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Background A rare disease is that an individual with a non-chimeric karyotype of 45,X develops into a male. We explored the genetic aetiology of an infertile male with an apparent 45,X karyotype, which was subsequently verified as cryptic translocation between chromosomes Y and 15. Methods DNA was extracted from the patient's peripheral blood. A range of genetic testing was performed, including conventional chromosomal karyotyping, short tandem repeat (STR) analysis for azoospermia factor ( AZF ) region, fluorescence in situ hybridization (FISH) with specific probes groups of  DXZ1/DYZ3 ,  DYZ3 / D15Z1/PML  and  SRY/D15Z1/PML , and chromosomal microarray analysis (CMA) for genomic copy number variations (CNVs). Results The patient was found to have an apparent 45,X karyotype. STR analysis showed that he possessed a short arm of the Y chromosome, including the  SRY  gene; however, he was missing the long arm of the Y chromosome, including  AZF a + b + c and Yqter. A FISH assay of  DXZ1  and  DYZ3  probes showed a green signal of the X centromere and a red of the Y centromeric signal on a D-group-sized chromosome. By FISH assaying with  D15Z1  and  DYZ3  probes, chromosomes 15 and Y centromeric signals appeared closely on a single chromosome, as the  PML  control probe ascertained. A further FISH assay with  D15Z1  and  SRY  probes revealed a signal of the  SRY  gene at the end of one arm of chromosome 15. The result of the CMA indicated a deletion with an approximate size of 45.31 Mb spanning from Yq11 to Yter. Conclusion Our study enriched the karyotype-phenotype correlation of Y and 15 chromosomes translocation. It strengthened the critical roles of molecular genetic techniques in identifying the chromosomal breakpoints and regions involved. Genetic aetiology can guide early intervention in childhood and assisted reproduction in adulthood.

Verification of a cryptic t(Y;15) translocation in a male with an apparent 45,X karyotype