A dark cloud is hovering over the Employment Non-Discrimination Act just as the U.S. Senate is poised, on Thursday afternoon, to pass the legislation for the first time in the measure’s 19-year history.

Senate Majority Leader Harry Reid moved Wednesday afternoon that all amendments pending on ENDA be withdrawn except for one submitted by Senator Pat Toomey (R-Penn.). Reid also signaled that, after the Toomey vote at 11:45 EDT, he expects the Senate to debate and then vote on ENDA at 1:45 EDT.

The Toomey Amendment is the cloud. It is strongly opposed by the Human Rights Campaign, Log Cabin Republicans, Freedom to Work, Senator Tammy Baldwin, ENDA chief sponsor Senator Jeff Merkley, and other LGBT civil rights supporters.

The Toomey Amendment seeks to dramatically expand the number and type of “religious” employers that would be exempt from ENDA.

According to a copy of a “summary” of the amendment, obtained by the Human Rights Campaign, the amendment would expand the definition of religious employers exempt from ENDA to include entities “managed by a church or religious organization, officially affiliated with a particular religion, or [that] teach a curriculum directed toward propagating a particular religion.”

“The amendment applies (and the organization is exempt from ENDA),” notes the summary, “even if the organization has both religious and secular functions.”

Paul Guequierre, an HRC spokesman, said HRC “strongly” opposes the Toomey Amendment because it would “dramatically diminish ENDA’s protections and create a dangerous license to discriminate against LGBT people.”

Freedom to Work President Tico Almeida issued a statement criticizing Toomey’s Amendment, saying it could enable “for-profit corporations to escape accountability by citing religion to unfairly terminate qualified gay and transgender employees.”

Log Cabin Republicans Executive Director Gregory Angelo said his group opposes Toomey’s amendment also.

Angelo and others say they support –or do not oppose—one Republican-led amendment to ENDA, submitted by Senator Rob Portman (R-Ohio) with Republican Senators Kelly Ayotte of New Hampshire, Orrin Hatch of Utah, Dean Heller of Nevada, and John McCain of Arizona.

The Portman Amendment “bans state and local governments from retaliating against religious groups that take action only permissible because of the religious exemption clause” in ENDA. It was approved by voice vote Wednesday morning.

Log Cabin’s Angelo said the Portman Amendment “made already solid religious exemptions even stronger.”

Section 6 of ENDA stated, “This Act shall not apply to a corporation, association, educational institution or institution of learning, or society that is exempt from the religious discrimination provisions of title VII of the Civil Rights Act of 1964.”

Portman, in explaining his amendment Wednesday, said that it was needed to protect religiously exempt organizations from “government retaliation.”

Senator Susan Collins (R-Maine), a strong supporter of ENDA, agreed, saying the Portman Amendment would prevent “subtle discrimination.”

“Then government cannot turn around and somehow retaliate against this employer based on his or her claiming a legitimate religious exemption as provided by ENDA,” said Collins.

HRC’s Guequierre said “the Democratic sponsors supported the amendment” and that “We did not oppose the Portman Amendment.”

On the floor of the Senate Wednesday evening, Baldwin did not mention the Toomey Amendment and noted only that she and supporters of the bill agreed to a “Republican amendment” on the measure –an apparent reference to the Portman Amendment. But a spokesman for Baldwin said she opposes the Toomey Amendment.

Some LGBT civil rights supporters, such as the activist group GetEQUAL, think the original bill’s religious exemption is harmful, saying it could “potentially allow religiously-affiliated institutions –from schools to hospitals — to have the legal permission to discriminate against LGBT workers.”

“Even worse,” said GetEQUAL, “it cements discrimination into law, and sets a backward precedent that affirms the second-class citizenship of LGBT Americans.”

Calls to the office of Senate Majority Leader Harry Reid (D-Nev.) had not been returned by deadline Wednesday night.

A ray of sunshine behind the Toomey Amendment is that, according to Reid’s comments on the floor, it will require 60 votes to pass and Democrats are not likely to go along with it even though Toomey was one of seven Republicans to provide the margin Monday to overcome a 60-vote procedural hurdle to get ENDA to the floor for consideration.

The Senate will take up the Toomey Amendment Thursday morning at 11:45, said Reid. The Senate will then take a pro forma vote to close debate on ENDA and proceed to the vote. Reid said he expects to call for the ENDA vote at 1:45 EDT.

Reid seemed happy with the bill proceedings overall.

“This is something we’ve done together,” he said. “Not everybody is satisfied but a lot of people are satisfied.”

As Senator Dick Durbin (D-Ill.) noted Tuesday that no senator used debate time for the cloture motion to express any opposition to ENDA. And no senator did so Wednesday. Most Republican senators who have spoken have used their time to criticize the Affordable Care Act.

The real trouble for ENDA lies with the Republican-controlled House. In opening Senate business Tuesday morning, Reid chastised House Speaker John Boehner for saying, through a spokesman, Monday, that he fears ENDA would lead to frivolous lawsuits.

“Coming from the man whose caucus spent $3 million in taxpayer dollars defending the unconstitutional Defense of Marriage law in court that is pretty rich,” said Reid. “According to a study by the United States Government Accountability Office – nonpartisan – in 21 states that have some protection against this kind of discrimination, relatively few lawsuits have resulted.”

Merkley also addressed Boehner’s fears about lawsuits, noting that the General Accounting Office study found only between two percent and six percent of all employment claims are LGBT-related.

Massachusetts Senator Elizabeth Warren (D-Mass.) did a pre-emptive strike against a frequent criticism of LGBT civil rights laws, that they creates “special rights” for LGBT people.

“ENDA doesn’t provide any special rights for any group,” said Warren. “It creates a level playing field…[and] makes sure that all workers are judged by the work they do.”

And in her remarks Wednesday, Baldwin seemed happy with how the legislation is proceeding.

“The tone of the debate here on the Senate floor has been remarkably dignified and cordial,” said Baldwin, comparing it to debate in the House when she served there. The tone, she said, “reflects the progress” the LGBT civil rights movement has made.