Structural analysis of a rare rearranged Y chromosome and its bearing on genotype-phenotype correlation

We report on a 9-year-old boy with a rare rearranged Y chromosome and borderline short stature (-2.0 SD). Standard metaphase chromosome analysis indicated a 46,X,i(Y)(q1O) karyotype, but high resolution G-banding showed an asymmetric band pattern for the rearranged Y chromosome. FISH and DNA studies for a total of 15 different Y chromosomal loci or regions showed that the rearranged Y chromosome was accompanied by: 1) a partial deletion of the short arm pseudoautosomal region (PAR1) involving SHOX, with the breakpoint distal to DXYS85; and 2) a partial duplication of Yq, with the breakpoint proximal to DAZ. The karyotype was determined as 46,X,?i(Y)(q1O).ish der(Y)(Yqter--> Yp11.3::Yq11.2-->Yqter)(DAZ++,DYZ3+,SRY +, SHOX-). The X chromosome and the autosomes were normal. The results suggest that haploinsufficiency of SHOX is primarily responsible for the borderline short stature, and that the deletion of the PAR1 may result in spermatogenic failure due to defective X-Y pairing and recombination in the PAR1.