Three rare diseases in one Sib pair: RAI1, PCK1, GRIN2B mutations associated with Smith–Magenis Syndrome, cytosolic PEPCK deficiency and NMDA receptor glutamate insensitivity

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Abstract

The National Institutes of Health Undiagnosed Diseases Program evaluates patients for whom no diagnosis has been discovered despite a comprehensive diagnostic workup. Failure to diagnose a condition may arise from the mutation of genes previously unassociated with disease. However, we hypothesized that this could also co-occur with multiple genetic disorders. Demonstrating a complex syndrome caused by multiple disorders, we report two siblings manifesting both similar and disparate signs and symptoms. They shared a history of episodes of hypoglycemia and lactic acidosis, but had differing exam findings and developmental courses. Clinical acumen and exome sequencing combined with biochemical and functional studies identified three genetic conditions. One sibling had Smith–Magenis Syndrome and a nonsense mutation in the RAI1 gene. The second sibling had a de novo mutation in GRIN2B, which resulted in markedly reduced glutamate potency of the encoded receptor. Both siblings had a protein-destabilizing homozygous mutation in PCK1, which encodes the cytosolic isoform of phosphoenolpyruvate carboxykinase (PEPCK-C). In summary, we present the first clinically-characterized mutation of PCK1 and demonstrate that complex medical disorders can represent the co-occurrence of multiple diseases.

Introduction

Genome-scale or “Next Generation” Sequencing (NGS) has become widely available for clinical use. The field of rare and new disease discovery leads the way in the application of NGS, and the NIH Undiagnosed Diseases Program (UDP) typifies this effort. The UDP features intensive phenotyping, diagnostic tools agnostic to disease causation, newly developed NGS analytics, and collaborative research aimed at establishing the disease-causality of candidate mutations by biochemists, cell biologists, and physiologists.

A traditional search for the cause of a heritable disease seeks a single, highly penetrant, large-effect gene. In this model, unusually severe or treatment-refractory presentations represent novel versions of known disorders and are considered to reflect the influence of genetic and/or environmental modifiers. However, case reports support the epidemiologic expectation that multiple rare disorders will occasionally occur in the same individual [1], [2]. Experience in the UDP has confirmed that a substantial number of apparently unique, undiagnosed medical conditions will, in fact, be the combinations of multiple genetic disorders in single individuals or families. Illustrating this, we present a non-consanguineous family with two affected children in which three different functionally verified mutations contribute to their phenotypes. For undiagnosed, unique and extensively investigated individuals such as those evaluated by the UDP, physicians should consider complex alternatives to a single, unifying genetic explanation.

The family reported here included two siblings who presented with variable developmental delay, hypotonia, and fasting hypoglycemia with lactic acidemia. One had prominent dysmorphic features and obesity; the other did not. Each had extensive metabolic and genetic testing by several specialists before the final diagnoses were confirmed by DNA sequencing, functional, and structural analyses.

Section snippets

Patients

The family was enrolled in clinical protocol 76-HG-0238, “Diagnosis and Treatment of Patients with Inborn Errors of Metabolism and Other Genetic Disorders”. The parents gave written informed consent for their children, who were enrolled in the NIH UDP. This initiative evaluates individuals and families in whom previous diagnostic investigations have been unrevealing [3], [4], [5].

NGS sequencing and SNP analysis

SNP oligo array analysis for filtering of exome sequence data was performed using Illumina Bead Array Platform and

Case reports

The propositae are two sisters born to non-consanguineous parents with Ashkenazi Jewish ancestry and a non-contributory family history.

Discussion

This family's unaffected parents had two daughters, each of whom had PEPCK-C deficiency (associated with proven instability of the mutant protein), one of whom had SMS (documented by RAI1 mutation), and the other of whom had a GRIN2B mutation (shown by functional assay of the p.E413G mutation's effect on GluN2B). The SMS explains the dysmorphisms and behavioral phenotype. Mutations in the GRIN2B gene have been associated with a wide range of neurological disorders, including intellectual

Conclusion

In the current era, in which multiple, sophisticated methodologies are employed for molecular diagnostics, more and more families with multiple genetic abnormalities are likely to be ascertained. This challenges the tenet of Occam's razor, i.e., that one explanation should account for all of a patient's symptoms. In particular, our family illustrates the need to consider additional diagnoses for cases that are present in an atypical fashion or are not fully explained by mutation(s) in a single

Acknowledgments

This work was supported by the Intramural Research Program of the National Human Genome Research Institute, by grant NS036654 (S.F.T.); by the NIH Undiagnosed Diseases Program (HSN268201300162P, H.Y.); the Center for Inherited Disorders of Energy Metabolism (D.S.K); the Allison Foundation, grant 116491 (R.W.H.); the National Center for Research Resources Grant P20 RR17708 and the Natural Sciences and Engineering Research Council of Canada (T.H.). Professor Richard W. Hanson died the same day

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