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Further Delineation of the Clinical Spectrum of KAT6B Disorders and Allelic Series of Pathogenic Variants

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Further Delineation of the Clinical Spectrum of KAT6B Disorders and Allelic Series of Pathogenic Variants ARTICLE © American College of Medical Genetics and Genomics Further delineation of the clinical spectrum of KAT6B disorders and allelic series of pathogenic variants Li Xin Zhang1, Gabrielle Lemire, MD2, Claudia Gonzaga-Jauregui, PhD3, Sirinart Molidperee, Gr. Cert1, Carolina Galaz-Montoya, MD3, David S. Liu, MD3, Alain Verloes, MD PhD4, Amelle G. Shillington, DO5, Kosuke Izumi, MD PhD6, Alyssa L. Ritter, MS LCGC7, Beth Keena, MS LCGC6, Elaine Zackai, MD7,8, Dong Li, PhD9, Elizabeth Bhoj, MD PhD7, Jennifer M. Tarpinian, MS CGC10, Emma Bedoukian, MS LCGC10, Mary K. Kukolich, MD11, A. Micheil Innes, MD12, Grace U. Ediae, BSc13, Sarah L. Sawyer, MD PhD14, Karippoth Mohandas Nair, MD15, Para Chottil Soumya, MD15, Kinattinkara R. Subbaraman, MD15, Frank J. Probst, MD PhD3,16, Jennifer A. Bassetti, MD3,16, Reid V. Sutton, MD3,16, Richard A. Gibbs, PhD3, Chester Brown, MD PhD17, Philip M. Boone, MD PhD18, Ingrid A. Holm, MD MPH18, Marco Tartaglia, PhD19, Giovanni Battista Ferrero, MD PhD20, Marcello Niceta, MD PhD19, Maria Lisa Dentici, MD19, Francesca Clementina Radio, MD PhD19, Boris Keren, MD21, Constance F. Wells, MD22, Christine Coubes, MD22, Annie Laquerrière, MD PhD23, Jacqueline Aziza, MD24, Charlotte Dubucs, MD24, Sheela Nampoothiri, MD25, David Mowat, MD26, Millan S. Patel, MD27, Ana Bracho, MD28, Francisco Cammarata-Scalisi, MD29, Alper Gezdirici, MD30, Alberto Fernandez-Jaen, MD31, Natalie Hauser, MD32, Yuri A. Zarate, MD33, Katherine A. Bosanko, MS CGC33, Klaus Dieterich, MD PhD34, John C. Carey, MD MPH35, Jessica X. Chong, PhD36,37, Deborah A. Nickerson, PhD37,38, Michael J. Bamshad, MD36,37, Brendan H. Lee, MD PhD3, Xiang-Jiao Yang, PhD39, James R. Lupski, MD PhD3,16 and Philippe M. Campeau, MD 2 Purpose: Genitopatellar syndrome and Say–Barber–Biesecker– four individuals who had increased nuchal translucency/cystic – KAT6B Young Simpson syndrome are caused by variants in the hygroma prenatally, and two fetuses with severe renal gene and are part of a broad clinical spectrum called KAT6B disorders, whose variable expressivity is increasingly being recognized. anomalies leading to renal failure. We also report an individual in which a pathogenic variant was inherited from a mildly Methods: We herein present the phenotypes of 32 previously unreported individuals with a molecularly confirmed diagnosis of a affected parent. KAT6B disorder, report 24 new pathogenic KAT6B variants, and Conclusion: Our work provides a comprehensive review and review phenotypic information available on all published individuals expansion of the genotypic and phenotypic spectrum of KAT6B with this condition. We also suggest a classification of clinical disorders that will assist clinicians in the assessment, counseling, subtypes within the KAT6B disorder spectrum. and management of affected individuals. Results: We demonstrate that cerebral anomalies, optic nerve hypoplasia, neurobehavioral difficulties, and distal limb anomalies Genetics in Medicine (2020) 22:1338–1347; https://doi.org/10.1038/s41436- other than long thumbs and great toes, such as polydactyly, are more 020-0811-8 frequently observed than initially reported. Intestinal malrotation and its serious consequences can be present in affected individuals. Keywords: KAT6B; KAT6B disorders; genitopatellar syndrome; Additionally, we identified four children with Pierre Robin sequence, Say–Barber–Biesecker–Young–Simpson syndrome; SBBYSS INTRODUCTION known as MYST4 and MORF) encodes a highly conserved Epigenetic regulation through histone acetylation is essential histone acetyltransferase that is part of the MYST family1 and for proper growth and development, and its role in human regulates the expression of multiple genes.2 Previous work has genetic diseases is increasingly recognized. KAT6B (formerly demonstrated that KAT6B preferentially acetylates lysine 14 Correspondence: Philippe M. Campeau ([email protected]). Affiliations are listed at the end of the paper. These first authors contributed equally: Li Xin Zhang, Gabrielle Lemire Submitted 30 January 2020; revised 9 April 2020; accepted: 9 April 2020 Published online: 19 May 2020 1338 Volume 22 | Number 8 | August 2020 | GENETICS in MEDICINE ZHANG et al ARTICLE of histone H3.2,3 KAT6B functions in a multisubunit complex interactions of KAT6B with interacting proteins leading to with other proteins including KAT6A, BRPF1, and ING5.4 clinical findings more specific to GPS,18 whereas the SBBYSS Exome sequencing has enabled identification of de novo phenotype would result from a loss of KAT6B functions. This heterozygous variants in KAT6B as the etiology of both has not yet been tested experimentally. Recently, more genitopatellar syndrome (GPS) (OMIM 606170) and proximal pathogenic variants in KAT6B exons 3, 7, 11, and Say–Barber–Biesecker–Young–Simpson syndrome (SBBYSS) 14–17 (for GPS, only in exons 17 and 18) were identified in – (OMIM 603736), a variant of Ohdo syndrome.5 7 individuals with GPS, SBBYSS, and the intermediate pheno- GPS is a skeletal dysplasia characterized by hypoplastic or type. The increasing identification of individuals with an absent patellae, flexion contractures of the hips and knees, intermediate phenotype having a variant previously identified agenesis of the corpus callosum, microcephaly, craniofacial in individuals with GPS or SBBYSS make phenotype predic- dysmorphisms, and genitourinary anomalies.8 Ohdo syn- tions based on genotype imprecise. drome was first described as a genetic condition characterized KAT6B pathogenic variants almost always occurred de novo by intellectual disability in association with congenital heart when parental testing has been performed. Recently, Kim disease and dysmorphisms.9 Subsequently, Young and et al. reported a family with an inherited pathogenic variant in Simpson reported a more severe phenotype later referred to exon 11 causing relatively mild disease in three individuals as the SBBYS variant of Ohdo syndrome, or SBBYS with SBBYSS.19 Another inherited pathogenic splice variant in – syndrome.10 12 SBBYSS is characterized by blepharophimosis, intron 5 has been found in six related individuals with mild dacryostenosis, ptosis, a mask-like facial appearance, and long SBBYSS phenotypes.20 GPS and SBBYSS are thus part of a thumbs/great toes.5 GPS and SBBYSS have been historically broad phenotypic spectrum and the variable expressivity of described as distinct disorders with respect to clinical findings KAT6B disorders is being increasingly recognized, motivating but with several overlapping features. Indeed, both the GPS research and delineation of an expanded allelic series. 1234567890():,; and SBBYSS phenotypes include significant global develop- Here, we review the clinical phenotypes of all reported mental delay/intellectual disability, hypotonia, genital individuals with molecularly confirmed KAT6B pathogenic abnormalities, patellar hypoplasia/agenesis, congenital heart variants in the literature and compare them with 32 newly defects, dental anomalies, hearing loss, and thyroid anoma- identified individuals with GPS, SBBYSS, and intermediate lies.13 To date, about 90 individuals with KAT6B disorders phenotypes. We aim to better define the phenotypic spectrum have been reported, including 18 with GPS, 58 with SBBYSS, of KAT6B disorders. We present 24 new KAT6B pathogenic and 13 described as having an intermediate phenotype. variants and have updated a publicly accessible Leiden Open The KAT6B pathogenic variant spectrum from previously Variation Database (LOVD) KAT6B variant database (https:// published individuals includes 56 variants: 22 substitutions, databases.lovd.nl/shared/genes/kat6b), which catalogs all 22 small intragenic deletions, 10 small intragenic duplications, known KAT6B pathogenic variants. and 2 small intragenic deletions associated with an insertion. The types of variants at the protein level include 33 frameshift, MATERIALS AND METHODS 19 nonsense, 2 missense, and 2 splicing defects. Pathogenic Individuals with molecularly proven KAT6B disorders from variants are most often located in exon 18, the last exon of the different clinical centers were included in this series. Some gene. More proximal pathogenic variants have typically been individuals presented with clinical features suggestive of a associated with milder phenotypes and are thought to lead to KAT6B disorder and underwent targeted KAT6B sequencing. nonsense-mediated decay (NMD) and KAT6B haploinsuffi- Molecular analysis via Sanger sequencing in these cases was ciency.5 Premature termination codons in the last exon or the performed at Baylor College of Medicine (Houston, TX, USA) last 50 nucleotides of the penultimate exon typically cause the or at Sainte-Justine Hospital Research Center (Montreal, QC, messenger RNAs (mRNAs) to escape the NMD pathway and be translated into aberrant proteins with either loss- or gain-of- Table 1 Major clinical features suggestive of GPS and SBBYSS. function effects.14,15 Interstitial 10q21.3q22.2 deletions encom- passing KAT6B have been reported in eight individuals who Major features suggestive of GPS Major features presented with some features overlapping with KAT6B suggestive of SBBYSS disorders, such as hypotonia, developmental delay, feeding • Genital anomalies • Long thumbs/great toes 16 difficulties, and craniofacial dysmorphisms. Of note, Pre- • Patellar hypoplasia/agenesis • Immobile mask-like face iksaitiene et al. reported a 5-Mb 10q22.1q22.3 deletion • Contractures at the hips, knees and/or • Blepharophimosis and/ KAT6B encompassing
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