RUNX2 is an essential transcription factor required for skeletal development and cartilage formation. Haploinsufficiency of RUNX2 leads to cleidocranial displaysia (CCD) a skeletal disorder characterised by defects in bones of intramembranous formation. CCD severity is related to the extent of crippling of the trans-activation function of RUNX2, indicating that skeletal differentiation is sensitive to the quantity of RUNX2 as well as function. The differentiation defect in intramembranous bone formation causes a characteristic hierarchy of affected skeletal sites in CCD. A notable feature of the RUNX2 protein is the polyglutamine and polyalanine (23Q/17A) domain coded by a repeat sequence. Since none of the known mutations causing CCD map in the Q/A repeat region, we hypothesised that repeat mutations may be related to a more subtle bone phenotypes and fracture endo-phenotypes. In fact, if RUNX2 variants are functional, the rank order of affected skeletal sites seen in CCD should be recapitulated in endo-phenotypes associated with osteoporosis, such as fracture and BMD. A common 11A variant had a strong relationship to fracture at bones of high intramembranous content (such as pelvis and ribs) compared with bones of largely endochondral content following closely the pattern of affected sites found in CCD. Furthermore, we found 22 rare heterozygotes for Q-repeat variant allele: (15Q, 16Q, 18Q and 30Q). Q-repeat variants alleles occurred at 0.004 frequency, and had a significant average decrease in BMD of 0.7SD measured over 12 BMD-related parameters (p=0.005). The transactivation function of RUNX2 was determined for 11A, 16Q and 30Q alleles using a reporter gene assay. Compared to wildtype 23Q/17A, the variants were quantitatively defective in transcription assays using synthetic targets genes: with Q variants more defective than 11A variants. These mutations significantly alter BMD and display impaired transactivation function, introducing a new class of functionally relevant RUNX2 mutants. Furthermore, the likelihood that fracture site is an important endo-phenotype for genome scans should alter thinking about mapping genes in osteoporosis.