The detection of a strong episignature for Chung-Jansen syndrome, partially overlapping with Börjeson-Forssman-Lehmann and White-Kernohan syndromes

Chung-Jansen syndrome is a neurodevelopmental disorder characterized by intellectual disability, behavioral problems, obesity and dysmorphic features. It is caused by pathogenic variants in the PHIP gene that encodes for the Pleckstrin homology domain-interacting protein, which is part of an epigenetic modifier protein complex. Therefore, we hypothesized that PHIP haploinsufficiency may impact genome-wide DNA methylation (DNAm). We assessed the DNAm profiles of affected individuals with pathogenic and likely pathogenic PHIP variants with Infinium Methylation EPIC arrays and report a specific and sensitive DNAm episignature biomarker for Chung-Jansen syndrome. In addition, we observed similarities between the methylation profile of Chung-Jansen syndrome and that of functionally related and clinically partially overlapping genetic disorders, White-Kernohan syndrome (caused by variants in DDB1 gene) and Börjeson-Forssman-Lehmann syndrome (caused by variants in PHF6 gene). Based on these observations we also proceeded to develop a common episignature biomarker for these disorders. These newly defined episignatures can be used as part of a multiclass episignature classifier for screening of affected individuals with rare disorders and interpretation of genetic variants of unknown clinical significance, and provide further insights into the common molecular pathophysiology of the clinically-related Chung-Jansen, Börjeson-Forssman-Lehmann and White-Kernohan syndromes.

Applying data science methodologies with artificial intelligence variant reinterpretation to map and estimate genetic disorder prevalence utilizing clinical data

Data science methodologies can be utilized to ascertain and analyze clinical genetic data that is often unstructured and rarely used outside of patient encounters. Genetic variants from all genetic testing resulting to a large pediatric healthcare system for a 5-year period were obtained and reinterpreted utilizing the previously validated Franklin© Artificial Intelligence (AI). Using PowerBI©, the data were further matched to patients in the electronic healthcare record to associate with demographic data to generate a variant data table and mapped by ZIP codes. Three thousand and sixty-five variants were identified and 98% were matched to patients with geographic data. Franklin© changed the interpretation for 24% of variants. One hundred and fifty-six clinically actionable variant reinterpretations were made. A total of 739 Mendelian genetic disorders were identified with disorder prevalence estimation. Mapping of variants demonstrated hot-spots for pathogenic genetic variation such as PEX6-associated Zellweger Spectrum Disorder. Seven patients were identified with Bardet-Biedl syndrome and seven patients with Rett syndrome amenable to newly FDA-approved therapeutics. Utilizing readily available software we developed a database and Exploratory Data Analysis (EDA) methodology enabling us to systematically reinterpret variants, estimate variant prevalence, identify conditions amenable to new treatments, and localize geographies enriched for pathogenic variants.

A Case of Beta-Propeller Protein-Associated Neurodegeneration With a Unique Truncating Variant in the WDR45 Gene and Uncommon Clinical and Radiologic Findings

Beta-propeller protein-associated neurodegeneration (BPAN), a subtype of neurodegeneration with brain iron accumulation, is caused by variants in the WDR45 gene. In this paper, we describe a patient with an atypical presentation of BPAN whose whole exome sequencing revealed a previously unattested truncating variant in the WDR45 gene (c.830+3G>C/p.Leu278Ter), the pathogenicity of which was verified by RNA transcriptomics. A number of uncommon neuroanatomic and clinical findings in our patient are discussed, expanding the phenotype associated with BPAN. This unique case challenges existing genotype-phenotype correlations and highlights the role of X chromosome skewing in shaping the clinical spectrum of BPAN.

Systematic analysis of variants escaping nonsense-mediated decay uncovers candidate Mendelian diseases

Protein-truncating variants (PTVs) near the 3' end of genes may escape nonsense-mediated decay (NMD). PTVs in the NMD-escape region (PTVescs) can cause Mendelian disease but are difficult to interpret given their varying impact on protein function. Previously, PTVesc burden was assessed in an epilepsy cohort, but no large-scale analysis has systematically evaluated these variants in rare disease. We performed a retrospective analysis of 29,031 neurodevelopmental disorder (NDD) parent-offspring trios referred for clinical exome sequencing to identify PTVesc de novo mutations (DNMs). We identified 1,376 PTVesc DNMs and 133 genes that were significantly enriched (binomial p < 0.001). The PTVesc-enriched genes included those with PTVescs previously described to cause dominant Mendelian disease (e.g., SEMA6B, PPM1D, and DAGLA). We annotated ClinVar variants for PTVescs and identified 948 genes with at least one high-confidence pathogenic variant. Twenty-two known Mendelian PTVesc-enriched genes had no prior evidence of PTVesc-associated disease. We found 22 additional PTVesc-enriched genes that are not well established to be associated with Mendelian disease, several of which showed phenotypic similarity between individuals harboring PTVesc variants in the same gene. Four individuals with PTVesc mutations in RAB1A had similar phenotypes including NDD and spasticity. PTVesc mutations in IRF2BP1 were found in two individuals who each had severe immunodeficiency manifesting in NDD. Three individuals with PTVesc mutations in LDB1 all had NDD and multiple congenital anomalies. Using a large-scale, systematic analysis of DNMs, we extend the mutation spectrum for known Mendelian disease-associated genes and identify potentially novel disease-associated genes.

Native American ataxia medicines rescue ataxia-linked mutant potassium channel activity via binding to the voltage sensing domain

There are currently no drugs known to rescue the function of Kv1.1 voltage-gated potassium channels carrying loss-of-function sequence variants underlying the inherited movement disorder, Episodic Ataxia 1 (EA1). The Kwakwaka'wakw First Nations of the Pacific Northwest Coast used Fucus gardneri (bladderwrack kelp), Physocarpus capitatus (Pacific ninebark) and Urtica dioica (common nettle) to treat locomotor ataxia. Here, we show that extracts of these plants enhance wild-type Kv1.1 current, especially at subthreshold potentials. Screening of their constituents revealed that gallic acid and tannic acid similarly augment wild-type Kv1.1 current, with submicromolar potency. Crucially, the extracts and their constituents also enhance activity of Kv1.1 channels containing EA1-linked sequence variants. Molecular dynamics simulations reveal that gallic acid augments Kv1.1 activity via a small-molecule binding site in the extracellular S1-S2 linker. Thus, traditional Native American ataxia treatments utilize a molecular mechanistic foundation that can inform small-molecule approaches to therapeutically correcting EA1 and potentially other Kv1.1-linked channelopathies.

The clinical and molecular spectrum of the KDM6B-related neurodevelopmental disorder

De novo variants are a leading cause of neurodevelopmental disorders (NDDs), but because every monogenic NDD is different and usually extremely rare, it remains a major challenge to understand the complete phenotype and genotype spectrum of any morbid gene. According to OMIM, heterozygous variants in KDM6B cause "neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities." Here, by examining the molecular and clinical spectrum of 85 reported individuals with mostly de novo (likely) pathogenic KDM6B variants, we demonstrate that this description is inaccurate and potentially misleading. Cognitive deficits are seen consistently in all individuals, but the overall phenotype is highly variable. Notably, coarse facies and distal skeletal anomalies, as defined by OMIM, are rare in this expanded cohort while other features are unexpectedly common (e.g., hypotonia, psychosis, etc.). Using 3D protein structure analysis and an innovative dual Drosophila gain-of-function assay, we demonstrated a disruptive effect of 11 missense/in-frame indels located in or near the enzymatic JmJC or Zn-containing domain of KDM6B. Consistent with the role of KDM6B in human cognition, we demonstrated a role for the Drosophila KDM6B ortholog in memory and behavior. Taken together, we accurately define the broad clinical spectrum of the KDM6B-related NDD, introduce an innovative functional testing paradigm for the assessment of KDM6B variants, and demonstrate a conserved role for KDM6B in cognition and behavior. Our study demonstrates the critical importance of international collaboration, sharing of clinical data, and rigorous functional analysis of genetic variants to ensure correct disease diagnosis for rare disorders.

Homozygous EXOSC3 c.395A>C Variants in Pontocerebellar Hypoplasia Type 1B: A Sibling Pair With Childhood Lethal Presentation and Literature Review

Pontocerebellar hypoplasia type 1B (PCH1B) is an autosomal recessive neurodegenerative disorder that involves hypoplasia or atrophy of the cerebellum and pons. PCH1B is caused by mutations in EXOSC3, which encodes a subunit of the RNA exosome complex. The most frequently observed mutation in PCH1B patients is a c.395A>C (p.D132A) missense variant, for which the homozygous mutation typically results in milder symptoms compared to compound heterozygous mutations or homozygous mutations for other pathogenic variants. In the present study, we report on a sibling pair harboring homozygous EXOSC3 c.395A>C missense variants who deteriorated more rapidly than previously described. These cases expand the spectrum of clinical manifestations of PCH1B associated with this variant, highlighting the need for further research to determine predictive factors of PCH1B severity.

Predominant Liver Cystic Disease in a New Heterozygotic PKHD1 Variant: A Case Report

BACKGROUND The polycystic kidney and hepatic disease 1 (PKHD1) gene codes for fibrocystin-polyductin, a protein that takes part in cell-signaling for cell differentiation, especially in kidney tubules and bile ducts. A homozygous or compound heterozygous defect in this gene can cause autosomal recessive polycystic kidney disease (ARPKD). Polycystic liver disease (PCLD) can also be caused by single heterozygous variants in the PKHD1 gene. ARPKD presents with renal insufficiency and cystic dilatation of bile ducts, although disease is not expected with a single heterozygous mutation. PCLD presents with multiple cysts in the liver and dilated bile ducts as well, but with less of an impact on the kidneys than with ARPKD. Our purpose in publishing this report is to introduce an as-yet unknown variant to the body of genetic defects associated with ARPKD and PCLD, as well as to argue for the likely pathogenicity of the variant according to the prevailing criteria used for classifying gene variants. CASE REPORT We present a patient with a de novo PKHD1 variant currently classified as a variant of unknown significance manifesting with bilaterally enlarged cystic kidneys and echogenic cystic structures in the hepatic portal system, indicative of cystic disease. CONCLUSIONS Given this patient's liver and kidney presentation that does not fully align with either ARPKD or PCLD, the authors believe that the single heterozygous variant in this patient's PKHD1 gene is worthy of reporting. This new single heterozygous variant in PKHD1 gene causing cystic kidney and cystic hepatic disease in the patient should be considered 'likely pathogenic' according to the criteria set by the American College of Medical Genetics.

Case report: A novel loss-of-function pathogenic variant in the KCNA1 cytoplasmic N-terminus causing carbamazepine-responsive type 1 episodic ataxia

Episodic ataxia is an umbrella term for a group of nervous system disorders that adversely and episodically affect movement. Episodes are recurrent, characterized by loss of balance and coordination and can be accompanied by other symptoms ranging from nausea to hemiplegia. Episodic Ataxia Type 1 (EA1) is an inherited, autosomal dominant disease caused by sequence variants in KCNA1, which encodes the voltage-gated potassium channel, KCNA1 (Kv1.1). Here we report a novel loss-of-function KCNA1 pathogenic variant [c.464T>C/p.Leu155Phe] causing frequent, sudden onset of clumsiness or staggering gait in the young female proband. The gene variant was maternally inherited and the mother, whose symptoms also began in childhood, has a normal MRI and EEG, slurred speech and dystonic movements involving upper extremities and mouth. Both mother and daughter are responsive to carbamazepine. Cellular electrophysiology studies of KCNA1-L155P potassium channels revealed complete but non-dominant loss of function, with reduced current and altered gating in heterozygous channels. To our knowledge this is the first EA1-associated pathogenic variant located in the KCNA1 cytoplasmic N-terminus, expanding the reported clinically sensitive domains of the channel.

Cognitive and visual diagnostic errors in dermatology: part 1

Sir William Osler famously, and ironically, stated that 'Medicine is a science of uncertainty and an art of probability'. The processes by which each physician metes out diagnostic uncertainty and navigates probabilities in dermatology is far from uniform. While certain ubiquitous cognitive and visual heuristics can enhance diagnostic speed, they also create pitfalls and thinking traps that introduce significant variation in the diagnostic process. Discussed in this part of a two-part article are various cognitive and visual heuristics as they pertain to skin disease, with an introduction and special attention paid to the heuristic methods classically applied by dermatologists. How to best address error and improve our thought processes will be addressed in part 2.

Diagnostic heuristics in dermatology, part 2: metacognition and other fixes

Diagnostic errors are the most common, costly and dangerous of medical mistakes. In part 1 of this series, we described how general and dermatology-specific cognitive and perceptual biases underlie most of our correct diagnoses, as well as being a source of diagnostic medical errors. In this second part of the series, we describe some tactics to combat diagnostic error. Metacognition, or thinking about how we think, is the central approach advocated to avoid errors of 'uncritical' diagnostic thinking. Current individual and medical cultural attitudes need to be modified in order to incorporate improvements in diagnosis. Algorithms, artificial intelligence and system changes are being developed to address error and improve diagnostic accuracy.

Juvenile Granulosa Cell Tumor of the Testicle - Report of a Neonatal Case with Positive Alpha-fetoprotein Immunohistochemical Staining

We report on a case of juvenile granulosa cell tumor of the testicle in a neonate, a rare testicular tumor in children. No genital ambiguity, anatomic abnormalities, nor sex chromosome aneuploidy was noted in this patient. In our case, despite positive staining for alpha-fetoprotein which is most consistent with yolk sac tumors, all clinical, gross anatomic, histologic, and other immunohistologic characteristics of the tumor remained consistent with the diagnosis of juvenile granulosa cell tumor. The alpha-fetoprotein positivity of the tumor remains unexplained.

A rare MeCP2_e1 mutation first described in a male patient with severe neonatal encephalopathy

Specific mutations in MECP2 cause Rett syndrome (RTT) in females whereas other mutations in the same gene cause several other syndromes in males, including X-linked intellectual disability (with and without spasticity) (OMIM 300055) and X-linked intellectual disability due to increased dosage of MECP2 (OMIM 300260). Males can also manifest an entity known as MECP2-related severe neonatal encephalopathy whose mutations are identical to those in females with RTT. We describe here the first case of MECP2-related severe neonatal encephalopathy caused by a mutation in exon one of MECP2, a mutation rarely identified in females with RTT. © 2016 Wiley Periodicals, Inc.

The structure and content of the medical subinternship: a national survey

OBJECTIVE

To describe the educational and administrative structure and content of internal medicine subinternship (SI) programs at medical schools throughout the United States.

DESIGN

A cross-sectional mailed survey of internal medicine SI directors at U.S. medical schools.

MAIN RESULTS

Responses were received from 100 (80%) of 125 eligible programs. Seventy-five percent of schools require a SI for graduation; 26% of these schools require the completion of a medical SI. Nationally, about 75% of all medical students opt to complete a medical SI. Dedicated SI administrative committees exist at 46% of medical schools. A minority of programs provide students with explicit curricula (31%) or exclusive conference time (36%). In 44% of programs, subinterns are used by hospital departments of medicine as intern substitutes. Subinterns are responsible for sign-out and cross-coverage in about half of the programs, and all patient orders entered by subinterns require cosignature. Subintern evaluation criteria include attending evaluation (100%), resident evaluation (80%), case write-ups (27%), supervised clinical examination (20%), written examination (14%), and oral examination (3%).

CONCLUSION

Although most medical schools offer an SI in internal medicine and many require it, the experience often lacks clearly defined curricular goals and often does not provide medical students with house-staff-level responsibilities. In an effort to ease the transition from undergraduate to postgraduate training, further studies are needed to define which educational and structural components of the medicine SI should be developed and emphasized.