De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith–Magenis syndrome

• Main Authors: Francesco Vetrini, Shane McKee, Jill A. Rosenfeld, Mohnish Suri, Andrea M. Lewis, Kimberly Margaret Nugent, Elizabeth Roeder, Rebecca O. Littlejohn, Sue Holder, Wenmiao Zhu, Joseph T. Alaimo, Brett Graham, Jill M. Harris, James B. Gibson, Matthew Pastore, Kim L. McBride, Makanko Komara, Lihadh Al-Gazali, Aisha Al Shamsi, Elizabeth A. Fanning, Klaas J. Wierenga, Daryl A. Scott, Ziva Ben-Neriah, Vardiella Meiner, Hanoch Cassuto, Orly Elpeleg, J. Lloyd Holder, Lindsay C. Burrage, Laurie H. Seaver, Lionel Van Maldergem, Sonal Mahida, Janet S. Soul, Margaret Marlatt, Ludmila Matyakhina, Julie Vogt, June-Anne Gold, Soo-Mi Park, Vinod Varghese, Anne K. Lampe, Ajith Kumar, Melissa Lees, Muriel Holder-Espinasse, Vivienne McConnell, Birgitta Bernhard, Ed Blair, Victoria Harrison, The DDD study, Donna M. Muzny, Richard A. Gibbs, Sarah H. Elsea, Jennifer E. Posey, Weimin Bi, Seema Lalani, Fan Xia, Yaping Yang, Christine M. Eng, James R. Lupski, Pengfei Liu
• Format: Article
• Language: English
• Published: BMC 2019-02-01
• Series: Genome Medicine
• Subjects: TCF20; 22q13; Neurodevelopmental disorders; Smith–Magenis syndrome; Haploinsufficiency; Loss-of-function variants
• Online Access: http://link.springer.com/article/10.1186/s13073-019-0623-0

Abstract Background Neurodevelopmental disorders are genetically and phenotypically heterogeneous encompassing developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), structural brain abnormalities, and neurological manifestations with variants in a large number of genes (hundreds) associated. To date, a few de novo mutations potentially disrupting TCF20 function in patients with ID, ASD, and hypotonia have been reported. TCF20 encodes a transcriptional co-regulator structurally related to RAI1, the dosage-sensitive gene responsible for Smith–Magenis syndrome (deletion/haploinsufficiency) and Potocki–Lupski syndrome (duplication/triplosensitivity). Methods Genome-wide analyses by exome sequencing (ES) and chromosomal microarray analysis (CMA) identified individuals with heterozygous, likely damaging, loss-of-function alleles in TCF20. We implemented further molecular and clinical analyses to determine the inheritance of the pathogenic variant alleles and studied the spectrum of phenotypes. Results We report 25 unique inactivating single nucleotide variants/indels (1 missense, 1 canonical splice-site variant, 18 frameshift, and 5 nonsense) and 4 deletions of TCF20. The pathogenic variants were detected in 32 patients and 4 affected parents from 31 unrelated families. Among cases with available parental samples, the variants were de novo in 20 instances and inherited from 4 symptomatic parents in 5, including in one set of monozygotic twins. Two pathogenic loss-of-function variants were recurrent in unrelated families. Patients presented with a phenotype characterized by developmental delay, intellectual disability, hypotonia, variable dysmorphic features, movement disorders, and sleep disturbances. Conclusions TCF20 pathogenic variants are associated with a novel syndrome manifesting clinical characteristics similar to those observed in Smith–Magenis syndrome. Together with previously described cases, the clinical entity of TCF20-associated neurodevelopmental disorders (TAND) emerges from a genotype-driven perspective.