Regulatory de novo mutations underlying intellectual disability.

The genetic aetiology of a major fraction of patients with intellectual disability (ID) remains unknown. De novo mutations (DNMs) in protein-coding genes explain up to 40% of cases, but the potential role of regulatory DNMs is still poorly understood. We sequenced 63 whole genomes from 21 ID probands and their unaffected parents. In addition, we analysed 30 previously sequenced genomes from exome-negative ID probands. We found that regulatory DNMs were selectively enriched in fetal brain-specific enhancers as compared with adult brain enhancers. DNM-containing enhancers were associated with genes that show preferential expression in the prefrontal cortex. Furthermore, we identified recurrently mutated enhancer clusters that regulate genes involved in nervous system development (CSMD1, OLFM1, and POU3F3). Most of the DNMs from ID probands showed allele-specific enhancer activity when tested using luciferase assay. Using CRISPR-mediated mutation and editing of epigenomic marks, we show that DNMs at regulatory elements affect the expression of putative target genes. Our results, therefore, provide new evidence to indicate that DNMs in fetal brain-specific enhancers play an essential role in the aetiology of ID.

Identifying phenotypic expansions for congenital diaphragmatic hernia plus (CDH+) using DECIPHER data.

Congenital diaphragmatic hernia (CDH) can occur in isolation or in conjunction with other birth defects (CDH+). A molecular etiology can only be identified in a subset of CDH cases. This is due, in part, to an incomplete understanding of the genes that contribute to diaphragm development. Here, we used clinical and molecular data from 36 individuals with CDH+ who are cataloged in the DECIPHER database to identify genes that may play a role in diaphragm development and to discover new phenotypic expansions. Among this group, we identified individuals who carried putatively deleterious sequence or copy number variants affecting CREBBP, SMARCA4, UBA2, and USP9X. The role of these genes in diaphragm development was supported by their expression in the developing mouse diaphragm, their similarity to known CDH genes using data from a previously published and validated machine learning algorithm, and/or the presence of CDH in other individuals with their associated genetic disorders. Our results demonstrate how data from DECIPHER, and other public databases, can be used to identify new phenotypic expansions and suggest that CREBBP, SMARCA4, UBA2, and USP9X play a role in diaphragm development.

RAC1 Missense Mutations in Developmental Disorders with Diverse Phenotypes.

RAC1 is a widely studied Rho GTPase, a class of molecules that modulate numerous cellular functions essential for normal development. RAC1 is highly conserved across species and is under strict mutational constraint. We report seven individuals with distinct de novo missense RAC1 mutations and varying degrees of developmental delay, brain malformations, and additional phenotypes. Four individuals, each harboring one of c.53G>A (p.Cys18Tyr), c.116A>G (p.Asn39Ser), c.218C>T (p.Pro73Leu), and c.470G>A (p.Cys157Tyr) variants, were microcephalic, with head circumferences between -2.5 to -5 SD. In contrast, two individuals with c.151G>A (p.Val51Met) and c.151G>C (p.Val51Leu) alleles were macrocephalic with head circumferences of +4.16 and +4.5 SD. One individual harboring a c.190T>G (p.Tyr64Asp) allele had head circumference in the normal range. Collectively, we observed an extraordinary spread of ∼10 SD of head circumferences orchestrated by distinct mutations in the same gene. In silico modeling, mouse fibroblasts spreading assays, and in vivo overexpression assays using zebrafish as a surrogate model demonstrated that the p.Cys18Tyr and p.Asn39Ser RAC1 variants function as dominant-negative alleles and result in microcephaly, reduced neuronal proliferation, and cerebellar abnormalities in vivo. Conversely, the p.Tyr64Asp substitution is constitutively active. The remaining mutations are probably weakly dominant negative or their effects are context dependent. These findings highlight the importance of RAC1 in neuronal development. Along with TRIO and HACE1, a sub-category of rare developmental disorders is emerging with RAC1 as the central player. We show that ultra-rare disorders caused by private, non-recurrent missense mutations that result in varying phenotypes are challenging to dissect, but can be delineated through focused international collaboration.

Novel de novo EEF1A2 missense mutations causing epilepsy and intellectual disability.

BACKGROUND: Exome sequencing has led to the discovery of mutations in novel causative genes for epilepsy. One such gene is EEF1A2, encoding a neuromuscular specific translation elongation factor, which has been found to be mutated de novo in five cases of severe epilepsy. We now report on a further seven cases, each with a different mutation, of which five are newly described. METHODS: New cases were identified and sequenced through the Deciphering Developmental Disabilities project, via direct contact with neurologists or geneticists, or recruited via our website. RESULTS: All the mutations cause epilepsy and intellectual disability, but with a much wider range of severity than previously identified. All new cases share specific subtle facial dysmorphic features. Each mutation occurs at an evolutionarily highly conserved amino acid position indicating strong structural or functional selective pressure. CONCLUSIONS: EEF1A2 should be considered as a causative gene not only in cases of epileptic encephalopathy but also in children with less severe epilepsy and intellectual disability. The emergence of a possible discernible phenotype, a broad nasal bridge, tented upper lip, everted lower lip and downturned corners of the mouth may help in identifying patients with mutations in EEF1A2.

How genetically heterogeneous is Kabuki syndrome?: MLL2 testing in 116 patients, review and analyses of mutation and phenotypic spectrum.

MLL2 mutations are detected in 55 to 80% of patients with Kabuki syndrome (KS). In 20 to 45% patients with KS, the genetic basis remains unknown, suggesting possible genetic heterogeneity. Here, we present the largest yet reported cohort of 116 patients with KS. We identified MLL2 variants in 74 patients, of which 47 are novel and a majority are truncating. We show that pathogenic missense mutations were commonly located in exon 48. We undertook a systematic facial KS morphology study of patients with KS at our regional dysmorphology meeting. Our data suggest that nearly all patients with typical KS facial features have pathogenic MLL2 mutations, although KS can be phenotypically variable. Furthermore, we show that MLL2 mutation-positive KS patients are more likely to have feeding problems, kidney anomalies, early breast bud development, joint dislocations and palatal malformations in comparison with MLL2 mutation-negative patients. Our work expands the mutation spectrum of MLL2 that may help in better understanding of this molecule, which is important in gene expression, epigenetic control of active chromatin states, embryonic development and cancer. Our analyses of the phenotype indicates that MLL2 mutation-positive and -negative patients differ systematically, and genetic heterogeneity of KS is not as extensive as previously suggested. Moreover, phenotypic variability of KS suggests that MLL2 testing should be considered even in atypical patients.

Adams-Oliver syndrome associated with bilateral anterior polar cataracts and optic disk drusen.

Adams-Oliver syndrome (AOS) (MIM 100300) was first described in 1945 as a condition of terminal transverse limb defects and aplasia cutis congenita. Since then, its clinical features have been found to be highly variable and include cardiac defects, abdominal wall defects, vascular malformations, brain abnormalities, and ocular anomalies. We report the case of a 3-year-old girl with AOS who was also found to have bilateral anterior polar cataracts and pseudopapilledema secondary to optic disk drusen. To the best of our knowledge, this is the first case of bilateral anterior polar cataracts and pseudopapilledema secondary to optic disk drusen to be reported in association with the AOS.

Inequality of use of cancer genetics services by members of breast, ovarian and colorectal cancer families in South East Scotland.

Some studies have found a deficiency of male, younger and more socially deprived individuals amongst referrals to and/or attendees at cancer genetics clinics. We investigated this inequality of use of genetics services from data on 4,178 Scottish patients with a family history of breast and/or ovarian cancer (BOC) or colorectal cancer (CRC) referred from 2000--2006. Some 98% BOC and 60% CRC referrals were female. Median age of female referrals was greater in the CRC than the BOC group (45.3 vs. 38.7 years, P < 0.001). Both groups of referrals were less socially deprived than the general population (P < 0.001) and the CRC less deprived than the BOC group (P < 0.001). Some 88% patients attended the first appointment offered. Attendance was greater in the CRC group (P < 0.001) and in older patients (P < 0.001) and in the BOC group was highly significantly lower in more socially deprived patients (P < 0.001). Male relatives may feel counselling is less relevant and relatives of both sexes may delay counselling until approaching the age of onset of cancer in a relative. We suggest that medical professionals and the general public may have more knowledge about the genetics of BOC than of CRC. Thus relatives in CRC families seeking counselling are likely to be those with access to more information. The lower attendance amongst more deprived relatives in BOC families may result from poor understanding of the reason for referral. These findings confirm the need to provide male, younger and more socially deprived relatives with more helpful information on cancer genetics.

Uptake of testing for BRCA1/2 mutations in South East Scotland.

We investigated the uptake of genetic testing by 54 families in South East Scotland with a BRCA1/2 mutation. At a median of 37 months since identification of the mutation, the overall rate of uptake of testing in 269 eligible family members was 32%. First-degree relatives were significantly (P<0.05) less likely to be referred for genetic counselling in more, compared to less, socioeconomically deprived families (46 versus 68%). Among relatives who attended for genetic counselling, females were more likely to be tested than males (76 versus 53%; P<0.05) and relatives with children more than those without children (82 versus 53%; P<0.001). Tested relatives were older than relatives who did not undergo testing (mean 41.9 versus 36.8 years, P<0.05) but did not differ in degree of relationship to the index case or in socioeconomic deprivation. Our results confirm the findings from other studies of substantially lower rates of uptake of genetic testing for BRCA1/2 mutations than anticipated in earlier predictions. Relatives in more socioeconomically deprived families were less likely to be referred for genetic counselling, which is a matter of concern. This may be partly the result of a lack of understanding of the testing process. Cascading currently does not work in breast cancer families and further work is required to investigate intrafamilial communication patterns, testing behaviour and counselling strategies.

Decreased cholesterol synthesis as a possible aetiological factor in malformations of trisomy 18.

We report a series of neonates and foetuses with trisomy 18 and abnormally low cholesterol levels and propose that down regulation of cholesterol synthesis in trisomy 18 is, in part, responsible for its phenotype. Cholesterol is a major structural lipid of cell membranes, as well as the precursor of steroid hormones and bile acids. Several human malformation syndromes have been identified biochemically as disorders of cholesterol biosynthesis. Trisomy 18, a multi-system malformation syndrome, has clinical features that overlap with those of disorders of cholesterol biosynthesis and dysregulation of this pathway may have a role in the developmental pathology.

Insights into the biochemical and genetic basis of glucokinase activation from naturally occurring hypoglycemia mutations.

Glucokinase (GCK) is a key regulatory enzyme in the pancreatic beta-cell and catalyzes the rate-limiting step for beta-cell glucose metabolism. We report two novel GCK mutations (T65I and W99R) that have arisen de novo in two families with familial hypoglycemia. Insulin levels, although inappropriately high for the degree of hypoglycemia, remain regulated by fluctuations in glycemia, and pancreatic histology was normal. These mutations are within the recently identified heterotropic allosteric activator site in the theoretical model of human beta-cell glucokinase. Functional analysis of the purified recombinant glutathionyl S-transferase fusion proteins of T65I and W99R GCK revealed that the kinetic changes result in a relative increased activity index (a measure of the enzyme's phosphorylating potential) of 9.81 and 6.36, respectively, compared with wild-type. The predicted thresholds for glucose-stimulated insulin release using mathematical modeling were 3.1 (T65I) and 2.8 (W99R) mmol/l, which were in line with the patients' fasting glucose. In conclusion, we have identified two novel spontaneous GCK-activating mutations whose clinical phenotype clearly differs from mutations in ATP-sensitive K(+) channel genes. In vitro studies confirm the validity of structural and functional models of GCK and the putative allosteric activator site, which is a potential drug target for the treatment of type 2 diabetes.