Assets at Boston’s five biggest family nonprofits rise to $3.5b

Holdings doubled over five years; giving isn’t always rising so fast

The top five foundations, which more than doubled in size over the last five reported years, are funded by fortunes made in cable television, hedge funds, real estate, and baseball. Their philanthropy is directed to health, cultural, and educational institutions in Boston and around the world, as well as to Jewish and Catholic causes.

Together, these foundations donated $168 million in 2013, up 20 percent from 2012. But in many cases, their giving has not kept up with the bulging growth of their assets over time.

For instance, the Barr Foundation is far and away the largest private foundation in Boston, with more than $1.5 billion in assets, up 18 percent from 2012. The fund, run by former cable TV magnate Amos B. Hostetter Jr. and his wife, Barbara, donated $52.1 million in 2013, down from $58.4 million in 2012.

Foundations must give away at least 5 percent of their assets yearly, and certain expenses can count toward that target if they are considered to be for charitable purposes. Of Barr’s $26.5 million in expenses, it applied $6.5 million to meeting the minimum.

That’s all perfectly lawful, according to Bruce Hopkins, a Kansas City, Mo., lawyer who specializes in nonprofits. But at big foundations with large staffs, that can mean less money going directly to the charities they aim to serve, if they are sticking to the 5 percent minimum distribution.

“In that sense it reduces what would otherwise go out to charities,’’ Hopkins said.

Barr gave millions of dollars to environmental causes, museums in Boston, and Harvard University. It also gave $5.4 million to Fidelity’s Charitable Gift Fund, rather than directly to operating charities.

Even including the allowed expenses, the Barr Foundation’s contribution in 2013 amounted to less than 5 percent of its average assets the prior year. A spokesman for the foundation, Stefan Lanfer, said that is because Barr has given more than 5 percent in past years, and under the IRS rules, “We were able to use the excess distributions from the prior years in order to distribute the required 5 percent in 2013.”

Other large Boston donors gave more in 2013 from smaller pools of money. The Klarman Family Foundation, run by Boston hedge fund manager Seth Klarman and his wife, Beth, donated $55.8 million, nearly double what they gave in 2012. Their foundation’s assets grew by nearly $100 million in that period, to $446.8 million, the city’s fifth-largest family fund.

Fidelity Investments chairman Edward C. “Ned” Johnson 3d’s foundation actually shrank in size in 2013, to $300.6 million. But the foundation, ranked number seven in a Globe review of filings, gave out about $82.4 million — more than anyone else in the top 10.

While the Klarmans have said publicly that they intend to give away the lion’s share of their wealth during their lifetimes, many philanthropists stick close to the 5 percent annual disbursements, in order to extend the life of their foundations.

The foundation of hedge fund manager Jonathon Jacobson and his wife, Joanna, rose to be the third-largest in Boston, with $493 million in assets, as the stock market surged in 2013. They increased their giving by 25 percent, to $20.6 million, or about 5.5 percent of the fund’s assets.

Spokesmen for Johnson, the Klarmans, and the Jacobsons declined to comment.

The Flatley Foundation, based in Braintree and funded by the real estate fortune of the late Thomas Flatley, was the second-largest of the group in 2013, with nearly $561 million in assets. The foundation donated $18.8 million that year, and with expenses gave close to the 5 percent minimum.

In addition to giving millions to Catholic causes and other charities, Flatley funds a lab that is conducting research on a cure for cystic fibrosis. Most of its top-paid executives are working in science and drug development. Its expenses for 2013 were $9.8 million.

Executives at Flatley were unavailable for comment.

The Yawkey Foundation, ranked number four on the list, with $470 million in assets, is funded with money from the Yawkey family’s sale of the Red Sox in 2002. The foundation gave $20.2 million in 2013, virtually the same amount it gave the prior year, even as assets grew by 8.5 percent.

A spokeswoman for the foundation was unavailable Friday.