Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders.

BACKGROUND: With the increasing number of genomic sequencing studies, hundreds of genes have been implicated in neurodevelopmental disorders (NDDs). The rate of gene discovery far outpaces our understanding of genotype-phenotype correlations, with clinical characterization remaining a bottleneck for understanding NDDs. Most disease-associated Mendelian genes are members of gene families, and we hypothesize that those with related molecular function share clinical presentations. METHODS: We tested our hypothesis by considering gene families that have multiple members with an enrichment of de novo variants among NDDs, as determined by previous meta-analyses. One of these gene families is the heterogeneous nuclear ribonucleoproteins (hnRNPs), which has 33 members, five of which have been recently identified as NDD genes (HNRNPK, HNRNPU, HNRNPH1, HNRNPH2, and HNRNPR) and two of which have significant enrichment in our previous meta-analysis of probands with NDDs (HNRNPU and SYNCRIP). Utilizing protein homology, mutation analyses, gene expression analyses, and phenotypic characterization, we provide evidence for variation in 12 HNRNP genes as candidates for NDDs. Seven are potentially novel while the remaining genes in the family likely do not significantly contribute to NDD risk. RESULTS: We report 119 new NDD cases (64 de novo variants) through sequencing and international collaborations and combined with published clinical case reports. We consider 235 cases with gene-disruptive single-nucleotide variants or indels and 15 cases with small copy number variants. Three hnRNP-encoding genes reach nominal or exome-wide significance for de novo variant enrichment, while nine are candidates for pathogenic mutations. Comparison of HNRNP gene expression shows a pattern consistent with a role in cerebral cortical development with enriched expression among radial glial progenitors. Clinical assessment of probands (n = 188-221) expands the phenotypes associated with HNRNP rare variants, and phenotypes associated with variation in the HNRNP genes distinguishes them as a subgroup of NDDs. CONCLUSIONS: Overall, our novel approach of exploiting gene families in NDDs identifies new HNRNP-related disorders, expands the phenotypes of known HNRNP-related disorders, strongly implicates disruption of the hnRNPs as a whole in NDDs, and supports that NDD subtypes likely have shared molecular pathogenesis. To date, this is the first study to identify novel genetic disorders based on the presence of disorders in related genes. We also perform the first phenotypic analyses focusing on related genes. Finally, we show that radial glial expression of these genes is likely critical during neurodevelopment. This is important for diagnostics, as well as developing strategies to best study these genes for the development of therapeutics.

Temple syndrome resulting from uniparental disomy is undiagnosed by a methylation assay due to low-level mosaicism for trisomy 14.

We describe a patient with Temple syndrome resulting from maternal uniparental disomy of chromosome 14 who also has low-level mosaicism for trisomy 14. UPD was initially suspected when SNP microarray analysis detected a large region of homozygosity on chromosome 14 and the patient's clinical features were consistent with the phenotype of upd(14)mat. However, SNP arrays cannot prove UPD, as homozygosity may also result from identity by descent. Methylation assays diagnose imprinting disorders such as Prader-Willi, Angelman and Temple syndromes; they detect methylation defects that occur in imprinted loci, which have parent-of-origin-specific expression and have the advantage of making a diagnosis without parental samples. However, in this patient methylation analysis using endpoint PCR detected biparental inheritance. Therefore, sequencing analysis was performed and diagnosed upd(14)mat. Re-examination of the microarray suggested that the explanation for the discrepancy between the array and methylation testing was low-level mosaicism for trisomy 14 and fluorescence in situ hybridization testing detected a trisomic cell line. Thus, this patient's Temple syndrome is a result of a maternal M1 error, which gave a trisomic zygote, followed by loss of the paternal chromosome 14 in an early mitotic division to give maternal UPD with low-level mosaicism for trisomy 14. The methylation assay detected the paternal allele in the trisomic line. The diagnostic failure of the methylation assay in this patient highlights a significant shortcoming of methylation endpoint analysis, especially for Temple syndrome, and underscores the need to use other methods in cases with mosaicism.