Hum Mutat. 2017 Dec;38(12):1774-1785. doi: 10.1002/humu.23339. Epub 2017 Sep 23.

Functional analysis of novel DEAF1 variants identified through clinical exome sequencing expands DEAF1-associated neurodevelopmental disorder (DAND) phenotype.

Chen L¹, Jensik PJ², Alaimo JT^3,⁴, Walkiewicz M^3,⁴, Berger S⁵, Roeder E^3,⁶, Faqeih EA⁷, Bernstein JA⁸, Smith ACM⁹, Mullegama SV^3,¹⁰, Saffen DW^1,^11,¹², Elsea SH^3,⁴.

Author information

1: Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China.
2: Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois.
3: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.
4: Baylor Genetics Laboratory, Houston, Texas.
5: Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.
6: Departments of Pediatrics, Baylor College of Medicine, San Antonio, Texas.
7: Department of Pediatrics Subspecialty, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia.
8: Department of Pediatrics, Stanford University School of Medicine, Stanford, California.
9: Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.
10: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California.
11: Institutes of Brain Science, Fudan University, Shanghai, China.
12: State Key Laboratory for Medical Neurobiology, Fudan University, Shanghai, China.

Abstract

Deformed epidermal autoregulatory factor-1 (DEAF1), a transcription factor essential for central nervous system and early embryonic development, has recently been implicated in a series of intellectual disability-related neurodevelopmental anomalies termed, in this study, as DEAF1-associated neurodevelopmental disorder (DAND). We identified six potentially deleterious DEAF1 variants in a cohort of individuals with DAND via clinical exome sequencing (CES) and in silico analysis, including two novel de novo variants: missense variant c.634G > A p.Gly212Ser in the SAND domain and deletion variant c.913_915del p.Lys305del in the NLS domain, as well as c.676C > T p.Arg226Trp, c.700T > A p.Trp234Arg, c.737G > C p.Arg246Thr, and c.791A > C p.Gln264Pro. Luciferase reporter, immunofluorescence staining, and electrophoretic mobility shift assays revealed that these variants had decreased transcriptional repression activity at the DEAF1 promoter and reduced affinity to consensus DEAF1 DNA binding sequences. In addition, c.913_915del p.K305del localized primarily to the cytoplasm and interacted with wild-type DEAF1. Our results demonstrate that variants located within the SAND or NLS domains significantly reduce DEAF1 transcriptional regulatory activities and are thus, likely to contribute to the underlying clinical concerns in DAND patients. These findings illustrate the importance of experimental characterization of variants with uncertain significance identified by CES to assess their potential clinical significance and possible use in diagnosis.

KEYWORDS:

SAND; clinical exome sequencing (CES); deformed epidermal autoregulatory factor-1 (DEAF1)-associated neurodevelopmental disorder (DAND); intellectual disability (ID); nuclear localization signal (NLS)