Yale University, the second-largest endowment in higher education, posted a 12.3 percent investment gain, beating Harvard University and many of its elite peers. The value of Yale’s endowment rose to a record $29.4 billion for the year ended June 30, the New Haven, Connecticut-based school said Monday in a statement. Some of the best-performing endowments have reported gains driven by private equity and venture capital. Yale’s return compares with a median 8.3 percent gain for endowments of all sizes, according to preliminary data compiled by consultant Cambridge Associates.