The clinical presentation varies among individuals, but typically includes global developmental delay, slow progress in mental and physical activities, autism, decreased muscle tone, epilepsy and dysmorphic features.

Mutations in the TET3 gene disrupt DNA demethylation during embryogenesis, an essential epigenetic process contributing to the early development of the nervous system.

[3] Decreased tone of muscles is most noticeable in early life, causing feeding difficulties and constipation in infants, and further impeding the development of speech and motor skills in children.

[4] Most individuals affected by Beck–Fahrner syndrome exhibit similar facial features, including a long face with a broad forehead, an open mouth appearance, protruding ears, arched eyebrows and a high-arched palate.

[4] Overgrowth may manifest in some individuals, presenting with characteristics such as a larger head size and tall stature;[3] rarely this may be correlated with enlarged kidneys and heart.

Congenital heart defects, pyloric stenosis, inguinal hernia, hypospadias and undescended testis have been observed less frequently.

[10] The mutations—which can be of various types like nonsense, missense or frameshift—disrupt the normal DNA demethylation process during early embryonic development and the formation of the nervous system.

GeneReviews recommends exome sequencing as the preferred diagnostic test due to the recent identification of the condition and the limited availability of TET3 gene analysis on most multigene panels.

This episignature can be assessed through whole blood genome-wide DNA methylation analysis,[11] and may serve as a tool to confirm the pathogenicity of a TET3 variant of uncertain significance.

Depending on specific symptoms, various medical specialists may be involved, including neurology for seizures and cardiology for heart defects.