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By genome-wide association studies, the <i>PRDM6</i> gene has been shown to affect multiple, apparently unrelated inherited traits, including bone density and body mass index. Therefore, it is considered a potentially pleiotropic gene. In this study, we identified a 12 bp deletion variant (NC_030814.1:rs651603667, g: 79985625-79985636delTTGACTGATCCA) within the <i>PRDM6</i> gene in a large sample (SBWC goats; <i>n</i> = 1044). All goat samples were collected in Shaanxi province in July 2018. The frequency of the wt allele was higher than the frequency of the del allele, and this mutation polymorphism confirmed to be consistent with the Hardy&#8722;Weinberg equilibrium (<i>p</i> &gt; 0.05). Further results showed that in a group of goats in the yearling period (18 months old, <i>n</i> = 567), this deletion variant of the <i>PRDM6</i> gene was associated with heart girth (<i>p</i> = 0.027), cannon circumference (<i>p</i> = 0.008), chest depth (<i>p</i> = 2.10 &#215; 10^&#8722;5), chest width (<i>p</i> = 0.004), body height (<i>p</i> = 0.032), body length (<i>p</i> = 0.044) and hip-width (<i>p</i> = 0.014). For adult SBWC goats (36 months old, <i>n</i> = 477), the effects of the 12 bp variation on growth-related traits were found to make no difference. These findings show that the 12 bp deletion within the goat <i>PRDM6</i> gene plays an important role in the early growth and development of goats. Using the 12 bp mutation, breeders can quickly and effectively select excellent individual goats at an early stage.