Establishing the phenotypic spectrum of ZTTK syndrome by analysis of 52 individuals with variants in SON

Abstract

Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome, an intellectual disability syndrome first described in 2016, is caused by heterozygous loss-of-function variants in SON. Its encoded protein promotes pre-mRNA splicing of many genes essential for development. Whereas individual phenotypic traits have previously been linked to erroneous splicing of SON target genes, the phenotypic spectrum and the pathogenicity of missense variants have not been further evaluated. We present the phenotypic abnormalities in 52 individuals, including 17 individuals who have not been reported before. In total, loss-of-function variants were detected in 49 individuals (de novo in 47, inheritance unknown in 2), and in 3, a missense variant was observed (2 de novo, 1 inheritance unknown). Phenotypic abnormalities, systematically collected and analyzed in Human Phenotype Ontology, were found in all organ systems. Significant inter-individual phenotypic variability was observed, even in individuals with the same recurrent variant (n = 13). SON haploinsufficiency was previously shown to lead to downregulation of downstream genes, contributing to specific phenotypic features. Similar functional analysis for one missense variant, however, suggests a different mechanism than for heterozygous loss-of-function. Although small in numbers and while pathogenicity of these variants is not certain, these data allow for speculation whether de novo missense variants cause ZTTK syndrome via another mechanism, or a separate overlapping syndrome. In conclusion, heterozygous loss-of-function variants in SON define a recognizable syndrome, ZTTK, associated with a broad, severe phenotypic spectrum, characterized by a large inter-individual variability. These observations provide essential information for affected individuals, parents, and healthcare professionals to ensure appropriate clinical management.

Fig. 1. Schematic representation of variants in SON.

Annotation is based on NM_138927.2. Although one variant p.(Val1918Glufs*87) is frequently present in our study cohort, overall, the variants do not seem to cluster and are spread out over the gene. Larger whole gene deletions observed in two individuals are not shown.

Fig. 2. Photos of individuals with a pathogenic variant in SON.

Individual 1 (5 years), 2 (2 years), 4 (4 years and 4 months), 7 (7 years), individual 10 (3 years and 6 months), 12 (6 years), 16 (4 years), 17, and individual 52 (3 years, 2 months). Variant annotation is based on NM_138927.2. Of note, individuals 16 and 52 were reported previously [11, 20].

Fig. 3. Functional analysis of non-haploinsufficiency variants.

A Real-time qPCR detecting the levels of SON and SON-targeted transcripts from Individual 18 with a SON missense variant (p.(Thr579Ser)). Three different pairs of the primers were used to measure the level of SON mRNA. Overall, the levels of SON and previously known targets of SON-mediated RNA splicing were not significantly downregulated in the affected individual. The mRNA levels of indicated genes were normalized to the level of TUBA1A mRNA. Errors bars represent mean ± SD from three technical replicates. For LoF variants, previous work [6] showed reduced expression of all genes tested in panel A, as well as aberrant splicing of exons as indicated in panel B. B In the reverse transcription and PCR analysis, exon skipping events in ADA and HDAC6, which were previously confirmed in individuals with SON loss-of-function variants, were not identified in Individual 18 with a SON missense variant (p.(Thr579Ser)).