PURPOSE: DYRK1A syndrome is among the most frequent monogenic forms of intellectual disability (ID). We refined the molecular and clinical description of this disorder and developed tools to improve interpretation of missense variants, which remains a major challenge in human genetics. METHODS: We reported clinical and molecular data for fifty individuals with ID harboring DYRK1A variants and developed i) a specific DYRK1A clinical score, ii) amino acid conservation data generated from one hundred of DYRK1A sequences across different taxa, iii) in vitro overexpression assays to study level, cellular localization, and kinase activity of DYRK1A mutant proteins, and iv) a specific blood DNA methylation signature. RESULTS: This integrative approach was successful to reclassify several variants as pathogenic. However, we questioned the involvement of some others, such as p.Thr588Asn, still reported as likely pathogenic, and showed it does not cause an obvious phenotype in mice. CONCLUSION: Our study demonstrated the need for caution when interpreting variants in DYRK1A, even those occurring de novo. The tools developed will be useful to interpret accurately the variants identified in the future in this gene. ACCEPTED MANUSCRIPT -CLEAN COPYand analyzed as previously described 20 , a total of n=774,590 probes were analyzed for differential methylation. Standard quality control metrics showed good data quality for all samples except Ind#20. Briefly, limma regression with covariates age, sex, and five predicted blood cell types identified a DNAm signature with a Benjamini-Hochberg adjusted p-value<0.05 and 10% methylation difference. Next, we developed a support vector machine (SVM) model with linear kernel trained on including non-redundant CpG sites 20 using the methylation values for the discovery cases vs. controls. The model generated scores ranging between 0 and 1 for tested samples, classifying samples as "positive" (score>0.5) or "negative" (score<0.5). Additional neurotypical controls (n=94) and DYRK1A LoF validation samples (n=6) were scored to test model specificity and sensitivity respectively, and samples with pathogenic KMT2A (n=8) and ARID1B (n=4) variants and DYRK1A missense and distal frameshift (n=11) variants were tested. RESULTS Identification of genetic variants in DYRK1A in individuals with IDWe collected molecular and clinical information from 50 individuals with ID (44 never reported and six previously reported 6,7 ) carrying a variant in DYRK1A identified in clinical and diagnostic laboratories: structural variants deleting or interrupting DYRK1A and recurrent or novel nonsense, frameshift, splice and missense variants (Table 1, Figure S1). When blood or fibroblast samples were available, we characterized the consequences of these variants on DYRK1A mRNA by RNA-sequencing and RT-qPCR (Figure S2, Supplementary Text). For one variant, c.1978del, occurring in the last exon of the gene (Ind #18), the mutant transcripts escape to nonsense mRNA mediated decay (NMD) and result in a truncated protein p.Se...

ABBSTRACTDYRK1A-related intellectual disability (ID) is among the most frequent monogenic form of ID. We refined the description of this disorder by reporting clinical and molecular data of forty individuals with ID harboring DYRK1A variants. We developed a combination of tools to interpret missense variants, which remains a major challenge in human genetics: i) a specific DYRK1A clinical score, ii) amino acid conservation data generated from one hundred of DYRK1A sequences across different taxa, iii) in vitro overexpression assays to study level, cellular localization, and kinase activity of DYRK1A mutant proteins, and iv) a specific blood DNA methylation signature. This integrative approach was successful to reclassify several variants as pathogenic. However, we questioned the involvement of some others, such as p.Thr588Asn, yet reported as pathogenic, and showed it does not cause obvious phenotype in mice, emphasizing the need to take care when interpreting variants, even those occurring de novo.

Objective: Monoallelic de novo gain-of-function variants in the voltage-gated sodium channel SCN8A are one of the recurrent causes of severe developmental and epileptic encephalopathy (DEE). In addition, a small number of de novo or inherited monoallelic loss-of-function variants have been found in patients with intellectual disability, autism spectrum disorder, or movement disorders. Inherited monoallelic variants causing either gain or loss-of-function are also associated with less severe conditions such as benign familial infantile seizures and isolated movement disorders. In all three categories, the affected individuals are heterozygous for a SCN8A variant in combination with a wild-type allele. In the present study, we describe two unusual families with severely affected individuals who inherited biallelic variants of SCN8A. Methods: We identified two families with biallelic SCN8A variants by diagnostic gene panel sequencing. Functional analysis of the variants was performed using voltage clamp recordings from transfected ND7/23 cells. Results: We identified three probands from two unrelated families with DEE due to biallelic SCN8A variants. Each parent of an affected individual carried a single heterozygous SCN8A variant and exhibited mild cognitive impairment without seizures. In both families, functional analysis demonstrated segregation of one allele with complete loss-of-function, and one allele with altered biophysical properties consistent with partial loss-of-function. Significance: These studies demonstrate that SCN8A DEE may, in rare cases, result from inheritance of two variants, both of which exhibit reduced channel activity. In these families, heterozygosity for the dominant variants results in less severe disease than biallelic inheritance of two variant alleles. The clinical consequences of variants 2278 | WENGERT ET al.