The Scottish international suffered the injury in the 2-1 win over Crystal Palace and now faces a lengthy spell on the sidelines.
McManus, who has played the majority of Boro's games this season, will undergo surgery on his ankle shortly.
His absence means Boro are likely to continue with a back-line made up entirely of Academy products - something first team coach Mark Proctor welcomes.
Jason Steele, Tony McMahon, Matthew Bates, David Wheater and Joe Bennett made up Boro's back-line against Swansea and impressed despite losing out to a late deflected goal.
The Academy at Boro is traditionally known for bringing through an array of homegrown talent, with the likes of Stewart Downing, Adam Johnson and Brad Jones all learning their trade on Teesside before making big money moves away.
Wheater, Bates and McMahon were all part of the Academy side that Proctor lead to FA Youth Cup glory back in 2004 and the first-team coach admits it is a proud moment to see players make the step up to first team action.
"They're doing a great job and they're very young but the good thing about it is they've all played together over the years," Proctor said.
"Especially Wheats and Batesy at centre back, they were the central pairing in the Youth Cup finals in 2003 and 2004 so they've grown up together.
"Joe's a little bit younger and Tony Mac was the captain so three out of the back four know each other like the back of the hand.
"Steeley has come through the development programme as well as Joe Bennett so they've very familiar with each others strengths and weaknesses.
"When any of the Academy lads come through the system and play in the first team and I've been in the stand, I feel as proud as punch but its not down to me solely, there's a multitude of coaches that are part of that process from nine to 18 and I'm the last one that gives them a little polish and passed them onto the first team.
"So when that happens its a great moment. I have been sat in the stands, not like a dad but certainly felt very proud and that's one of the big parts of the job that's kept me here, I find that a thrill to be part of that process.
"I've done it myself, you know what its like to make your league debut and its a big moment for us. Its great to see the back five as academy products."
The sales of Downing, Johnson and Jones have raised over £20m for Boro in a difficult financial climate and Proctor believes is it imperative the Teessiders continue to bring through youngsters to benefit the club both on and off the field.
"I think in the present climate, money is tight and if you analyse the last two years, the Academy has done a terrific job," Proctor said.
"Downing, Johnson, Jones, that might be over £20m and that's helped us in difficult times.
"It's really important that we continue the conveyor belt which we've managed to do over the last few years.
"Our production line is as good as anyone's I think, were always seen as an elite Academy and hopefully we can continue that."
Proctor himself was a product of Boro's youth system, making his debut in 1979 and he knows from his own experience that being thrown in at the deep end can reap benefits for up and coming players.
He also believes that now more than ever, players coming through have a great chance of breaking into the first team with the club limited to what they can spend compared to previous years.
"I think sometimes, opportunities are given a bit early, through circumstances and sometimes you find when you throw them into the pool, they actually can swim and they're OK,
"I look back to me in 79, we didn't have a great budget, John Neal brought me in and I came through.
"I constantly say to the young players here they've got a great opportunity now to come through compared to when we were spending money on the likes of (Fabrizio) Ravanelli and Juninho, but were a different club now and they will get that opportunity."
Source: Northern Echo
Source: Northern Echo