosis originated by the anomalous configuration of this chromosome abnormality and large deletion which occurred in Yp-PAR1.

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The study has been partially supported by the “EcoFoodFertility” project. The authors wish to thank Mr. Domenico Incarnato, CNR-ISPAAM of Naples for his excellent technical assistance.

Author information




DC performed array CGH and GTG-banding karyotypes and contributed to the data interpretation; AI and AP performed CBA- and RBA-banding karyotypes, all FISH-mapping analyses and contributed to the data interpretation; LM recruited the subject and performed the sperm analysis; OC provided the BAC clones; CS acquired some data and contributed to the data interpretation; MLV performed hormonal analyses, skeletal X-graph and contributed to the data interpretation; MU revised critically the manuscript for important intellectual content; LI and VV conceived the study and wrote the paper. All authors revised the manuscript and approved the final version.

Corresponding author

Correspondence to Leopoldo Iannuzzi.

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We have the informed consent from the patient for this publication.

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Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. In particular, all studies conducted under the EcoFoodFertility project have been approved by the Ethical Committee, Coordination Service of the ASL Napoli 3, Naples, Italy, as reported in the Directive Determination N. 56 of July 15, 2015.

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Communicated by: Michal Witt

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Cancemi, D., Iannuzzi, A., Perucatti, A. et al. Duplication of Yq- and proximal Yp-arms with deletion of almost all PAR1 (including SHOX) in a young man with non-obstructive azoospermia, short stature and skeletal defects. J Appl Genetics 58, 481–486 (2017). https://doi.org/10.1007/s13353-017-0412-7

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  • Y-chromosome aberration
  • Yq duplication
  • PAR1 deletion
  • Male infertility
  • Azoospermia
  • Short stature
  • Skeletal anomalies