In individuals with Coffin–Lowry syndrome, phosphorylation of transcriptional regulators is reduced due to the weakened activity of RSK2 kinase activity. RSK2 is normally activated by the ERK MAP kinase. Mutated RSK2 may be deficient for activation by ERK, or its kinase activity may be reduced despite activation by ERK. The most common mutation in RPS6KA3 is an early stop codon that fails to produce a functional protein, indicating that disease etiology most likely arises from loss-of-function effects. Substitution mutations (which alter a single amino acid) have also been shown to give rise to the disease. RSK2 is  highly expressed in the brain, specifically in the neocortex, hippocampus, and Purkinje cells, all of which are involved in cognitive function and behavior. There is some experimental evidence that RSK2 regulates synaptic transmission and plasticity in neuronal cell types. Diagnosis
Affected individuals are often short in stature. Behavioral symptoms include aggression and depression, but these may be secondary to the emotional consequences of significant physical disabilities associated with the disorder.Coffin–Lowry patients may be affected by chewing and swallowing difficulties, for which there are diagnostic assessments. Among these are the Videofluoroscopic Swallowing Evaluation (VFSE), the Karaduman Chewing Performance Scale, and the Penetration Aspiration Scale (PAS) which is used to evaluate accidental aspiration of food particles. The Pediatric Assessment Tool (PEDI-EAT-10) also includes measurement of severity of dysphagia (difficulty in swallowing).
Genetics
Coffin–Lowry syndrome is an X-linked disorder resulting from loss-of-function mutations in the RPS6KA3 gene, which encodes RSK2 (ribosomal S6 kinase 2). Multiple mutations have been identified in RPS6KA3 that can give rise to the disorder, including missense mutations, nonsense mutations, insertions and deletions. Individuals with CLS rarely have affected parents, suggesting that most incidents arise from de novo mutations in the germline. The lack of an inheritance pattern may be due to the fact that affected individuals are unlikely to parent children. In 20–30% of cases, however, there is a family history of disease. In these cases, the disorder is typically inherited from the maternal parent. Because RPS6KA3 is located on the X chromosome, males (who possess only one copy of the X chromosome) display more severe symptoms than females. Affected females usually possess one mutated copy of the RPS6KA3 gene and one wild type copy. Random inactivation of one copy of the X chromosome in females mitigates the impact of possessing a mutant allele. Occasionally females are born with two mutated alleles. In these cases the symptoms are as severe as in males with the disease. Cell physiology
Mutations in the RPS6KA3 gene can result in expression of an RSK2 protein (ribosomal S6 kinase 2) with reduced or absent kinase function. RSK2 is a downstream component of the MAPK (mitogen-activated protein kinase) cascade that is itself a kinase. RSK2 phosphorylates cellular proteins (including histone H3, and CREB), which regulate eukaryotic gene expression.