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De novo variants represent a significant cause of neurodevelopmental delay and intellectual disability. A genetic basis can be identified in only half of individuals who have neurodevelopmental disorders (NDDs); this indicates that additional causes need to be elucidated. We compared the frequency of de novo variants in patient-parent trios with (n = 2,030) versus without (n = 2,755) NDDs. We identified de novo variants in TAOK1 (thousand and one [TAO] amino acid kinase 1), which encodes the serine/threonine-protein kinase TAO1, in three individuals with NDDs but not in persons who did not have NDDs. Through further screening and the use of GeneMatcher, five additional individuals with NDDs were found to have de novo variants. All eight variants were absent from gnomAD (Genome Aggregation Database). The variant carriers shared a non-specific phenotype of developmental delay, and six individuals had additional muscular hypotonia. We established a fibroblast line of one mutation carrier, and we demonstrated that reduced mRNA levels of TAOK1 could be increased upon cycloheximide treatment. These results indicate nonsense-mediated mRNA decay. Further, there was neither detectable phosphorylated TAO1 kinase nor phosphorylated tau in these cells, and mitochondrial morphology was altered. Knockdown of the ortholog gene Tao1 (Tao, CG14217) in Drosophila resulted in delayed early development. The majority of the Tao1-knockdown flies did not survive beyond the third instar larval stage. When compared to control flies, Tao1 knockdown flies revealed changed morphology of the ventral nerve cord and the neuromuscular junctions as well as a decreased number of endings (boutons). Furthermore, mitochondria in mutant flies showed altered distribution and decreased size in axons of motor neurons. Thus, we provide compelling evidence that de novo variants in TAOK1 cause NDDs., (Copyright © 2019 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

Calcium/calmodulin-dependent protein kinase II (CAMK2) is one of the first proteins shown to be essential for normal learning and synaptic plasticity in mice, but its requirement for human brain development has not yet been established. Through a multi-center collaborative study based on a whole-exome sequencing approach, we identified 19 exceedingly rare de novo CAMK2A or CAMK2B variants in 24 unrelated individuals with intellectual disability. Variants were assessed for their effect on CAMK2 function and on neuronal migration. For both CAMK2A and CAMK2B, we identified mutations that decreased or increased CAMK2 auto-phosphorylation at Thr286/Thr287. We further found that all mutations affecting auto-phosphorylation also affected neuronal migration, highlighting the importance of tightly regulated CAMK2 auto-phosphorylation in neuronal function and neurodevelopment. Our data establish the importance of CAMK2A and CAMK2B and their auto-phosphorylation in human brain function and expand the phenotypic spectrum of the disorders caused by variants in key players of the glutamatergic signaling pathway., (Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

Objective: Published data may suggest that the cholesterol-lowering effect of mutation R46L in the proprotein convertase subtilisin/kexin type 9 (PCSK9) gene in familial hypercholesterolemia (FH) heterozygotes, is less pronounced than in normocholesterolemic subjects., Methods: 1130 unrelated subjects with molecularly defined FH were screened for mutation R46L in the PCSK9 gene and cell culture experiments were performed to study the effect of high concentrations of low density lipoprotein (LDL) on the binding of PCSK9 to the LDL receptor (LDLR)., Results: 2.7% of the subjects were carriers of the R46L mutation and they had a non-significant 6% lower value for total serum cholesterol than non-carriers. This reduction is lower than the 8-9% reduction in total serum cholesterol levels previously observed in normocholesterolemic subjects. Cell culture experiments showed that increasing concentrations of low density lipoprotein (LDL) in the media, decreased the amount of PCSK9 internalized and decreased the PCSK9-mediated degradation of the LDLR., Conclusion: High levels of LDL, as seen in untreated FH heterozygotes, compete against wild-type PCSK9 for binding to the LDLR. Thus, in the presence of high LDL levels, wild-type-PCSK9, which has twice the binding affinity of R46L-PCSK9 to bind to the LDLR, may not be significantly more potent in degrading the LDLR than R46L-PCSK9. These data may suggest that targeting PCSK9 as monotherapy in FH heterozygotes, may not prove to be very effective., (Copyright 2009 Elsevier B.V. All rights reserved.)

Background: Familial hypercholesterolemia (FH) patients with the splice site mutation c.313+1, G>A in intron 3 of the low density lipoprotein receptor (LDLR) gene, present with a phenotype similar to that of FH patients in general. However, a mild phenotype would have been expected from the published data showing that the mutation only causes skipping of exon 3., Methods: Epstein Barr virus-transformed lymphocytes from eight c.313+1, G>A heterozygotes and two c.313+1, G>A homozygotes were subjected to studies of the LDLR at the mRNA and protein levels., Results: Mutation c.313+1, G>A not only causes skipping of exon 3, but also causes inclusion of intron 3. No functional LDLR was produced from the transcript with inclusion of intron 3. The transcript with skipping of exon 3 produced a receptor which had markedly reduced ability to internalize low density lipoprotein., Conclusion: The findings that the mutation c.313+1, G>A in the LDLR gene also generates a mutant transcript with inclusion of intron 3, explains why the mutation c.313+1, G>A may result in a severe phenotype.

Screening for mutations in the low density lipoprotein receptor (LDLR) gene has identified more than 1000 mutations as the cause of familial hypercholesterolemia (FH). In addition, numerous intronic mutations with uncertain effects on pre-mRNA splicing have also been identified. In this study, we have selected 18 intronic mutations in the LDLR gene for comprehensive studies of their effects on pre-mRNA splicing. Epstein-Barr virus (EBV) transformed lymphocytes from subjects heterozygous for these mutations were established and mRNA was studied by Northern blot analyses and reverse transcription polymerase chain reactions. Furthermore, functional studies of the LDLRs were performed by flow cytometry. The results of the wet-lab analyses were compared to the predictions obtained from bioinformatics analyses using the programs MaxEntScan, NetGene2 and NNSplice 0.9, which are commonly used software packages for prediction of abnormal splice sites. Thirteen of the 18 intronic mutations were found to affect pre-mRNA splicing in a biologically relevant way as determined by wet-lab analyses. Skipping of one or two exons was observed for eight of the mutations, intron inclusion was observed for four of the mutations and activation of a cryptic splice site was observed for two of the mutations. Transcripts from eight of the mutant alleles were subjected to degradation. The computational analyses of the normal and mutant splice sites, predicted abnormal splicing with a sensitivity of 100% and a specificity of 60%. Thus, bioinformatics analyses are valuable tools as a first screening of the effects of intronic mutations in the LDLR gene on pre-mRNA splicing.

Objective: The normal function of proprotein convertase subtilisin/kexin type 9 (PCSK9) is to mediate degradation of the low density lipoprotein (LDL) receptors. However, the exact mechanism for this function remains to be determined. Characterization of how the naturally occurring mutations in the PCSK9 gene affect the function of PCSK9, may provide important insight into the mechanism by which PCSK9 degrades the LDL receptors., Methods: DNA sequencing of the 12 exons with flanking intron sequences of the PCSK9 gene was performed in 1336 unrelated hypercholesterolemic subjects. In vitro assays and bioinformatics analysis were employed to characterize the functional consequences of a novel mutation. EXPERIMENTAL RESULTS: One subject was heterozygous for the novel mutation S462P in exon 9 of the PCSK9 gene. Based upon Western blot analysis of transiently transfected HepG2 cells, S462P-PCSK9 was almost completely retained in the endoplasmic reticulum (ER) even though it did undergo autocatalytic cleavage. Thus, only trace amounts of S462P-PCSK9 were detected in the culture media of transfected cells. Flow cytometric experiments revealed that the S462P-PCSK9 mutant was unable to degrade the LDL receptors., Discussion: The markedly reduced secretion of S462P-PCSK9 makes S462P a loss-of-function mutation. Ser462 is one of the few residues in the C-terminal domain which is conserved in all known PCSK9 homologs. A hydrogen bond between the side-chain of Ser462 and the backbone of beta-strand 6 of the C-terminal domain, appears to be essential for the proper folding of the C-terminal domain. The S462P mutation is believed to disrupt the normal folding of the C-terminal domain leading to retention of the mutant protein in the ER.