The first murder victim in Catherine Aird's The Religious Body is a nun in her forties who converted to Catholicism and entered the convent at eighteen-and-a-half. The police have to visit her mother in person to inform her of her daughter's death, because they can't get her to acknowledge that she had a daughter long enough to get to her via telephone.
This is the main character aspect of Barty Crouch Junior in Harry Potter. Though in this case it's less "went into a career his father didn't like" and more "joined a fascist dark wizard cult and helped torture two dark-wizard catchers (who were also parents) into incurable insanity". At first the situation is framed to the reader as though Junior is a hapless innocent who was lumped in with the real villains because he was in the wrong place at the wrong time, being run through a Kangaroo Court by his cruel and selfish father because of the damage the court case did to his career and reputation... but it's eventually revealed that Junior really was 100% guilty, and a fanatical Sadist to boot. Although it isn't clear if Barty Senior knew this for certain when slapping his son with a life sentence.
The movie version subverts this. Barty Crouch Jr. was ratted out by Igor Karkaroff in the middle of the latter's trial, which he was observing. He tried to walk out before he could be ousted, but his accuser was too quick, and Mad Eye Moody managed to subdue him. He was dragged before his father, and eagerly greeted him, but Crouch Sr. looked on him with disappointment and dismissed him.
Barty Crouch Jr.: Hello father! (sticks out tongue and retracts it like a snake)
Barty Crouch Sr.: (looks at Jr. in disappointment) You are no son of mine.
Also Sirius Black, who was disowned by his parents and burnt off the family tree after he ran away. This is his family's standard procedure - an uncle who left Sirius money in his will got the same treatment, as did his cousin Andromeda when she married a Muggle-born.
In the Doctor Who New Adventures novel Lungbarrow, the best example of this is the titular house's Kithriarch, Quences. While not exactly father and son, Quences viewed the Doctor as his favourite member of the house. After it was predicted that the Doctor would be the most influential Time Lord since Rassilon (which was actually a pretty damn accurate prediction), Quences doted on him and had him studying at the Time Lord Academy, hoping that he would become the first member of the house to become Lord Cardinal. The Doctor obviously didn't see eye to eye with Quences and had other plans, which resulted in this trope.
The Dragonlance series does this twice with the elven king. First he disowns his daughter, (and declares he has no daughter when someone tries to talk to him about it), and later he does the same with his younger son. (This time there's a line that goes along the lines of "He made a gesture as if to indicate that he had only one child now").
Earlier, Tywin disowns his other son Jaime when he refuses to go along with Tywin's plans and quit the Kingsguard. Tywin's not exactly Father of the Year material.
Ironically enough, another character states that Tyrion is Tywin's only true son, due to their extremely manipulative natures. Tywin refuses to speak with her for a very long time after she makes this observation.
Randyll Tarly threatened to arrange a hunting "accident" for his fat and bookish son Sam if Sam didn't join the Night's Watch (thus forfeiting his inheritance). After Sam did so, Randyll didn't spare him a second thought.
This was actually the title of an early-1970s-vintage Doonesbury paperback; it quoted the punchline of one of the included strips, an exclamation by "Marvelous Mark" Slackmeyer's father.
This happened to Courtney Thane in Quills Window. It is not until late in the book, however, that we find out what the cause of estrangement was.
In the Vorkosigan Saga, General Count Piotr Vorkosigan has no grandson, because Miles was born handicapped. Physical deformities are reviled on Barrayar, and Piotr sees Miles as a mutant. He refuses to allow a deformed boy to become Count Vorkosigan, tried to kill the boy at least once (three times if you count when he attempted to have the Uterine Replicator dumped), and forbids Aral and Cordelia from using his name as Miles's given name, as is Barrayaran tradition. Miles (who would have been Piotr Miles) is renamed Miles Naismith, and gets the last laugh - growing up to become not only Lord Vorkosigan, but a soldier, spy, and the first Imperial Auditor in the Vorkosigan family.
If it had been possible for Piotr to disinherit Miles directly, he would have done so, but he could only disinherit Aral, and Piotr was not quite angry enough to disown his only living child. Disinheriting his sole blood heir also required the consent of of the Emperor, or in this case the Emperor's Regent... who happened to be his sole blood heir. (Having pointed this fact out to his father, Aral notes that if Piotr wants his permission then he can have it, which rather took the wind out of the old man's sails.) As it was, though, he threw Aral and Cordelia out of his homes and stripped Aral of his incomes from Vorkosigan district; they did not even begin to reconcile until Miles was five.
In Sense and Sensibility, Mrs. Ferrars first disowns her eldest son Edward when he refuses to break off his engagement to the eminently unsuitable Lucy Steele; later she disowns her younger son Robert when hesteals Lucy's affections away from Edward and marries her himself! She eventually is persuaded to accept them both back into the family, but never restores to Edward the inheritance that she took from him and conferred upon Robert.
Played with in Airman. The villain arranges for the protagonist, Conor, to hear his father declaring "I no longer have a son". Conor believes that his father has disowned him, but his father said it because he believed Conor to be dead.
In the Star Trek: The Next Generation novel Nightshade, a character has this reaction to learning his wife had given their son the genetic treatments he's been protesting against.
In L. Jagi Lamplighter's Prospero Lost, when Miranda appeals to Theo on the grounds his brother is poisoned and dying, Theo says he has no brother.
In Gone with the Wind, middle daughter Suellen has been brow-beating her dementia-stricken father into signing a document proclaiming his loyalty to the Union, thus enabling the family to receive restitution for loss of property. This would be a major affront to any hard-core Southerner, but Suellen is taking advantage of her father's weak mind in order to accomplish this. However, just as he's about to sign the papers, she slips up, revealing what they are. This is enough to snap her father out of his dementia, confront her over what she's done and declare, "You're no daughter of mine!" before storming out.
Legacy of the Force: after Jacen tortured to death Boba Fett's daughter, Han Solo tells him he is no longer his son. Later, he will state that Dath Caedus is not Jacen Solo, in the "That Man Is Dead" sense.
Rainflower renames her son Crookedkit and disowns him after he badly breaks his jaw, because she can't see past his disfigured face.
When it is revealed to Crowfeather that Lionblaze, Hollyleaf, and Jayfeather are his (illegitamite) kits, he refuses to believe it, saying in front of the whole Gathering that his only son is Breezepelt.
Yellowfang and Raggedstar encounter the father of the latter and Scorchwind: a kittypet named Hal. When they tell them this, he rejects anything having to do with mating with a wild cat.
A brotherly example is with Dustpelt and Ravenpaw. According to Word of God, Dustpelt is embarrassed of Ravenpaw's personality and refuses to admit they're brothers.
When Quiet Rain, hears all Clear Sky had done to get the others to hate him, she disowns Clear Sky and refuses to forgive him. But on her deathbed, she finally forgive him.
In Gene Stratton-Porter's Freckles, his grandfather's attitude. When he gets a letter telling him that his disobedient son and his wife are dead, leaving an infant grandson, he files the letter away. Nothing is done until he dies and his other son finds the letter.
In Stephen King's short story "Word Processor of the Gods", the protagonist discovers a typewriter which makes everything typed on it come true. He then erases his son from existence with it, and thinks "I have no son". The narration then states: "How many times had he heard that melodramatic phrase in bad novels?"
Inverted in the Horus Heresy novel "Know No Fear", when the primarch Lorgar responds to an invocation of his father, the Emperor, with a whisper of "I am an orphan".
In Seanan McGuire's October Daye novel A Local Habitation, Sylvester says his only blood relatives are his daughter and niece; Toby starts to object, and he says he has no brother. (And after what the brother did to his wife, and daughter, and Toby, no wonder.)
In one Cicada short story about a young woman in Taliban-controlled Afghanistan, when the woman's long-distance relationship with a Canadian man comes to light, her own brother, Alam, says "Your sin is beyond measure, Ayesha. I have no sister," when she is set to be stoned to death. Even considering the Values Dissonance at play, it's quite shocking because he was shown to be a Nice Guy compared to their other brother, who was quite a Jerkass.
Carr, in Fancy Apartments, reveals that his parents disowned him. He doesn't explain why, however.
In The Bible, Hosea marries a prostitute who bears three children. Two of them he names "Lo-Ruhama" and "Lo-Ammi", which literally mean "not loved" and "not mine".
One of the 1632 stories has a Jewish musician named Isaac Fremdling was disowned in this way by his father, after refusing to abandon his music studies and follow in his father's footsteps as a rabbi. It's a more nuanced portrayal than most, Isaac explains that his father gave him plenty of chances, and only cast him out after he refused in front of the entire jewish community of their hometown at which point his father could hardly go back on his word. He also states that the process was very traumatising for his father, who never believed Isaac would choose music over family and community, and that he aged twenty years in five minutes when he realised he would have to disown his son.
A tragic posthumous variation occurs in The Last of the Mohicans: Reed-that-bends, a young Huron warrior guilty of cowardice is condemned to be killed and forgotten by the tribe's elders. A short while after the execution, Magua arrives not knowing what occurred, and has the misfortune to mention his name, which causes everybody to look at Reed-that-bends' father, which obliges him to disown his dead son:
"It was a lie," he said, "I had no son. He who was called by that name is forgotten; his blood was pale; and it came not from the veins of a Huron; the wicked Chippewas cheated my squaw. The Great Spirit has said that the family of Wiss-entush should end; he is happy who knows that the evil of his race dies with himself. I have done." [...] But the stern customs of his people had made too severe an exaction of the feeble old man. The expression of his eye contradicted his figurative and boastful language, while every muscle in his wrinkled visage was working with anguish. Standing a single minute to enjoy his bitter triumph, he turned away, as if sickening of the gaze of men, and veiling his face in his blanket, he walked from the lodge with the noiseless step of an Indian, seeking, in the privacy of his own abode, the sympathy of one like himself, aged, forlorn, and childless.
In The Murder on the Links Madame Renaud disowns her son Jack for being involved in his father's murder, and promises she would forbid Jack to touch the inheritance of Paul Renaud. It's actually a ruse to lure Marthe, who had murdered Paul so that she can get his inheritance via marrying Jack.
Subverted at the end of the Discworld novel The Truth, when William confronts his father Lord De Worde after having exposed the latter man's conspiracy to remove Vetinari from power, and spills out a bunch of jewels, saying that he's paying back the cost of raising him, so they will no longer be related. His father refuses the gesture and as he heads off into unofficial exile announces that William is most definitely a De Worde.
Words of Radiance (second book of The Stormlight Archive): In the flashbacks, Shallan's father has four sons, until he decides that he only has three because the oldest did something unforgivable.