We report on a man with short stature, bilateral early-onset cataracts, HH and an inherited 44.8 kb deletion of chromosome Xq28 encompassing the entirety of FUNDC2, exons 2–3 of CMC4, and exons 2–5 of MTCP1. Clinical evaluation excluded other known genetic and acquired causes of HH, including Klinefelter syndrome, testicular torsion, previous infection, or exposure to radiation or medications. This evidence concerns the gene CMC4 and Klinefelter syndrome.