"I have no son" when it comes to Alluka from Hunter × Hunter. The Zoldyeks were notably known for, among many things, having only sons, and Alluka was presumed to be one as well, but she is "not to be thought of as human or as family."
Ranma ½: Genma has done this to Ranma a few times. However Genma does this for petty reasons, like Ranma stealing his food, or being beaten in a sparring match. Or if, y'know...he's a girl at the moment. This is Genma's default threat and response for all petty grievances, although in something of a subversion, whenever Ranma really is in trouble or needs help Genma is the one that he always turns to and has gone to lengths to help his son. Taking anything in Ranma 1/2 seriously leads directly to something bad, but Genma is a hideously abusive parent, and probably the main reason Ranma relies on him at all is that with the long training trip he's never known anyone else long.
In Code Geass Lelouch gives up his claim to the Brittanian Imperial Throne in outrage after his father (the Emperor) shows complete indifference to Lelouch's mother and sister, who were killed and crippled, respectively. The Emperor then verbally demolishes his ten-year-old son with a particularly harsh declaration of this trope, before sending Lelouch and his sister to Japan to serve as hostages, meant to be killed if Brittania ever invades. Less than a year later, Brittania does invade, and (as far as the Emperor knows) condemns his children to death.
The Emperor: You are dead. You have always been dead to me, dead from the moment you were born. Who gave you the fine clothes you wear, a comfortable home, the food you eat, and your very life? All of those, I have given to you. In short, you are nothing to me because you have never existed!
This trope is more directly inverted when Lelouch accidentally forces princess Euphemia to commit genocide against the Japanese population, an act which causes the Japanese people to rise up in open revolt, giving Lelouch the chance to drive Brittania out of Japan once and for all. His father's reaction to this? Ha! Finally, an act which proves him worthy to be my son!
Also remember that out of all his children, Charles actually liked Lelouch and Nunnally the most and sent them over to Japan for their safety. The Nightmare of Nunnally manga reshapes them into more sympathetic characters, as well.
In AIR, Minagi's mother does this, although to be completely fair this was after the dream she had about the time she miscarried Michiru caused her to ever forget she had a daughter, and they make up later.
Uptown Girl Nadeshiko Kinomoto was cut off from her highly wealthy family after she married a poor, humble student-teacher (and protagonist's father) in Cardcaptor Sakura; more hatred was directed at the husband (both for being of a lower class and because she was a school student when she married him), but she was disowned anyway. Interestingly, she wasn't upset with this, and her living family, especially her cousin, talk of her as if she were a saint.
Inverted with Portgas D. Ace and his father. Ace disavows his father so completely that he uses his mother's surname, Portgas, and says that "my only dad is Whitebeard." His dad was dead before he was born anyway.
A variation on the trope is the basis of Baby 5's up-until-then-funny quirk: when she was a little girl, her mother harshly abandoned her after telling her she's a bother, and isn't useful or needed. She's had a habit of doing things for others if she thinks that they need her ever since.
Both inverted and played straight with Sanji and his family. He disowned and estranged himself from his family ever since he was a child, and wants nothing to do with them. When he meets with his father again after 13 years, he straight up tells him he doesn't consider him a father. Said father feels the same, and doesn't considert Sanji a son of his, or anything more than a means to an end.
Another inversion occurs in Yu-Gi-Oh! in the Milliennium World arc when Seto's father, Akhenaden, was trying to have his son join The Darkside and kill Kisara, who harbors the Blue-Eyes White Dragon as her soul. Seto calls him out by telling him his real father died bravely in the battlefield. In the anime, Seto says this after Akenaden kills Kisara, who then proceeds to stabs him with a knife (not the Millennium Rod's hidden knife).
Played straight and just a bit literally in Wandering Son.Cool Big Sis Yuki is shown to have a tough time with her mother, whose visits are just stressful, and her father, who's more or less told Yuki not to come home, because she's a Transsexual. The fact that she's "Mama" of a gay bar probably doesn't help, either.
Sibling version in Saki: Teru constantly denies that she has a sister (Saki) due to an implied tragedy in the past, and the last time Saki saw Teru, Teru refused to speak with her at all. When Saki learned from Mihoko that Teru told this to a reporter, she became depressed and wondered whether there was any hope of reconciling with her.
In Chapter 129, Awai asks Teru if Saki is her sister. Teru starts to say no, but then says that Saki is her sister.
The Cain Saga has one played for both comedy and drama during the Red Ram arc, when Oscar is introduced initially as one of Emmeline's suitors. He takes Mary off on a trip fairly late in the story, when it's become pretty clear Jack the Ripper is one of the people in the story, and when Cain telephones the baron Oscar said was his father to ask if he knows where his son is right now he gets "there's no one called Oscar in this household." Cain understandably freaks.
After everything is sorted out with the real culprit and Cain has lost another Love Interest, Oscar's line when confronted is the spectacularly unclear "Aargh! That old bastard denied I was his son?"
Turns out Oscar was pretty-much-disowned for being useless and dissolute and getting kicked out of college repeatedly after his fiancee died. No reconciliation is ever shown, but then apart from coming under suspicion over the Rose Scar thing Oscar is a comic relief character for the rest of the series.
Pandora Hearts: Zai Vessalius is this way to his son, Oz Vessalius, calling him "it" and saying he's filthy. Though, actually, it's more of a subversion considering that the real Oz Vessalius was stillborn and Zai replaced his dead child with Jack Vessalius, who was trapped in an ever-repeating Fountainof Youth due to the Abyss rejecting his soul, and also that Oz himself is the Bloodstained Black Rabbit who was responsible for carrying out the Tragedy of Sablier, there's no reason why Zai WOULDN'T consider him filthy. Not only that, it seemed like an example of Even Evilhas Standards when he is revolted by Jack asking him to "replace" his dead son and dismissing his son's death. Basically, Jack just rubbed his son's death in the dirt and asked him to replace him with an imposter. Justified Trope indeed.
Kyoko Katsunuma is told this by her parents because she tarnished their rep by being a sukeban (delinquent girl). She sorta was luckier than other examples, though: this happened right when her counselor and until-then Big Brother Mentor, Katsuya Honda, was about to ask them for permission to marry her (she was a minor back then); once he saw how badly the Katsunumas treated her with his own eyes, he gave them a very deserved tongue-lashing and took Kyouko into his home.
Momiji had one of the most brutal examples of this trope happen to him when his mother rejected him for his Zodiac curse. Just before her memory was wiped, he overheard her calling him "that creature" and stating that she regrets ever giving birth to him. Not only does she refuse to see him as her son, she refuses to even consider him human.
In Shibatora, "Surprise Acquittal" Kuma Gorou, a defense attorney with his own TV show, implied to be an Amoral Attorney, is called in by his son, who's been arrested for violation of juvenile prostitution mediation, juvenile prostitution solicitation, and anti-child pornography laws, to be his defense attorney. However, it turns out that Kuma Gorou is actually a Crusading Lawyer, who immediately recognizes his son's guilt and disowns him, saying that he encouraged his son to study law, not because he needed a successor, but because he hoped it would improve his son's character. He rescinds his disownment, to the detriment of his own career and public image, on the condition that his son confess to everything.
In Girls und Panzer, Hana gets temporarily disowned when her mother finds out about her doing tankery, but her mother later comes around and they reconcile. Miho's mother decides that as she is not living up to the family's standards, she will be disowned. In the anime, Shiho has not told Miho as of the end of the first season, but claps after her victory over Maho. In the manga, Shiho sends Kikuyo, one of the family maids, to tell Miho that if she loses against Pravda, she will be disowned; Miho has not reacted to this apart from becoming a Stepford Smiler.
An surprisingly heartwarming variation on this happens in the Land of Tea arc in Naruto. Idate Morino, who had always been regarded as cowardly and unfit to be a ninja by his brother Ibiki, ends up separated from Ibiki through an incident that Idate thought had resulted in Ibiki's death. He joins the Wasabi family, and after saving his clan from dissolution by winning a race with Team 7's help, sees Ibiki again, who says that he doesn't recognize him as his brother, since his brother was a coward, in a roundabout So Proud of You way.
This is KingJikochuu'sfirst reaction when Regina doesn't want to destroy the human world for him. His second reaction is casting a thunder on her. When he wants her to come back to him, she reminds him what he said to her. He "apologizes" for that. Though, it's obvious his apologize is not meant seriously. He brainwashes her.
Kazuma and Genma in Kaze no Stigma. Kazuma wasn't a fire mage like the rest of the family, so Genma disowned him and kicked him out. Slowly subverted through the rest of the series mostly through Ren, Kazuma's brother and resident Morality Chain.
Fairy Tail: Invoked in chapter 491: Irene transforms Hisui into a mouse for this very reason, intending for her father to be disgusted by his daughter's new form and throw her away. The exact opposite happens, as Toma makes it clear that no matter what form Hisui is in, she's still his daughter, and swears on his life that he'll do anything to return her to normal.