Molecular Pathogenesis
RPS6KA3
(RSK2), the gene associated with CLS, encodes a growth factor-regulated serine/threonine kinase that is a member of the Ras signaling cascade. Humans have four closely related RPS6KA (RSK) genes; each gene has two non-identical kinase catalytic domains, both of which are required for maximal activity [Yntema et al 1999, Yang et al 2004]. Members of the RSK family participate in cellular events such as proliferation and differentiation.
Gene structure. The RPS6KA3 transcript NM_004586.2 comprises 22 exons; it is named for ribosomal S6 kinase (alternate name: RSK2). For a detailed summary of gene and protein information, see Table A, Gene.
Pathogenic variants. Pathogenic variants in RPS6KA3 are distributed throughout the gene with no evidence of clustering associated with a specific phenotype.
In the largest study to date (250 individuals), 71 pathogenic variants were found in 86 unrelated families. Almost 60% caused or predicted protein truncation; 38% were missense variants, 20% nonsense variants, 18% errors of splicing, and 21% intragenic deletions or insertions [Delaunoy et al 2001].
A smaller study of 106 unrelated individuals with suspected CLS found 28 pathogenic variants (26%). Of the 28 pathogenic variants, 60% caused or predicted protein truncation; 36% were missense, 21% nonsense, 11% errors of splicing, and 32% intragenic deletions or insertions [Abidi & Schwartz, unpublished].
Splice site pathogenic variants and an intronic LINE-1 insertion that disrupts the normal function of the protein have been reported [Zeniou et al 2002, Martínez-Garay et al 2003, Zeniou et al 2004]. (For more information, see Table A.)
Recently, Schneider et al [2013] have identified a deep intronic pathogenic variant that results in an aberrant protein. This finding warrants analysis for pathogenic variants at the RNA level in all individuals with a highly suggestive clinical diagnosis of CLS and in whom exon screening has failed to detect a pathogenic variant.
Full- and partial-gene duplications have been reported. Matsumoto et al [2013] report a microduplication including the entire RPS6KA3 in a family with mild ID, ADHD, localization-related epilepsy, and pervasive developmental disorder (PDD). Marques Pereira et al [2007] report an in-frame, tandem multiexon duplication in an individual with CLS. Given the high frequency of Alu sequences within the gene, they suggest that these may be a relatively common event; however, additional studies are needed.
Normal gene product. Ribosomal protein S6 kinase alpha-3 (RPS6KA3) is involved in kinase activation in a number of pathways including ras-MAPK, protein kinase C, and adenyl cyclase [Harum et al 2001, Pereira et al 2010]. RPS6KA3 regulates neurite formation [Ammar et al 2013], mediates activation of PLD1 to produce the lipids required for exocytosis [Zeniou-Meyer et al 2008, Zeniou-Meyer et al 2009], and regulates the release of neurotransmitters [Zeniou-Meyer et al 2010].
Association of RPS6KA3 with nonsyndromic XLMR (MRX19; see Genetically Related Disorders) as well as CLS indicates that the gene is critical for cognitive function. RPS6KA3 expression shows both temporal and spatial restriction in human embryogenesis, with homogeneous brain expression from the telencephalon to the rhombencephalon at nine weeks' gestation [Guimiot et al 2004]. RPS6KA3 has also been shown to activate CREB (cAMP response element binding protein), which is involved in neuronal survival and conversion from short- to long-term memory [Harum et al 2001].
RPS6KA3 also plays an important role in maintaining genomic stability by mediating cell cycle progression and DNA repair [Lim et al 2013]. Through the MAPK/RSK pathway and the epidermal growth factor (EGF)-stimulated phosphorylation of histone H3, it appears to play a role in stimulation of the cell cycle between G0 and G1.
Abnormal gene product. Pathogenic variants in RPS6KA3 give rise to both CLS and nonsyndromic XLMR. The pathogenic variants in individuals with CLS result in the loss of kinase activity of the gene product. However, the pathogenic variant associated with MRX19 occurs outside the kinase domains and results in reduction of RPS6KA3 activity, suggesting that the brain is more sensitive to levels of RPS6KA3 activity than are the other organ systems affected in CLS.
In a sample of seven individuals, Harum et al [2001] showed a correlation between IQ and the degree of attenuation of the RPS6KA3-mediated CREBtide phosphorylation response in lymphoblasts.
Yang et al [2004] proposed that lack of phosphorylation of ATF4 by RPS6KA3 may interrupt the normal regulatory role of ATF4 in osteoblast differentiation, accounting for some of the bone anomalies seen in CLS, as well as possibly explaining the progressive nature of the kyphoscoliosis