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Interrupted/bipartite clavicle as a diagnostic clue in Kabuki syndrome

DOI: 10.1002/ajmg.a.38131

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Citation for published version (APA): Haanpää, M., Schlecht, H., Batra, G., Clayton-Smith, J., & Douzgou, S. (2017). Interrupted/bipartite clavicle as a diagnostic clue in Kabuki syndrome. American Journal of Medical , Part A, 173(4), 1115-1118. https://doi.org/10.1002/ajmg.a.38131 Published in: American Journal of , Part A

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Download date:23. Sep. 2021 American Journal of Medical Genetics: Part A

Interrup ted/bipartite clavicle as a Diagnostic Clue in Kabuki Syndrome.

Journal:For American Peer Journal of MedicalReview Genetics: Part A Manuscript ID 16-0645.R2

Wiley - Manuscript type: Clinical Report

Date Submitted by the Author: n/a

Complete List of Authors: Haanpää, Maria; Central Manchester University Hospitals NHS Foundation Trust, Manchester Centre for Genomic Medicine; TYKS, Department of Clinical Genetics Schlecht, Helena; Central Manchester University Hospitals NHS Foundation Trust, Manchester Centre for Genomic Medicine Batra, Gauri; Central Manchester University Hospitals NHS Foundation Trust, Department of Perinatal Histopathology Clayton-Smith, Jill; St Mary's Hospital, Medical Genetics Research Group and Regional Genetics Service; University of Manchester Faculty of Medical and Human Sciences, Institute of Evolution, System and Genomics Douzgou, Sofia; Central Manchester University Hospitals NHS Foundation Trust, Manchester Centre for Genomic Medicine; University of Manchester Faculty of Medical and Human Sciences, Institute of Evolution, System and Genomics

Keywords: bipartite clavicle, Interrupted clavicle, Kabuki syndrome, KMT2D

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John Wiley & Sons, Inc. Page 1 of 17 American Journal of Medical Genetics: Part A

1 2 3 Interrupted/bipartite Clavicle as a Diagnostic Clue in Kabuki Syndrome. 4 5 6 7 M. Haanpää 1,2 , H. Schlecht 1, G Batra 3, J. Clayton-Smith 1,4 , S. Douzgou 1,4*. 8 9 10 11 1 12 Manchester Centre for Genomic Medicine, Central Manchester University hospitals 13 14 NHS Foundation trust, UK Manchester Academic Health Sciences Centre, 15 16 Manchester M13 9WL, Manchester M13 9WL, United Kingdom. 17 18 2 For Peer Review 19 Turku University Hospital, Finland. 20 3 21 Department of Perinatal Histopathology, Central Manchester University Hospitals 22 23 NHS Foundation Trust, Manchester M13 9WL, United Kingdom. 24 25 4 Institute of Evolution, Systems and Genomics, Faculty of Medical & Human 26 27 Sciences, University of Manchester, United Kingdom. 28 29 30 31 32 33 *corresponding author 34 35 Email: [email protected] 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 John Wiley & Sons, Inc. American Journal of Medical Genetics: Part A Page 2 of 17

2 1 Haanpää et al 2 3 Abstract 4 5 Kabuki syndrome is a rare developmental disorder characterized by typical facial 6 7 features, postnatal growth deficiency, mild to moderate intellectual disability and 8 9 KMT2D KDM6A 10 minor skeletal anomalies. It is caused by mutations of the and genes 11 12 while recently RAP1A and RAP1B mutations have been shown to rarely contribute to 13 14 the pathogenesis. We report two patients’ presentation of Kabuki syndrome caused by 15 16 different KMT2D mutations, both including an interrupted/bipartite clavicle. The 17 18 For Peer Review 19 clinical diagnosis of Kabuki syndrome may be challenging, especially in younger 20 21 patients and we suggest that the observation of a bipartite clavicle may be an 22 23 additional diagnostic clue to prompt investigation for Kabuki syndrome. We also 24 25 hypothesize that bipartite/pseudofractured clavicles or other skeletal defects may be 26 27 under-recognized features of the clinical presentation of the 28 29 30 disorders. 31 32 33 34 35 36 37 38 39 40 41 42 43 Keywords: Interrupted clavicle, bipartite clavicle, Kabuki Syndrome, KMT2D 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 John Wiley & Sons, Inc. Page 3 of 17 American Journal of Medical Genetics: Part A

3 1 Haanpää et al 2 3 Introduction 4 5 6 7 Kabuki syndrome (KS; OMIM 147902), first described by Niikawa et al. 8 9 10 [1981] and Kuroki et al. [1981], is characterized by distinctive craniofacial features 11 12 highlyarched and interrupted eyebrows, elongated palpebral fissures with an eversion 13 14 of the lateral third of the lower eyelid, a broad and depressed nasal tip with a short 15 16 columella, downturned mouth with a full lower and a thin upper lip, large and 17 18 For Peer Review 19 prominent ears, mild to moderate intellectual disability, postnatal growth deficiency, 20 21 persistence of fetal fingertip pads, minor skeletal abnormalities and various internal 22 23 organ malformations [Bogershausen and Wollnik, 2013]. 24 25 Kabuki syndrome is a heterogeneous condition and pathogenic mutations in 26 27 KMT2D and KDM6A have been identified by numerous studies. Both KMT2D and 28 29 30 KDM6A, two major components of the ASCOM methyltransferase complex, are 31 32 important for chromatin state and transcriptional activation [Goo et al., 2003]. 33 34 Recently, it has been suggested that the KS pathophysiology overlaps with that of the 35 36 RASopathies, on the basis of the aberrations or dysfunction of the MAPK pathway in 37 38 RAP1A RAP1B 39 both. Mutations in the genes and cause similar craniofacial 40 41 abnormalities and have been recently identified as new KS genes [Bogershausen et 42 43 al., 2016]. Chromatin-modifying enzymes such as KMT2D play a fundamental role in 44 45 cell differentiation during embryonic development and mutations in these genes 46 47 manifest the same anatomical defects such as skeletal changes [Bogershausen et al., 48 49 KMT2D 50 2015]. Mutations in are found in 55-80% of the patients with KS [Banka et 51 52 al., 2012], whereas deletions or mutations of KDM6A are responsible for 9-14% of the 53 54 cases [Miyake et al., 2013b]. 55 56 57 58 59 60 John Wiley & Sons, Inc. American Journal of Medical Genetics: Part A Page 4 of 17

4 1 Haanpää et al 2 3 Skeletal abnormalities occur in about 80% of patients with KS. A patient with 4 5 Kabuki syndrome and bilateral bipartite clavicles compatible with pseudoarthrosis 6 7 was first described by Fryns and Devriendt [1998]. Hinrichs et al. [2002] described 8 9 10 two more patients with KS, one with a right hypoplastic clavicle and the other with a 11 12 bipartite right clavicle including a missing medial third. However, this specific feature 13 14 has not been listed as a component manifestation of KS in OMIM, Orphanet or in 15 16 Genereviews, and many clinicians are unaware of it. Here we report a fetus and a 17 18 For Peer Review 19 young boy who both have this rare feature associated with Kabuki syndrome and we 20 21 review the literature for a similar clinical presentation in other chromo-domain 22 23 remodeling disorders (ChRDs). 24 25 26 27 Clinical reports 28 29 30 Patient 1: 31 32 This was the second pregnancy of a Caucasian, non-consanguineous couple. A 33 34 previous pregnancy resulted in a healthy boy. Antenatal scans showed left-sided cleft 35 36 lip and palate, severe left hydronephrosis with oligohydramnios and normal fetal 37 38 39 growth. There were concerns late in pregnancy about reduced fetal movements with 40 41 the fetus maintaining position between scans with abnormal positioning of the hands 42 43 and feet suspicious for arthrogryposis. On these grounds, the couple opted for 44 45 termination. Consent was given for external examination and full autopsy, post- 46 47 mortem photographs, and genetic testing. Fetal growth parameters at 36 weeks of 48 49 th th 50 gestation were: weight 2.88kg (50 centile, length 50cm (97 centile) and OFC 51 th 52 31.5cm (25 centile). We recognized a facial gestalt characterized by widely spaced 53 54 eyes and long palpebral fissures (Figure 1). There was a left-sided cleft lip and palate 55 56 and apparent brachycephaly. The chest appeared a little short with apparently high-set 57 58 59 60 John Wiley & Sons, Inc. Page 5 of 17 American Journal of Medical Genetics: Part A

5 1 Haanpää et al 2 3 nipples. Limbs, abdomen, external genitalia, anus and back appeared normal. There 4 5 were no contractures, talipes or limb deformities, although there were fetal pads. 6 7 Full autopsy revealed that the right clavicle was incomplete. There was a 8 9 10 lateral piece of clavicle articulating with the acromion and a medial piece articulating 11 12 with the sternum. Both fragments were well corticated, indicating that this was an 13 14 interrupted/bipartite clavicle. Twelve ribs were present on the left side, in contrast to 15 16 11 on the right side. 17 18 For Peer Review 19 20 21 Patient 2: 22 23 A fifteen-month-old boy was referred for a genetic evaluation to determine the cause 24 25 of his poor weight gain and persistent gastro-esophageal reflux. He had been born at 26 27 term with a birth weight of 3.25 kg (50 th centile). Following birth, he was noted to be 28 29 30 hypoglycemic and became jaundiced within 24 hours. He required tube feeding for 31 32 the first day and then established breast feeding. Weight gain was poor, and he 33 34 required treatment with Omeprazole and Domperidone for reflux. He had surgery for 35 36 inguinal hernia and orchidopexy for undescended testes at three months of age and 37 38 39 had recurrent episodes of otitis media requiring antibiotics. A chest X-ray was carried 40 41 out to investigate the possibility of aspiration and revealed some shadowing 42 43 suggestive of infection in the right lung and a bipartite clavicle on the right side 44 45 (Figure 2). He sat at ten months of age and said his first words at 15 months. He had 46 47 good social skills, normal hearing and normal eyesight. On examination, his weight 48 49 th th nd 50 was 8.1 kg (0.4 centile) and occipitofrontal circumference was 44.7 cm (0.4 -2 51 52 centile). He had apparently long palpebral fissures and joint laxity. Small fingertip 53 54 pads were noted. An echocardiogram was normal. 55 56 57 58 59 60 John Wiley & Sons, Inc. American Journal of Medical Genetics: Part A Page 6 of 17

6 1 Haanpää et al 2 3 Mutation analysis and Results 4 5 In both patients, initial microarray analysis was performed on OGT ISCA 8x60K 6 7 oligo array analysed with Cytosure Interpret v4.4.6 software against the GRCh37 8 9 10 Genome build. The average resolution of this array is 180 kb and showed normal 11 12 results. 13 14 In view of the constellation of clinical features, Kabuki syndrome was 15 16 suspected and KMT2D mutation analysis was carried out. DNA was extracted from 17 18 For Peer Review 19 the spleen of patient 1 and from peripheral lymphocytes of patient 2. The coding 20 21 sequence of KMT2D including splice donor and acceptor sites was amplified by long 22 23 range PCR and sequenced on an Illumina MiSeq with a minimum of 100 x coverage. 24 25 Variant calling was carried out using an in-house custom bioinformatics pipeline. 26 27 MLPA analysis was carried out to detect whole exon deletions or duplications. 28 29 KMT2D 30 In the first patient, the c.1452-5T>G variant in intron 44 of gene was 31 32 identified. This variant has not been previously reported in Kabuki syndrome and it is 33 34 not in the HGMD database. Splice site analysis using Alamut v.2.3.5 predicts that this 35 36 variant may affect normal splicing of KMT2D and may therefore be harmful. Parental 37 38 de novo 39 testing showed normal results confirming that this was a mutation in the 40 41 fetus. In the second patient, the heterozygous variant c.6595delT in exon 31 of 42 43 KMT2D was found. This is a frameshift mutation which is predicted to be pathogenic 44 45 and has been reported in a previous patient with Kabuki syndrome [Ng et al., 2010]. 46 47 Parental testing showed that this was a de novo finding. 48 49 50 51 52 Discussion 53 54 Kabuki syndrome is a recognizable syndrome with characteristic facial 55 56 features and various associated symptoms. The diagnosis is usually suspected on 57 58 59 60 John Wiley & Sons, Inc. Page 7 of 17 American Journal of Medical Genetics: Part A

7 1 Haanpää et al 2 3 clinical grounds. Characteristic facial features along with congenital malformations 4 5 (cardiac, renal, ano-rectal, skeletal) can lead to a clinical diagnosis that may be 6 7 confirmed with genetic testing. However, given the evolving phenotype that becomes 8 9 10 more obvious over time, a clinical diagnosis may be challenging in a fetus or newborn 11 12 especially because the characteristic facial features become more evident during 13 14 childhood [Dentici et al., 2014]. In this report, we describe an additional diagnostic 15 16 clue for Kabuki syndrome that proved useful in arriving at a diagnosis in a fetus and a 17 18 For Peer Review 19 young child. 20 21 A bipartite clavicle has been described as a component manifestation of other 22 23 genetic syndromes including chromosomal abnormalities such as chromosome 2q23.1 24 25 and 10p11-12 microdeletion syndromes which may be excluded by microarray 26 27 analysis. Other syndromic conditions where bipartite/pseudofractured clavicles are 28 29 30 part of a variable phenotype are Goltz syndrome (OMIM 305600) that can be 31 32 distinguished because of the cutaneous abnormalities; 33 34 (IRF6 -related disorder) (OMIM 119300) in which lip pits; ankyloblepharon or 35 36 syndactyly usually occur; and the branchio-oto-renal syndrome (OMIM 113650) 37 38 39 which is distinguished by the presence of branchial cysts and/or external ear 40 41 anomalies. Short clavicles with a widened medullar cavity have been described in 42 43 type IX Ehlers-Danlos syndrome [Sartoris et al., 1984]. Other differential diagnoses 44 45 that may be excluded on X-ray are unilateral, congenital pseudoarthrosis of the 46 47 clavicle (OMIM 118980); cleidocranial dysplasia (OMIM 119600) with hypoplastic 48 49 RUNX2 50 or aplastic clavicles caused by gene mutations; mandibuloacral dysplasia 51 52 (OMIM 248370) that presents with hypoplastic clavicles, persistently wide sutures 53 54 and multiple wormian bones; and limb/pelvis-hypoplasia/aplasia syndrome (OMIM 55 56 57 58 59 60 John Wiley & Sons, Inc. American Journal of Medical Genetics: Part A Page 8 of 17

8 1 Haanpää et al 2 3 276820) that is distinguished by severe malformations of upper and lower limbs with 4 5 a severely hypoplastic pelvis. 6 7 Chromatin remodeling is an epigenetic mechanism that controls DNA 8 9 10 accessibility to transcription. The group of disorders of chromatin remodeling is 11 12 increasingly recognized and skeletal defects have been observed as part of the 13 14 phenotypic spectrum of genetic syndromes caused by mutations in genes that interact 15 16 in chromatin remodeling complexes. Floating-Harbor syndrome (FHS) (OMIM 17 18 For Peer Review 19 136140) is one of these disorders and is characterized by typical craniofacial features, 20 21 short stature, delayed osseous maturation, expressive-language deficits, and skeletal 22 23 anomalies caused by mutations in the SRCAP . Pseudoarthrosis of the clavicle has 24 25 been seen in several individuals with FHS [Hood et al., 2012]. Coffin-Siris syndrome 26 27 (CSS) is characterized by development delay of varying degree, distinctive facial 28 29 30 features, , feeding difficulties and hypoplasia/aplasia of the fifth fingernails. 31 32 One patient with CSS has been described with hypoplastic clavicles in the lateral 33 34 portions of both sides [Schinzel, 1979]. Like KMT2D , SRCAP and the genes causing 35 36 CSS are chromatin-remodeling factors. Although clavicular anomalies have not been 37 38 39 reported in other conditions caused by chromatin remodeling genes, skeletal 40 41 anomalies occur in many. For example, absent patellae occurs in the KAT6B- 42 43 associated disorders [Gannon, et al., 2014] and Weiss et al. [2016] recently described 44 45 CHD4 mutations causing an intellectual disability syndrome with dysmorphism and 46 47 skeletal anomalies, including vertebral fusions and tarsal coalition. CHD4 is a core 48 49 50 component of the nucleosome remodeling complex. 51 52 In KS numerous de novo mutations have been described and mutations are 53 54 distributed throughout the gene. The large majority of the mutations are nonsense or 55 56 frameshift. Most identified mutations are truncating, likely leading to 57 58 59 60 John Wiley & Sons, Inc. Page 9 of 17 American Journal of Medical Genetics: Part A

9 1 Haanpää et al 2 3 haploinsufficiency. Splice-site mutations are responsible for about 9% of pathologic 4 5 allelic variants in KMT2D [Bogershausen and Wollnik, 2013]. The mutation found in 6 7 the fetus has not been previously reported and is not found in human mutation 8 9 10 databases, but it is likely to be pathogenic as it is predicted to affect a splice site. 11 12 Some physical features are present more commonly in patients with KS and a KMT2D 13 14 mutation compared to clinically diagnosed patients without a KMT2D mutation 15 16 [Makrythanasis et al., 2013], however correlations between mutation type and the 17 18 For Peer Review 19 phenotype have not yet been definitely established [Miyake et al., 2013a]. There are a 20 21 few patients with bipartite clavicles described in the literature, but specific details of 22 23 their mutations are not known. Both of our patients had mutations, albeit different 24 25 ones, in the most common KS gene KMT2D . It will be interesting to see whether there 26 27 is a correlation between a bipartite clavicle and mutations in KMT2D . 28 29 30 In conclusion, the spectrum of clinical features in Kabuki syndrome is wide 31 32 and diagnosis can be difficult in very young patients. There have not been previous 33 34 observations of Kabuki syndrome in a fetus with bipartite clavicle and therefore this 35 36 report further expands the phenotypic spectrum and clinical variability of Kabuki 37 38 39 syndrome. Moreover, this report proposes that bipartite clavicles may be, amongst 40 41 other skeletal abnormalities, a diagnostic clue for syndromes caused by mutations in 42 43 chromatin-remodeling genes. 44 45 46 47 Conflict of interest 48 49 50 The authors declare no conflict of interest. 51 52 53 54 Acknowledgements 55 56 We would like to thank the families for consenting to publication. 57 58 59 60 John Wiley & Sons, Inc. American Journal of Medical Genetics: Part A Page 10 of 17

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14 1 Haanpää et al 2 3 Hiraki Y, Kitanaka S, Matsubara Y, Makita T, Taguri M, Nakashima M, Tsurusaki Y, 4 5 Saitsu H, Yoshiura K, Matsumoto N, Niikawa N. 2013a. MLL2 and KDM6A 6 7 mutations in patients with Kabuki syndrome. Am J Med Genet A 161A:2234-2243. 8 9 10 Miyake N, Mizuno S, Okamoto N, Ohashi H, Shiina M, Ogata K, Tsurusaki Y, 11 12 Nakashima M, Saitsu H, Niikawa N, Matsumoto N. 2013b. KDM6A point mutations 13 14 cause Kabuki syndrome. Hum Mutat 34:108-110. 15 16 17 Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, 18 For Peer Review 19 Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, Smith JD, Rieder 20 21 22 MJ, Yoshiura K, Matsumoto N, Ohta T, Niikawa N, Nickerson DA, Bamshad MJ, 23 24 Shendure J. 2010. identifies MLL2 mutations as a cause of Kabuki 25 26 syndrome. Nat Genet 42:790-793. 27 28 29 Niikawa N, Kuroki Y, Kajii T, Matsuura N, Ishikiriyama S, Tonoki H, Ishikawa N, 30 31 Yamada Y, Fujita M, Umemoto H. 1988. Kabuki make-up (Niikawa-Kuroki) 32 33 syndrome: a study of 62 patients. Am J Med Genet 31:565-589. 34 35 36 Niikawa N, Matsuura N, Fukushima Y, Ohsawa T, Kajii T. 1981. Kabuki make-up 37 38 syndrome: a syndrome of mental retardation, unusual facies, large and protruding 39 40 ears, and postnatal growth deficiency. J Pediatr 99:565-569. 41 42 43 Paulussen AD, Stegmann AP, Blok MJ, Tserpelis D, Posma-Velter C, Detisch Y, 44 45 Smeets EE, Wagemans A, Schrander JJ, van den Boogaard MJ, van der Smagt J, van 46 47 Haeringen A, Stolte-Dijkstra I, Kerstjens-Frederikse WS, Mancini GM, Wessels MW, 48 49 Hennekam RC, Vreeburg M, Geraedts J, de Ravel T, Fryns JP, Smeets HJ, Devriendt 50 51 52 K, Schrander-Stumpel CT. 2011. MLL2 mutation spectrum in 45 patients with 53 54 Kabuki syndrome. Hum Mutat 32(2):E2018-2025. 55 56 57 58 59 60 John Wiley & Sons, Inc. Page 15 of 17 American Journal of Medical Genetics: Part A

15 1 Haanpää et al 2 3 Sartoris DJ, Luzzatti L, Weaver DD, Macfarlane JD, Hollister DW, Parker BR. 1984. 4 5 Type IX Ehlers-Danlos syndrome. A new variant with pathognomonic radiographic 6 7 features. Radiology 152:665-670. 8 9 10 Schinzel A. 1979. The Coffin-Siris syndrome. Acta Paediatr.Scand. 68:449-452. 11 12 13 Weiss K, Terhal PA, Cohen L, Bruccoleri M, Irving M, Martinez AF, Rosenfeld JA, 14 15 Machol K, Yang Y, Liu P, Walkiewicz M, Beuten J, Gomez-Ospina N, Haude K, 16 17 Fong CT, Enns GM, Bernstein JA, Fan J, Gotway G, Ghorbani M, DDD Study, van 18 For Peer Review 19 Gassen K, Monroe GR, van Haaften G, Basel-Vanagaite L, Yang XJ, Campeau PM, 20 21 22 Muenke M. 2016. De Novo Mutations in CHD4, an ATP-Dependent Chromatin 23 24 Remodeler Gene, Cause an Intellectual Disability Syndrome with Distinctive 25 26 Dysmorphisms. Am J Hum Genet 99:934-941. 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 John Wiley & Sons, Inc. American Journal of Medical Genetics: Part A Page 16 of 17

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 For Peer Review 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 Figure 1. Facial features of the fetus.

48 457x609mm (180 x 180 DPI) 49 50 51 52 53 54 55 56 57 58 59 60 John Wiley & Sons, Inc. Page 17 of 17 American Journal of Medical Genetics: Part A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 For Peer Review 19 20 21 22 23 24 25 26 27 28 Figure 2. Chest X-ray shows a bipartite clavicle on the right side. 29 30 244x155mm (300 x 300 DPI) 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 John Wiley & Sons, Inc.