Truncating SRCAP variants outside the Floating-Harbor syndrome locus cause a distinct neurodevelopmental disorder with a specific DNA methylation signature

Abstract

Summary Truncating variants in exons 33 and 34 of the SNF2-related CREBBP activator protein ( SRCAP ) gene cause the neurodevelopmental disorder (NDD) Floating-Harbor syndrome (FLHS), characterized by short stature, speech delay, and facial dysmorphism. Here, we present a cohort of 33 individuals with clinical features distinct from FLHS and truncating (mostly de novo ) SRCAP variants either proximal (n = 28) or distal (n = 5) to the FLHS locus. Detailed clinical characterization of the proximal SRCAP individuals identified shared characteristics: developmental delay with or without intellectual disability, behavioral and psychiatric problems, non-specific facial features, musculoskeletal issues, and hypotonia. Because FLHS is known to be associated with a unique set of DNA methylation (DNAm) changes in blood, a DNAm signature, we investigated whether there was a distinct signature associated with our affected individuals. A machine-learning model, based on the FLHS DNAm signature, negatively classified all our tested subjects. Comparing proximal variants with typically developing controls, we identified a DNAm signature distinct from the FLHS signature. Based on the DNAm and clinical data, we refer to the condition as “non-FLHS SRCAP -related NDD.” All five distal variants classified negatively using the FLHS DNAm model while two classified positively using the proximal model. This suggests divergent pathogenicity of these variants, though clinically the distal group presented with NDD, similar to the proximal SRCAP group. In summary, for SRCAP , there is a clear relationship between variant location, DNAm profile, and clinical phenotype. These results highlight the power of combined epigenetic, molecular, and clinical studies to identify and characterize genotype-epigenotype-phenotype correlations.

Molecular Genetics and Pathogenesis of the Floating Harbor Syndrome: Case Report of Long-Term Growth Hormone Treatment and a Literature Review

“…It is also important to note that several variants at the very end of exon 34 are also present in gnomAD ( Figure 2 ), suggesting that even variants that fall inside exon 34 but outside the pathogenic mutation hotspot, do not cause FHS. At the same time, a recent report by Rots et al ( Rots et al (2021) ) suggested that proximal SRCAP variant might cause another neurodevelopmental disorder, characterized by an altered DNA methylation pattern. However, high frequency of proximal pLoF variants in SRCAP suggests that such a phenotype should be much more common than FHS and/or have incomplete penetrance.…”

“…All the studies of FHS genetics emphasize the importance of variants in exons 33 and 34 for FHS. It has been suggested that the truncated SRCAP protein variants act in a dominant negative manner ( Messina et al (2016) ) and escape nonsense-mediated decay ( Rots et al (2021) ). However, it remains unclear how the genetic changes observed in FHS patients are connected to the phenotype.…”

“…Hence, expression of multiple CREB target genes related to growth and development (e.g., PIT-1 transcriptional regulator or myostatin,, a key regulator of muscle growth ( Zuloaga et al (2013) )) is likely to be altered in FHS. These effects are complemented by a general effect of FHS-causing mutations on DNA methylation pattern ( Rots et al (2021) ). Taken together, all these factors may drive the phenotypic manifestation of FHS ( Figure 3 ).…”

DNA methylation signature associated with Bohring-Opitz syndrome: a new tool for functional classification of variants in ASXL genes

“…Our research group and others have shown that neurodevelopmental disorders caused by pathogenic variants in genes encoding epigenetic regulators can be associated with genome-wide changes in DNA methylation (DNAm), termed “DNAm signatures” [ 13 – 19 ]. To date, DNAm signatures for more than > 50 disorders have been defined.…”

“…These DNAm signatures are likely established via crosstalk between histone modifications and DNA methylation. Although the exact mechanisms underpinning DNAm signatures are not yet fully elucidated [ 20 ], a rapidly expanding body of work has emerged demonstrating that DNAm signatures have diagnostic utility in classifying variants of uncertain significance (VUS) [ 13 – 19 ].…”