A teaching union has launched a study after signs that the wild swings in Thursday's GCSE results have hit schools in disadvantaged areas hardest.

Brian Lightman, general secretary of the Association of School and College Leaders (ASCL), warned of an "emerging pattern" whereby schools in poorer neighbourhoods have been most affected by the volatility in grades.

"We've got some schools that are 10 or 12 percentage points below their expected pass rate. Some are reporting it in one subject such as maths or English. One school I've got, which is an academy, had predicted it would get 44% 5 A*-Cs and it has got 30%," he said.

"A range of schools have had unexpected results," Lightman said. "But certainly the pattern appears to be that schools with a high number of students from disadvantaged backgrounds have been affected more. There are big risks to social mobility here and opportunities for those young people."

Experts at the headteachers' union will look at a sample of unexpected results to find why grades have fallen. Before the release of results, Ofqual, the exam regulator, said some schools should expect variation on last year after an overhaul of the system, with a return to end-of-course exams and changes to the way English is assessed.

Across the country, however, it says headline figures are stable. Overall the results for England, Wales and Northern Ireland showed a very modest increase in the proportion of pupils getting at least grade C, up 0.7 percentage points to 68.8%. Grades in English fell by almost two percentage points – from 63.6% in 2013 to 61.7%.

Analysis released by the regulator suggests that schools have seen most variation in English grades.

"This appears to be less in schools that used a linear approach in 2013 and more pronounced in schools that have previously used a modular approach and those that used re-sitting," the regulator said.

Ofqual compared schools where more than half of pupils previously resat at least one GCSE, with secondaries where the resit rate was below 50%. It found that schools in which resitting was common saw their C grade results drop by an average of 3.66 percentage points on last year. Other schools saw falls of 1.18 points. An analysis of schools where the majority of pupils sit modular exams showed the same trend.

Lightman said the variations experienced by a number of schools cannot be easily explained: "Ofqual have put forward various reasons for why this has happened, and in some cases that will undoubtedly be right, but other schools are unable to explain their grades."

Underperformance will have serious consequences for both schools and students, he added. "The difference between a C and a D is starting a college course, or – not starting that course because you've got to retake your English and maths first. A drop from an A* or A might mean you're not selected for an elite university that you might previously have been eligible for.

"If a school has got below the floor target, which is 40% getting five A*-Cs, that could mean it being put in special measures if it is not seen to have improved enough."

Dame Joan McVittie, headteacher of Woodside high school in Tottenham, north London, said the proportion of her students getting five A*-Cs including English and maths fell 17 percentage points, from 62% to 45%. The school, which is based in a deprived area, was expecting a pass rate of 72%.

She says accusations that schools whose grades have dipped were simply "gaming the system" are insulting. "I've seen comments in the press about how these are schools that have been gaming and getting their comeuppance. We stopped using modular exams two years ago as we got better able at preparing children.

"The other accusation is that schools were fiddling the coursework on speaking and listening [an element now removed from the exam]. Well, the coursework goes off to be moderated by the exam board and because our students always make high levels of progress in speaking and listening, for the last two years we've had the [exam] board in supervising our assessments. There's no opportunity in my school for gaming. It's just a paltry excuse put forward by Ofqual."

"We've got children who want to go on to study law and medicine. Across the board they've got good grades, and then a D in English. They can't get into university to study law with a D in English GCSE."

Many heads are keeping a low profile about variations in English grades, she added. "They know that overall it affects their five A-C pass rate, which affects the tenure on their job. They're keeping very quiet."