Jane L. Schuette

Haploinsufficiency of SF3B4, a Component of the Pre-mRNA Spliceosomal Complex, Causes Nager Syndrome

Nager syndrome, first described more than 60 years ago, is the archetype of a class of disorders called the acrofacial dysostoses, which are characterized by craniofacial and limb malformations. Despite intensive efforts, no gene for Nager syndrome has yet been identified. In an international collaboration, FORGE Canada and the National Institutes of Health Centers for Mendelian Genomics used exome sequencing as a discovery tool and found that mutations in SF3B4, a component of the U2 pre-mRNA spliceosomal complex, cause Nager syndrome. After Sanger sequencing of SF3B4 in a validation cohort, 20 of 35 (57%) families affected by Nager syndrome had 1 of 18 different mutations, nearly all of which were frameshifts. These results suggest that most cases of Nager syndrome are caused by haploinsufficiency of SF3B4. Our findings add Nager syndrome to a growing list of disorders caused by mutations in genes that encode major components of the spliceosome and also highlight the synergistic potential of international collaboration when exome sequencing is applied in the search for genes responsible for rare Mendelian phenotypes.

Guidelines for Writing Letters to Patients

Patient letters provide a permanent record of the genetic counseling that was provided and are unique in medical care; rarely do other health care providers send summaries written specifically to their patients and families. We surveyed genetic counseling training program directors and found that while the acquisition of patient letter-writing skills was considered important, there were no specific guidelines made available to students. To develop letter-writing guidelines, we evaluated patient letters, reviewed references on professional correspondence, surveyed the medical literature, and worked with a writing consultant. The guidelines we subsequently developed and present here include a format for writing patient letters, suggestions on presenting medical information in understandable terms, and wording considerations. These patient letter-writing guidelines are intended to serve as a guide for teaching students this important skill and as a resource for practicing health care professionals.

TAF1 Variants Are Associated with Dysmorphic Features, Intellectual Disability, and Neurological Manifestations.

We describe an X-linked genetic syndrome associated with mutations in TAF1 and manifesting with global developmental delay, intellectual disability (ID), characteristic facial dysmorphology, generalized hypotonia, and variable neurologic features, all in male individuals. Simultaneous studies using diverse strategies led to the identification of nine families with overlapping clinical presentations and affected by de novo or maternally inherited single-nucleotide changes. Two additional families harboring large duplications involving TAF1 were also found to share phenotypic overlap with the probands harboring single-nucleotide changes, but they also demonstrated a severe neurodegeneration phenotype. Functional analysis with RNA-seq for one of the families suggested that the phenotype is associated with downregulation of a set of genes notably enriched with genes regulated by E-box proteins. In addition, knockdown and mutant studies of this gene in zebrafish have shown a quantifiable, albeit small, effect on a neuronal phenotype. Our results suggest that mutations in TAF1 play a critical role in the development of this X-linked ID syndrome.

Parents’ Perspectives on Variants of Uncertain Significance from Chromosome Microarray Analysis

Chromosomal microarray analysis (CMA) for unexplained anomalies and developmental delay has improved diagnosis rates, but results classified as variants of uncertain significance (VUS) may challenge both clinicians and families. We explored the impact of such results on families, including parental knowledge, understanding and interpretation. Semi-structured telephone interviews were conducted with parents (N = 14) who received genetic counseling for a VUS in their child. Transcripts were analyzed through an iterative coding process. Participants demonstrated a range of recall and personal interpretation regarding whether test results provided a causal explanation for their children’s health issues. Participants maintained contradictory interpretations, describing results as answers while maintaining that little clarification of their child’s condition had been provided. Reported benefits included obtaining medical services and personal validation. Parents described adaptation/coping processes similar to those occurring after positive test results. Recall of terminology, including “VUS” and precise CMA abnormalities, was poor. However, most demonstrated conceptual understanding of scientific uncertainty. All participants expressed intentions to return for recommended genetics follow-up but had misconceptions about how this would occur. These results provide insight into the patient-and-family experience when receiving uncertain genomic findings, emphasize the importance of exploring uncertainty during the communication process, and highlight areas for potential attention or improvement in the clinical encounter.

De novo missense variants in PPP2R5D are associated with intellectual disability, macrocephaly, hypotonia, and autism

Protein phosphatase 2A (PP2A) is a heterotrimeric protein serine/threonine phosphatase and is involved in a broad range of cellular processes. PPP2R5D is a regulatory B subunit of PP2A and plays an important role in regulating key neuronal and developmental regulation processes such as PI3K/AKT and glycogen synthase kinase 3 beta (GSK3β)-mediated cell growth, chromatin remodeling, and gene transcriptional regulation. Using whole-exome sequencing (WES), we identified four de novo variants in PPP2R5D in a total of seven unrelated individuals with intellectual disability (ID) and other shared clinical characteristics, including autism spectrum disorder, macrocephaly, hypotonia, seizures, and dysmorphic features. Among the four variants, two have been previously reported and two are novel. All four amino acids are highly conserved among the PP2A subunit family, and all change a negatively charged acidic glutamic acid (E) to a positively charged basic lysine (K) and are predicted to disrupt the PP2A subunit binding and impair the dephosphorylation capacity. Our data provides further support for PPP2R5D as a genetic cause of ID.

Novel DICER1 mutation as cause of multinodular goiter in children

The aim of this report was to present a rare case of an adolescent with multinodular goiter (MNG) found to have a DICER1 mutation.

Duplication 2p25 in a Child with Clinical Features of CHARGE Syndrome

CHARGE syndrome is a dominant disorder characterized by ocular colobomata, heart defects, choanal atresia, retardation of growth and development, genital hypoplasia, and ear abnormalities including deafness and vestibular disorders. The majority of individuals with CHARGE have pathogenic variants in the gene encoding CHD7, a chromatin remodeling protein. Here, we present a 15‐year‐old girl with clinical features of CHARGE syndrome and a de novo 6.5 Mb gain of genomic material at 2p25.3–p25.2. The duplicated region contained 24 genes, including the early and broadly expressed transcription factor gene SOX11. Analysis of 28 other patients with CHARGE showed no SOX11 copy number changes or pathogenic sequence variants. To our knowledge, this childs chromosomal abnormality is unique and represents the first co‐occurrence of duplication 2p25 and clinical features of CHARGE syndrome. We compare our patients phenotype to ten previously published patients with isolated terminal duplication 2p, and elaborate on the clinical diagnosis of CHARGE in the context of atypical genetic findings.

CTNNB1 mutation associated with familial exudative vitreoretinopathy (FEVR) phenotype

Familial exudative vitreoretinopathy (FEVR) is a rare genetic disorder of retinal vascular development that can result in retinal detachment and blindness. A pathologic hallmark of FEVR is peripheral retinal avascularity, which promotes ischemia, neovascularization, and ultimately vitreoretinal traction and detachment of the retina in severe cases. Mutations in five genes have been associated with the FEVR phenotype, and many of these genes play an essential role in Wnt signaling. Wnts are glycoproteins that bind to specific transmembrane receptors to initiate intracellular signaling cascades, and normal Wnt signaling within developing retinal endothelial cells is crucial to the formation of a well-vascularized retina. We report a patient with a heterozygous mutation in the CTNNB1 gene, which codes for the protein beta-catenin. Beta-catenin is the final mediator of gene transcription in canonical Wnt signaling. To the best of our knowledge, this is the first report of a CTNNB1 mutation that has been linked to the FEVR phenotype. A 22-month-old boy was referred to the W. K. Kellogg Eye Center for evaluation of “depth perception problems.” The patient’s past medical history included lipomyelomeningocele, failure to thrive, short stature, developmental delay, and behaviors on the autism spectrum. The patient was born at 34 and 1/7 week gestation with a birth weight of 1842 g. Newborn screening was normal. The patient had previously been evaluated by Pediatric Genetics and a heterozygous mutation in the CTNNB1 gene was identified by clinical whole exome sequencing (GeneDx, Gaithersburg, MD). The mutation was characterized as an insertion of five base pairs (c.2112_2116dupAGAAC; p.P706QfsX31), causing a frameshift of the protein and likely complete loss-of-function, resulting in haploinsufficiency. The mutation was not found in the mother, who was the only parent available for testing. Based on the type of mutation and the patient’s clinical features, it was presumed to be causative of his developmental delay and congenital anomalies. At his initial visit to the eye center at age 22 months, the patient’s exam was notable for bilateral hyperopic astigmatism. Spectacles were prescribed and the patient was to follow-up in 6 months, but he was lost to followup for over 14 months. On return visit, he was noted to have a left eye preference and dilated examination revealed an abnormality in the right eye concerning a retinal detachment. Examination under anesthesia showed normal anterior segments of both eyes. Fundoscopic examination of the right eye revealed an exudative macular detachment with retinal elevation in the peripapillary area extending to the inferotemporal periphery (Figure 1A). Also present were the initial stages of retinal fold formation in the posterior pole with a falciform fold in the inferotemporal periphery. Vitreous overlying this fold was abnormal and generating traction, and exudates were present at the base of the fold. The retinal periphery was markedly avascular. Fundoscopic examination of the left eye revealed an elevated optic nerve, a normal macula, and premature pruning of the temporal retinal vessels (Figure 1C). Fluorescein angiography revealed early leakage from the abnormal retinal vessels (Figure 1B). The peripheral vessels were pruned off with complete avascularity of the far periphery. The left eye showed similar peripheral vascular pruning temporally more than nasally (Figure 1D). The findings on EUA were consistent with the FEVR phenotype. To prevent disease progression, the patient underwent laser photocoagulation of the peripheral retina of the right eye during the initial EUA. He subsequently underwent prophylactic laser photocoagulation of the left eye several weeks later. Our patient with a CTNNB1 mutation and intellectual disability exhibited the ocular findings pathognomonic for FEVR: peripheral retinal avascularity and retinal detachment in a child whose natural history was not consistent with retinopathy of prematurity (ROP). These findings are significant because, to the best of our knowledge, this is the first reported case of a CTNNB1 mutation associated with the FEVR phenotype. Furthermore, as normal CTNNB1 expression is essential for proper canonical Wnt signaling, the combination of the patient’s genotype and phenotype supports the current paradigm that abnormal Wnt signaling contributes to the development of FEVR. The Wnt signaling pathway is a complex, highly conserved pathway that regulates cellular differentiation and proliferation. Traditionally, Wnt signaling has been

Yield of additional genetic testing after chromosomal microarray for diagnosis of neurodevelopmental disability and congenital anomalies: a clinical practice resource of the American College of Medical Genetics and Genomics (ACMG)

PurposeChromosomal microarray (CMA) is recommended as the first-tier test in evaluation of individuals with neurodevelopmental disability and congenital anomalies. CMA may not detect balanced cytogenomic abnormalities or uniparental disomy (UPD), and deletion/duplications and regions of homozygosity may require additional testing to clarify the mechanism and inform accurate counseling. We conducted an evidence review to synthesize data regarding the benefit of additional testing after CMA to inform a genetic diagnosis.MethodsThe review was guided by key questions related to the detection of genomic events that may require additional testing. A PubMed search for original research articles, systematic reviews, and meta-analyses was evaluated from articles published between 1 January 1983 and 31 March 2017. Based on the key questions, articles were retrieved and data extracted in parallel with comparison of results and discussion to resolve discrepancies. Variables assessed included study design and outcomes.ResultsA narrative synthesis was created for each question to describe the occurrence of, and clinical significance of, additional diagnostic findings from subsequent testing performed after CMA.ConclusionThese findings may be used to assist the laboratory and clinician when making recommendations about additional testing after CMA, as it impacts clinical care, counseling, and diagnosis.

A novel DICER1 mutation causes multi-nodular goiter in children

The aim of this report was to present a rare case of an adolescent with multinodular goiter (MNG) found to have a DICER1 mutation.