We describe a rare case of syndromic HH with short stature and cataracts in a 35-year-old man, in whom we identified a 44.8 kb microdeletion of chromosome Xq28 involving the entirety of FUNDC2 and most of CMC4 and MTCP1. Further genetic and expression analyses suggest a novel link between CMC4 and FUNDC2 and apoptosis, inflammation and FSH and SCB regulation in men, which is strongly supported by the finding that the disrupted pathways of upregulated DEGs overlap between our patient and men with 47,XXY. Here, FUNDC2 is linked to cataract.