The House of Representatives passed the Tax Cuts and Jobs Act on Thursday by a 227 to 205 vote. The bill, roundly criticized by leaders in the nonprofit sector, marks a significant step in what has been an accelerated process for the most significant tax reform in more than three decades.

The House Bill includes a doubling of the standard deduction — up to $24,400 for joint filers and $12,200 for individuals, no universal charitable deduction, a repeal of the estate tax, and repeal of the Johnson Amendment — which prohibits 501(c)(3) organizations from engaging in partisan politics. The doubling of the standard deduction, alone, will cost the sector some $13 billion per year, according to the Lilly Family School of Philanthropy.

The Senate Finance Committee’s version of the bill, released last week, features some stark contrasts, including no repeal of the Johnson Amendment and an expanded exemption within the estate tax, but no complete repeal.

Hadar Susskind, senior vice president of government relations for the Council on Foundations (CoF), said that the council has realized that the House bill is essentially set and has turned attentions to the Senate. Maintaining the Johnson Amendment and inserting some sort of universal charitable deduction are among current efforts. CoF leadership has also supported Sen. John Thune’s (R-SD) Charity Act, which would bring a flat 1-percent excise tax on private foundations, as opposed to 1.4 percent in both the House and Senate.

The comprehensive reform has put nonprofits in a unique position. Advocates are used to fighting off one provision at a time. Now, everything is on the table, according to Vikki Spruill, president and CEO of CoF. In some respects the charitable sector has been left alone in that the charitable deduction remains. The practical effect of provisions such as the doubled standard deduction, however, have great impacts, including the potential loss of millions of itemizers.

“First off, we are very disappointed with how this is happening,” Spruill said. “Sadly, the impacts of this bill are going to be felt for a really long time.”

Not unlike foundations, private higher-education institutions face a 1.4 percent annual excise tax on endowment income in both the House and Senate bills. The Senate bill limits the provision to institutions with assets of $250,000 per full-time student or greater as compared to the House’s $100,000 demarcation. Jessica Sebeok, associate vice president and counsel for policy for the Association of American Universities (AAU), noted that the proposed tax has caught some members by surprise.

The drafting process for both bills has been unique in its secrecy, Sebeok added. AAU and related organizations have been thrust into a position of reacting on the fly to express concerns all while universities communicate with elected representatives who might be on the same plane of confusion as they are.

“Certainly, a lot of the initial drafting was done in some secrecy,” Sebeok said. “This was done behind many closed doors, it was not inclusive. There was not a lot of input allowed or welcomed even from other members of the majority.”

Sebeok believes that Congressional Republicans, eager to seize momentum, will try to push forward to get something on President Donald Trump’s desk by the end of the year with the 2018 midterm election cycle looming.

Laura Kalick, tax consulting director for BDO USA’s National Healthcare and Nonprofit & Education practices, on the other hand, expects some scaling back of provisions before anything is set in stone. The Houses’ repeal of the estate tax, for instance, might end up looking more like the Senate’s expanded exemption. The current estate-tax exemptions of $5.49 million for individuals and $10.98 million for couples, as they are, affect only about two out of every 1,000 estates in the U.S., according to  Aaron Dorfman, president and CEO of the National Committee for Responsive Philanthropy (NCRP).

The Joint Committee on Taxation (JCT) estimated that after 2023, most taxpayers would see a tax increase. Donors of all income levels give a little more when they have a little more money but the proposed tax cuts championed by most Republicans will have “miniscule effects,” Dorfman said, and aren’t “significant enough to make up for bad tax policy.”

Both bills enable individuals to deduct up to 60 percent of their adjusted gross income for charitable contributions, up from 50 percent. In practice, however, Kalick noted the limited scope of such a provision with few donors willing or able to give 50 percent of their earnings to charity, let alone 60 percent.

“If anybody thinks that that’s a great bone to charity, that’s absurd,” Kalick said.

The Senate has also moved to eliminate the Affordable Care Act’s individual mandate, likely to sweeten the legislation for more conservative senators, as it would reportedly save about $318 billion over 10 years. The consequence is that it also conflates tax reform with unsuccessful attempts to reform healthcare, Kalick said, potentially leading to some roadblocks on the way to consensus.

Kalick believes that extending the process into 2018 with a more nuanced bill is more palatable for many representatives than voting in favor of something that might be unpopular coming into an election year.

“I don’t think it’s going to happen,” said Kalick of tax reform in 2017. “People are looking at it and saying ‘This doesn’t make sense.’”

• Senior editor Mark Hrywna contributed to this report.

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