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A male newborn presented with hypospadias and differential testicular volumes. Short femur length was detected four times during pregnancy, at 23, 31, 32 and 33 weeks, by ultrasonographic examination. Chromosome analysis was performed on peripheral lymphocytes obtained from the infant and his parents. Fluorescent in situ hybridization (FISH), using sex determining region Y (SRY)/DXZ1 and DYZ3 probes, was performed to verify the deletion of the SRY gene (located on Yp11.3 region) and the activation of Y chromosomal centromeres. Single nucleotide polymorphism (SNP)‑array comparative genomic hybridization (CGH) was used to detect copy number variations in the infant. The results revealed a ~2.2 Mb mircodeletion on Yp11.32 containing the short stature homeobox (SHOX) gene. According to the above examinations, the abnormal Y chromosome of the patient was identified as a dicentric derivate of the Y chromosome with pseudoinactivation of one of the two centromeres. The karyotype is therefore: 45,X[20]/46,X,idic(Y)(p11.3).ish psu idic(Y)(p11.3) (SRY++, DYZ3++). array Yp11.32 (118,551‑2,393,500)x0[26]/46,X,ishY(SRY+, DYZ3+)[4]. The combination of cytogenetic, FISH and SNP‑array CGH technologies was beneficial for diagnosing the karyotype accurately, predicting the prognosis, and preparing an effective treatment plan for the patient.

Hypospadias in a male infant with an unusual mosaic 45,X/46,X,psu idic(Y)(p11.32)/46,XY and haploinsufficiency of SHOX: A case report