The prospect of meeting Lesley Glaister was a little daunting.

Rarely interviewed, and thus somewhat mysterious, the author of 12 novels is a master of the sinister and creepy. Her books create a sense of someone peering over your shoulder or skulking behind the door, and her latest, the eerily atmospheric Little Egypt, made me shudder; certain passages were read through half-closed eyes, the way you watch grisly scenes in a film - desperate to know what happens, but not wanting to disturbing images imprinted on your mind.

So would Glaister and her books have anything in common? I am happy to report that she is one of the least alarming writers you could imagine. Laughingly, she tells me, "I am as normal as anything!". An exceptionally youthful-looking, bird-like woman, wearing zebra print boots and a jumper the colour of a Tuscan summer sky, she chats over rooibos tea in a Morningside cafe as if there is nothing darker on her mind than the prospect that it might rain.

But, of course, we know better. Glaister's imagination turns on the weird and unsettling, the murderous and morbid, creating classy emotional thrillers, as in Now You See Me, about a homeless girl who finds a berth in someone's basement, or As Far As You Can Go, about a young British couple who answer an advert for a housekeeper in the Australian outback and discover themselves dangerously far from civilisation.

She returns to some of her previous themes in Little Egypt, whose story bounces between England and Egypt and begins in the present day, with 80-plus Isis living in the dilapidated mansion of the title with her twin brother, Osiris. Her grand old house is surrounded by motorway and shopping mall, Isis having sold off the land piecemeal to pay the bills. Every week, she meets a property developer for coffee, toying with his proposal of buying the house and allowing her and her twin to move somewhere comfortable in their twilight years. She would sell in a flash, one realises, were it not for the terrible secret the developers would discover when they began to demolish the place.

Flitting between today and the 1920s, when Isis and Osiris were brought up by their eccentric Egyptologist parents, Little Egypt is a testament to sibling love and adult neglect, and the power of obsession to destroy lives forever. Written with unshowy elegance and compassion, its revelations are quietly devastating. As the story unfolds, and the house begins to crumble, it becomes clear that Little Egypt has as much character as its occupants. Since this is not the first time a house has taken a part in Glaister's fiction, one wonders if she is particularly drawn to buildings and the roles they can play.

"I am quite fascinated by the atmosphere in houses," she says, in her soft, middle-English accent. "You know that thing when you are house-hunting, and you can walk into a house that's perfect in every way and yet you could never live there? It's like online dating. The person might have every single thing right - politics, everything physical about them - but then you meet them and there's just nothing. I think there's a kind of chemistry with people and houses. People affect houses, obviously, but I think some houses affect people too."

The conversation moves on, but later Glaister returns to the subject, as if she's been thinking about it all the time we've been talking. "I sometimes have an image that the house is like the head, and the people in it are like the dreams. It's there as a thought. I do feel that sometimes as I'm walking through a house, it's like walking through a mind. A house is always settling down and making noises, and groaning."

Born in 1956 and brought up in Suffolk, the third of four children to a customs officer and his musical wife, Glaister later lived for many years in Sheffield, where she brought up her own family. Twice divorced, in 1997 she began a relationship with her now husband, the poet and novelist Andrew Greig, and the pair shuttled between Sheffield and Orkney. Since 2006 they have lived in Edinburgh. Half the year Glaister teaches creative writing at the University of St Andrews, the other six months she works on her latest novel.

Although it had been her ambition to write since childhood when, as she has written, she found it a comforting process, she did not become a writer until she was pregnant with her third son. Her first novel, Honour Thy Father (1990), won the Somerset Maugham Prize and Betty Trask Prize, and since then she has written books as if like clockwork. Does she still find writing comforting?

"I do find the act of writing soothing, even when it's quite dark," she replies. "There's something really satisfying, almost like putting your finger on a nerve, and finding the right word."

She believes that "the best kind of writing is like a window pane, allowing you to see through it to the story, rather than looking at the surface." Such clarity and the texture and grit in her stories have drawn her many plaudits and a reputation that led one reviewer to describe her as a latter-day Daphne du Maurier and another to wonder why she doesn't sell as well as Kate Atkinson.

Yet for all the praise, Glaister keeps a low profile, seeming not to seek the limelight, even though her husband is one of the country's best-known literary figures. Asked what it is like when two writers live together, she is refreshingly honest.

"There was quite a lot of negotiation about mental space, personal space. When we first got together I was very much a novelist and Andrew was very much a poet. And then he became a novelist. I had to negotiate my place then, we both did. So there was some jostling. There's no competition, and we are pleased for each other when we are successful, and sympathetic when not. And it's nice being with someone who completely understands, and I would say now that that's the strongest thing.

"But it has taken years for us to negotiate our way into that. As a woman I feel slightly apologetic about complaining or wanting something. I don't actually think that my books are important. They are important to me, and I hope they are important to some readers. This sounds horrible - I don't mean this as a criticism - I think Andrew thinks his books are important, in Scottish cultural terms. He sees himself as part of a canon, and I just feel, I'm just writing stories. But then he is part of something, and I'm not. I've never been part of any particular school or movement."

Glaister's upbringing may in part explain this lack of attention-seeking. Her father had been a prisoner-of-war in Japan, and could not bear to talk about it. "I remember a horrible time," she says, "when he used to make us play these scary games. They were only word games, but they were quite scary because you had to respond at the right moment. So he would go" - she thumps the table twice - "'Word Associations'. He had one horrifying game called Last Of The Summer Wine, when you had to say Last Of The Summer Wine in a different accent when he pointed at you."

She laughs. "Anyway, one of these games you had just to say your favourite word, and I said 'Mitsubishi', completely innocently, because I just thought it was a nice word, and it was awful. There had been this jolly atmosphere until I'd said it and then it was as if I'd said a terribly rude swear word and the whole thing shattered, and it was just awful. So we'd get into that quite febrile state, but there was this sense that at any minute it could all come crashing down."

There was another unnerving element in the family home that might also explain Glaister's talent at unsettling her readers. She explains that one of her much older brothers had joined a cult. "As a child I wasn't so close to him particularly. By the time I was a teenager he was away. I did find it strange when he was there because he was so different. And also scary. You'd walk into a room and think you were on your own and then suddenly you'd realise he was meditating under a blanket. I used to find that frightening. And he had a blissed out look on his face which was again not at all as he used to be. That was a strange transformation."

Such shape-shifting lies at the heart of Glaister's work, the banal becoming terrifying, the ordinary suddenly sinister. No wonder there's a touch of the haunted house about all her fiction.

Little Egypt is published by Salt, £9.99. Lesley Glaister is appearing at Aye Write! with Andrew Greig on April 10