University of Groningen

De novo variants in CDK13 associated with syndromic ID/DD van den Akker, W. M. R.; Brummelman, I.; Martis, L. M.; Timmermans, R. N.; Pfundt, R.; Kleefstra, T.; Willemsen, M. H.; Gerkes, E. H.; Herkert, J. C.; van Essen, A. J. Published in: Clinical Genetics

DOI: 10.1111/cge.13225

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Citation for published version (APA): van den Akker, W. M. R., Brummelman, I., Martis, L. M., Timmermans, R. N., Pfundt, R., Kleefstra, T., Willemsen, M. H., Gerkes, E. H., Herkert, J. C., van Essen, A. J., Rump, P., Vansenne, F., Terhal, P. A., van Haelst, M. M., Cristian, I., Turner, C. E., Cho, M. T., Begtrup, A., Willaert, R., ... Schuurs-Hoeijmakers, J. H. M. (2018). De novo variants in CDK13 associated with syndromic ID/DD: Molecular and clinical delineation of 15 individuals and a further review. Clinical Genetics, 93(5), 1000-1007. https://doi.org/10.1111/cge.13225

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Download date: 30-09-2021 This articleisprotected bycopyright.Allrightsreserved. Accepted Article Netherlands, Centre Utrecht, Utrecht, TheNetherlands, Utrecht, Centre Utrecht, Genetics,Maastricht University Ho Terhal Johanna C. Herkert Johanna C. 20877, USA, 20877, USA, other conflict ofinterest. anynot awareof We are employeesof GeneDx. are Willaert and R. Cho, A.Begtrup, M. interest Conflict of Stegmann # z a National Military Medical Center, Bethesda, Maryland, USA, Center,Bethesda,National MilitaryMedical Maryland, Willem M.R. van M.R. Willem den Akker Timmermans Washington University School of Medicine, St. Louis, Missouri, USA, USA, Missouri, St.University Louis, Medicine, Washington School of Florida,USA,Children's Orlando, Hospital Orlando, The Netherlands, Groningen, [email protected] 9101, 6500 HB, TheNetherlands. Tel.00 31 243613946 Univ Department ofHuman Genetics,Radboud Begtrup Netherlands, Equal contributionEqual Corresponding author: Janneke H.M. Schuurs-Hoeijmakers MD, PhD. MD, PhD. Corresponding author:Janneke H.M.Schuurs-Hoeijmakers Genetics, ofHuman Radboud Univ Department

molecular andclinicaldelineation article as doi: 10. differencesbetween version lead to this may been through the copyediting, typesetting, pagination andproofreading process, which This article hasbeen accepted for publication andundergone full peer review but has not De novo c , Mieke M. van Haelst g , RebeccaWillaert i , BertB.A.deVries az h e b Division ofGenetics Genomic and Medicine, DepartmentofPediatrics, Division ofGenetics Metabolism,Department and ofPediatrics, Nemours ofGenetics, UniversityDepartment Center University of Medical Groningen, , Rolph Pfundt Running title: variantsin b , Anthonie J. van Essen, Anthonie J. 1111/cge.13225 All contributors have read and approved the submission to the journal. † Deceased

g a , Emily Fassi , Emily , Iris Brummelman cd

a De novo CDK13variants associated with ID/DD a , IngridCristian , TjitskeKleefstra andJanneke Schuurs-Hoeijmakers H.M. CDK13 spital, Maastricht, The Netherlands spital,Maastricht, TheNetherlands h associated with associatedwith , Koen L.I.van, Koen Gassen c review review Department of Genetics, University Medical University ofGenetics, Department d

AMC/VUmc, Clinical Genetics,Amsterdam,AMC/VUmc, The Clinical b† e , Patrick Rump , ClessonE. Turner az

ersity Medical Center, Nijmegen, PO Box Medical ersity a , Lavinia M. Martis Lavinia , ersity Medical Center, Nijmegen,The ersity Medical

, Marjolein H.Willemsen Marjolein , of 15individualsandafurther and the Versionof Record. Please cite this f Department of Genetics, Walter Reed Department ofGenetics, g b GeneDx, MD Gaithersburg, , FleurVansenne syndromic ID/DD; c , Alexander P.A. , Alexander f az , MeganT.Cho , Renée N. i Department ofHuman Department a# a

, Erica H. Gerkes b , PaulienA. g , Amber b , This articleisprotected bycopyright.Allrightsreserved. Accepted Article Facial Dysmorphism, Keywords IDsyndrome. ofthis described management recently testing Basedonthisis needed. overview work-up we clinical suggestionsand provide for à vue diagnosis of this syndrome and t vue and à diagnosis ofsyndrome this clinicallybe a recognizable facial appearance. endhave ofat the domainmight thekinase a obvious genotype-phenotype although twoindividuals codons correlation, harbouring astop an anddoesis provided ofallnotdemonstrate An publishedcases individuals. overview known cohort, thecurrent42%ofall butinatleast of individuals intwo were present problems,variety (neonatal) hypotonia and a of characteristics of the individuals includemild to severe delay, ID,developmental behavioural transcripts inlymphoblastoidcells from an in recurrentvariant. frame-shift demons We the domain ofCDK13. wedescribe Furthermore, twononsensevariants and a novel report and fifteen individuals of assessment clinical defectsassociatedcongenital andintellectualwithheart disability Here,wepresentthe (ID). De novo Abstract variants in the encoding -dependentbeen gene (CDK13) have inkinasethe 13 variants : CDK13 , Congenital HeartDefects,

Intellectual Disability, Splice-site variant, Whole-Exome Sequencing Sequencing Whole-Exome variant, Splice-site Disability, Intellectual herefore genome-wideor trate the synthesis of two aberrant thesynthesis oftwo trate milderphenotype. Overall seems there notto facial dysmorphism. Congenital heart defects Congenital defects dysmorphism. facial heart The variabilityThe the phenotypesimpedes an in dividual with a splice-site variant. Clinical Clinical splice-sitevariant. dividual witha de novo de novo de variants gene-panel driven genetic missense variants within , Developmental Delay, Delay, Developmental CDK13

This articleisprotected bycopyright.Allrightsreserved. Accepted Article the syndromic phenotypicof spectrum individuals with with the 25previously reported individuals, enables us to provide animproved description of variantsfor the firsttimenonsense we describe in individuals with In the present study, we performed a clinical evaluation of fifteen previously unreported on 13previously individuals reported (5,7). update on16cases,which (8) provideincludedan clinicalinformation colleagues extensive recurrentvariant (p.Asn842Ser)reportedinseven non-relatedindividuals. Hamilton and is of note allthat reported variants in that study are developmental delay(DD)/ID,def heart congenital

Bostwick characteristics oftheseindividualsincluded reported from the Deciphering Disorders Developmental projectCommon phenotypic (7). among otherfeatures. delay, variousdisability facialdevelopmental intellectual and motor (ID)and dysmorphisms defects, mainly of the ventral atrial and septa (6).In addition, theseindividuals showed reported (5-8).Sifrim andcolleagues describe seven individuals with congenital heart Recently, splicingRNA (2,3)anditsmousehomologue regulates of elongation (4). axonal phosphorylation of RNApolymeraseII(1). Furt conjunction with cyclinK, a complex protein kinase.serine/ Thiskinase uses ATPas source of phosphate groupsandin forms, CDK13 (cyclin-dependent kinase 13,OMIM et al et de novode . (5)describe nineindividuals, another showing asimilarphenotypewith de novo de missensevariantslocated inthekinasedomain of

A further six female individuals with individuals A further six female

CDK13 variants. Importantly, inadditionnovel missense variants, to whichregulates positively transcription through ID and dysmorphic facial characteristics. 603309)isaubiquitously expressed hermore, CDK13isinvolvedin alternative ects, hypotonia and facial dysmorphisms. It It facial dysmorphisms. ects,hypotonia and CDK13 de novo de novo . This extended cohort, combined de novo variants in in variants missense variants, missense withone

CDK13 CDK13 CDK13 variants were were variants have been have been . This articleisprotected bycopyright.Allrightsreserved. Accepted Article identificationindividuals offour with 10) resultedin Genetics attheTheNetherlands) (9,the Radboudumc (Nijmegen, Human of attheDepartment (-WES) sequencing child-parents whole-exome Clinical andexaminationvariantsRecruitment ofindividualsCDK13 with Individuals andmethods sequencing according to standardaccording to protocols.sequencing of cyclohexamide. wereculturedinthepresence/absence that fromcells isolated was mRNA mediated decay, followingtransformation standard procedures(13) linesbloodvirusfrom peripheral byEpstein-Barr weregenerated cells cell lymphoblastoid To study the effects of a splice-sitevariant in intron 7 of mRNA analysis shown clinical photographs. InformedArnhem-Nijmegen NL36191.091.11). consent of the Radboud University Medical Center (CommissieMensgebonden Onderzoek Regio their naturalhistory reviewed. studyThis was approved was by the institutional board review Allindividualshttp://gnomad.broadinstitute.org/). wereexamined by aclinical geneticist and fromaswell theExAc database(12) as All NM_003718.4. andhere previously reportedvariantsreported Table absent (Suppl 3)are and the United States ofAmerica. The reference sequence used for in sequencing different exome undergone clinical in individual was identified by single-case WES. Ten additional individuals with monozygotic twinandsamevariant detected insister by the re-sequencing. was her Another CDK13 wererecruited baseda‘genotype-first on GeneMatcher approach’and had via (11) CDK13 mRNA was mRNA analyzedbythesynthesis Sanger ofcDNAand de novo the extended version of this database (gnomAD,

variants in . To checkfortheoccurrence ofnonsense- geneticlaboratories in TheNetherlands was obtained for publication wasobtainedforofthe CDK13 CDK13 in mRNA from Individual 10, inmRNA . One is individual a

CDK13 de novo is RefSeq isRefSeq variants This articleisprotected bycopyright.Allrightsreserved. Accepted Article mutant transcripts mutant transcripts were apparently notaffected by decay. nonsense-mediated It is of note variant, 8andweremissingexons while9 thereadingin framewasconservedexon 10. The splicecryptic sitein exon 8leading toan was present,thewild-type supposedly derivedfrom Individual Thecorrectly Three differenttranscriptsspliced(Fig.1B). mRNA 9. weredetected downstreamfrom im mRNA region of exon 6 was predicted tointerfere with the correct splicing ofintron7. To test this, weanalysed the acceptor variant c.2601-2A>G detected in the monozygotic twin pair (Individuals9 and10) splice- site isused.The analternative translational start that possible transcript itisalso but involve alower protein productionin the cell ofnonsense-mediatedbecause decay of this The consequence ofthisvariantindividuals. The frame-shiftvariantc.484dup leading to p.Ala162fs was observedin threeindependent mediated of decay the transcriptsmight occurleading to a clearin reductionproteinlevel. protein.nonsense-Alternatively, the third of missing one by CDK13 adysfunctional result in c.3073C>T,arep.Arg999* expectedto and p.Arg1025*) nonsense variants (c.2995C>T, anticipated tobe deleterious by different pr were conserved highly regionsCDK13 and missensevariants affect evolutionary of (aa833-845)(6),wasobservedin fiveofthe fifteenindividuals. all Taken together, regionATP-binding (aa711-734)(Fig.1A). The p. of CDK13(aa697-1029),which twoarein (p threevariants, novel, which are missense alllead in of to changes theproteindomain kinase Thefourdifferent Individualwere not availablefortesting. parents13 of the individual; present among thiscohort.Thevariants were shownto have occurred 1). Inaddition to missense variants, nonsense variants and asplice-acceptorvariant were Genetic characterisation Results We identified abroadrangeWe of CDK13 out-of-frame coding sequence. In the third splice out-of-frame coding sequence. Inthe thirdsplice ediction Table algorithms (Supp. 2). The two on on protein synthesis is notknown andmight variants amongthe fifteenindividuals (Table mortalised lymphoblastoid cells derived from cellsmortalised lymphoblastoid derived from .Gly714Asp) orclose to (p.Arg737Cys) the Asn842Ser substitutionAsn842Ser within kinase- the CDK13 allele. Another transcript allele. Another useda de novo in all but one This articleisprotected bycopyright.Allrightsreserved. Accepted Article phosphorylation activity of CDK13. None of thereported of CDK13.None phosphorylation activity Phenotypic characterisation ExAC/gnomAD databases. that all common (9/13). Furthermore, gynaecomastia was seen in three of the six male individuals. It It individuals. seen inthreeofthesixmale was common Furthermore, gynaecomastia (9/13). hypotoniccharacterized bya posturewithsl relativeshort statue(-1.75 SD). The individuals general some was appearance of SD) and showed microcephaly (-2.5 whereas twoindividuals inthreecases, was present (>2.5SD) Macrocephaly andstrabismus. blepharophimosis abnormalities, included philtrum ten individuals. Variable dysmorphic facial wereseen inmostfeatures individuals and (Fig.2) obesity (14),therebyexplainingin herhyperphagiaoverweight. wasand Hypotonia reported melanocortin 4 receptor, and variants of CDK13 Individual(Individuals in reported. tothe2, 7,11,13)hyperphagia 11had, addition was cases four Notably, in mostly neonate. (10/15), as frequently reported were problems developed speechattheir theages lastexamination medical at and11 years. of8 Feeding (Individual commonly reported Speech (7/8)andtwoindividualshadnot 3). were problems leukodystrophy(Individual 5),periventricular(Individual malformation 8)andChiari oftheputamen ofpart of focal atrophy consisting MRI, have cerebral anomalies on (2/15). Not allindividuals underwent spectrum disor diverse, autism included and but IQ measurement showed a score of85.Behavioural problems were frequent and 14 displayedDDandbehaviouralproblems Individual severeID. had although Individual 5 and/or ID(15/15). The degree ofIDvariablewas and varied mostly mild from to moderate, 1). Extensive clinical descriptions givenare in and13 Individuals 5 wereexamined(Table attheageof22and54, respectively y), whereas The oftheindividualsmajority were examined (96male) at ayoung female, age (<14 variant, apaternallyinherited frame-shift variant of CDK13 variants seemtoaffecttheprotein

cerebralimaging butIndividuals 3,5,8wereshown to this gene are associated with hyperphagia and withhyperphagia are associated gene this ders (5/15), ADHD (4/15) andders ADHD(4/15) hyperactivity (5/15), Supp. Table 1. AllDD Table 1. Supp. individuals displayed oping shoulders (6/14) andflatfeetwere kinase domain and this likely disturbsthe likely kinasedomain andthis CDK13 variants werepresent in the MC4R , encoding for the encoding , This articleisprotected bycopyright.Allrightsreserved. Accepted Article al 43%). (17/40,Bostwick Interestingly, syndrome both CDK13 the with in individuals variant encountered this mostfrequentlyOvervariantsis far, the havethe beenreported so that all p.Asn842Serthe recurrent foundinfivecases.variant substitution to missensewas leading milder showa phenot might the kinase domain, phenotype correlation individuals although 15 14and harboringcodona stop atthe end of Discussion at theageof 24y. show screening ofIndividualarteriosus. 5 Cardiac defects; 6hadanatrialheart Individual defectseptum andIndividual 9hadapatent ductus 9 outof in performed was Echocardiography whethertheis breast tissue unknown was addition nonsense and frame-shift variantsin inwe describe here 3). Notably, Table (5-8)(Suppl. werereported and onesplice-sitevariant publicationsIn previous onindividuals with Spectrum ofreportedvariants including ID/DDwithbehavioural prob alsokinasedomain. individuals affectthischaracteristics The sharedphenotypic several and theactivesiteof thekinasebinding site of protein, the CDK13 and more variantsspecifically, cluster mostlyin andclose to the ATP domain thekinase in all cluster is thatthey variants the missense interesting observation of for one not individual available were for the parents Atesting. common characteristic and in variants unreported individuals with characteristics themolecularWe evaluated previously clinical phenotypes offifteen and . (5) and Hamilton. (5)and

et al . (8) report another variant. (8)report at this amino positionacid (c.2525A>G, lemsvarious and dysmorphisms. facial CDK13 CDK13 domain. The truncating and splice-site variants splice-sitevariants and domain.The truncating CDK13 13 individuals. Two individuals had congenital congenital had Two individuals 13 individuals. , of which fourteen wereproven whichfourteen , of glandular oforigin orabenign fat deposit. ype. Among our groupoffifteenindividuals, ype. Among ed borderline dilation of the right ventricle oftherighted borderline dilation variants,variants onlymissense (n=24) . We could notdetect a clear genotype- de novo , and , and et This articleisprotected bycopyright.Allrightsreserved. Accepted Article database include individuals withseve does not sense andtwoframe-shiftvariants variants 2017)non- contains high-confidence the gnomADdatabase (November, nine noted that suppor which (15), Genomic Variants Database of entire the including copy-number losses variants are as well expected to result in haploinsufficiency the result of to well expected asvariants are variousof the Functional experiments might deeperinsiprovide Furthermore,Hamilton etal.(8)performed tolerated within domain. thekinase individuals healthy regions proteinamong ofthe incomparison withCDK13 variation thereductiondomain other of in genetic in thekinase locate as in thekinase domain all other reported missense variantsmarkeddo. The variantsleading top.Arg737Cysan domain. The whichp.Asn842Asp) introduces anegative in charge theactive siteproteintheof kinase missense mutations located in the genotype-phenotype that(someof)the currentlyit correlation.is stillfeasible However, a not observe could we that might explain model a haploinsufficency variants, and genetic of This observation might suggest that there is models Mechanistic the kinase regionof CDK13 (Supp. Table 1andFig. 2). indistinguisha nonsensevariants clinically were ofthekinaseImportantly,terminal end with theseindividualsdomain. theframe-shift and p.Ala162fs) andwedescribeindividualswithnon-sensevariantsat theC- two located report threeunrelatedindividualswe with negative mechanism, althoughthis is not substantiated by functional studies. In this study, insight intomolecular thepossible basis of gain toinvestigate andto theeffectof protein variantsCDK13structure modelling on de novo variants in in variants CDK13 CKD13 kinase domain have a dominant negative effect. have adominant kinase domain negativeeffect. pathogenicity. Theauthors pathogenicity. presume adominant . a similar mode of actiona similar mode betweenthe twogroups

CDK13 (of which twice).(of ThegnomAD oneispresent The here reported frame-shift and non-sense The herereported frame-shift andnon-sense an identical frame-shift variantan identicalframe-shift (c.484dup, ble from those carrying missense variants in in ble fromthosecarryingvariants missense d p.Arg880Cys were not reported before and d p.Arg880Cys reportedbeforeand werenot re paediatric disease, but mild phenotypes phenotypes re but mild paediatric disease, ght into the precisemolecular mechanisms (12), indeed suggests that little variationis (12), indeedsuggeststhatlittle ts a haploinsufficiency mode of action. ts a modeofaction. It ishaploinsufficiency gene are strikingly absent from the genearestrikingly absent from CDK13 gene. In addition, gene.Inaddition, in silico

This articleisprotected bycopyright.Allrightsreserved. Accepted Article identified among theirwith sevenidentified individuals among cohort defects individuals) withselectedcongenital forindividuals heart (1,891 colleagues and not reveal consistencyfa didvariants of the most features. frequently reported Stratification of theindividuals accordingto their genetic the individuals,withthin lips, lid abnor eye shoulders (inpresentvarietystudy, 43%). A of facial dysmorphisms frequentlyare in seen hypotoniais the possiblyreflected high by observed more than in 75% of the individuals,mostly at theneonatal stage. Post-neonatal different reports. performedinallindividuals. Hypotonia Cerebral wasnot is imaging behavioural aspects. Thefrequency ofstruct varietybehavioural byaof accompanied genotype-phenotypeis inall is correlation.present ID/DD individuals mostly and variantsgene specificand aclinical phenotype.study Our does thereforenot support aclear areAs reviewed. previouslymentioned, thereis correlationno obvious specific between andthosereportedpreviouslyindividualstotalin thisstudy 2713male (5-8).In female and In Table1,we presentoverview an ofthemain Clinical spectrum andsuggestions forclinical practise kinase domain ofCDK13andabrogateitscatalytic function. of kinase domain in the individuals. Therefore, based onour current dat of interestincluded.the concerned be Itwould toexploremight bemedical history of the natural course of thisnatural courseof syndrome.The i closelymonitor the identified currently group of individuals to improve description of the individualsinvestigatedage theoffourteen), are youngchildren werecommendto (below with newly discovered studies16/38 (42%),Table2) all (over as well haddefects. theotherindividuals septalIn studies,wereobserved congenital heart defects CDK13 CDK13 variants inthe clinical work-up.Because of most the lead lead to astructural functionalof the and/or deformation dentification of individuals with ofindividuals dentification this cial appearance per variant (Table 2).Sifrim and malities andabroadnose/nasalas bridge the problems, althoughnot all studies report on . We suggest echocardiography for individuals suggest echocardiography for We . incidence of pesincidence of planus (9/13)and sloping a, we hypothesize thatthe variants missense ural anomalies varied brain between the clinical features of the individuals featuresofthe clinical described de novo variants in CDK13 CDK13 (6). All these syndrome This articleisprotected bycopyright.Allrightsreserved. Accepted Article studies (5, 8)reported a recognisable facialgestalt their among individualswith heart defects, andbehaviouralmost features. hypotonia asthe problems frequent Previous intellectualdo showasyndromic disability phe social aspect of social aspect current research.We concludethatindividualswith inhas theformationmeanwhile resulted of panel analysis (including CDK13 needed. Language delay proactivespeech therapy.clinical requires As recognition ofthe specialrequires attention,close monitoring enabling early intervention tosupport feeding if increased seizurerisk. Thehighincidence cardiacandneurologi assessment should include, management.Earlysuggestions forclinical work-upand thefollowing we provide current Based onthe clinicalof findings all cases, (www.humandiseasegenes.com). reported additional individuals that will identified years over be thecoming novo variation seems todivert further. with diagnosis. Also, clinical theincreasingnumberofindividualsdescribed, although the facial phenotype might notbe specific norconsistent enoughtoenable àvue studyvariants. Our confirms thepresence ofdysmorphic featuresinallindividuals, facial variants of syndrome will challenging, be agenotype- CDK13 we established a website tocollect detailed clinical information of CDK13

), will in), newsyndrome. becrucial diagnosing this To withfurther delineate theclinical associated spectrum ofhypotonianeonataland feedingproblems parent groups on social groups on media, animportant social parent notype, with facial dysmorphisms,congenital notype, with first WESorIDgene approach, byeither c evaluation withspecialc evaluation attention for de novo

CDK13 variants variants CDK13 de de

This articleisprotected bycopyright.Allrightsreserved. Accepted Article 917-86-319 and912-12-109and Development toB.B.A.d.V.). (ZON-MWgrants Research Health bythe Dutch Organization for supported is financially study analysis. This Center, Nijmegen, forgenerating the lymphobl we appreciatethesupport of theDepartmen theirparen We aregrateful toallindividuals and Acknowledgements t of Human Genetics,Radboud University ts for participatingin this study. Furthermore, astoid cell lines and performing mRNA linesastoid cell performing mRNA and This articleisprotected bycopyright.Allrightsreserved. Accepted Article mutation in presently reported and published individuals andtranscript (5-8), analysis of a splice-site Fig. 1. legends Figure protein arederived fromKohoutekand Blazek,2012(16). of transcriptTheNM_003718.4. functionaldomains the indicated based wild-type on the studiesthose reportedinearlier depicted below are theprotein inblue. Numbering ofaa is instudyCDK13variants.red and this areshown aboveproteinin Thevariantsthereported Disability. and/or Intellectual Supplementary TableReported 3. Supplementary TableLocation conservation 2. and ofmissense variants in Supplementary TableofindividualsClinical features 1. variantsin with information Supporting Fig. 2. tothedeletion of60aa’swhichkinase theencoded leads intheof protein. domain one, exons8 and9 are skipped and in exon 10t second c.2620,whereasinthe atposition sitesplice-acceptor is used transcript, cryptic a whereas twoother transcriptsa consequence are variant.splice-acceptor The wild-type transcr the c.2601-2A>G with 9 fromIndividual derived cells lymphoblastoid transcripts in detected Facial features of individuals Facialfeaturesof with Localisation oftheamino-acid (aa) residuesubstitutions inCDK13 protein ofall the CDK13 . (a) Schematic localisationof allpresently andearlier Schematic reported . (a)

CDK13 de novo variants associated with Developmental Delay variants with associated Developmental Delay ipt is presumably from the unaffected allele, ipt isthe unaffectedallele, from presumably variants in in variants he wild-type open-reading frameisused, of the splice-acceptor variant.of thesplice-acceptor thefirst In CDK13 (b) Overview ofthevarious presented in presented this study. CDK13. CDK13

. de novo

This articleisprotected bycopyright.Allrightsreserved. Accepted Article 10. Lelieveld SH, Reijnders MR, Pf MR, Reijnders SH, Lelieveld 10. with persons in sequencing exome Diagnostic al. BonBWet MH, van J,Willemsen Ligt de severeintellectual disability. EnglN J Med 2012:367: 1921-1929. 9. 2017. Med Genet MJ,al Canham Net Hamilton RC, Caswell J disability. intellectual and delay developmental of form syndromic a cause of CDK13 domain kinase 8. Prevalen S. Disorders Developmental Deciphering 542: 433-438. Nature 2017: disorders. developmental 7. 1060-1065. and syndromic for architectures genetic Distinct al. A et MP,Wilsdon Hitz A, Sifrim identified defects congenital heart nonsyndromic 6. 9: 73.disorders. Genome Med2017: of CDK13- characterisation molecular and al.Phenotypic PoseyJE et S, McLean BL, Bostwick developmental intellectual and features facial dysmorphic defects, heart related congenital 5. 21. a through elongation axonal regulate Cdk13 and Cdk12 et al. CK GT,Huang Lin HR, Chen Cdk5ex signalingpathway thatmodulates common 4. 2158-2172. maintains complex K/Cdk12 Cyclin The al. K et Bartholomeeusen J, D,Kohoutek Blazek 25: 2011: Dev genes. response damage of DNA expression of regulation via stability genomic 3. cellula and Molecular processing. 12 kinase cyclin-dependent human of Characterization etal. JM X, Gilmore K,Gao Liang domain C-terminal in complexes CDK13 and (CDK12) 2. GreifenbergAK, HonigPilarova D, K et al. Structuraland Functional Analysis ofthe 2016:14: 320-331. reports Cell Cdk13/Cyclin K Complex. 1. References Kohoutek J, Blazek D. Cyclin Kgoes with Cdk12and Cdk13. Cell division 2012: 7: 12. 16. MacDonald JR, Ziman R, YuenRK et al. The Database of Genomic Variants: a curated D986-992. 42: 2014: Res Acids Nucleic genome. human in the variation structural of collection 15. Clinical al. GS et Yeo JM, Keogh IS, Farooqi melanocortin 4 receptor gene.Engl N JMed 2003:348: 1085-1095. 14. 197-204. 10: fibroblasts.2006: MolDiagn Ther and for genes 12 reference of H.Comparison H,Kremer van Bokhoven Brouwer de AP, lines cell lymphoblastoid virus-transformed in Epstein-Barr levels expression of gene normalization 13. LekM,Karczewski KJ,Minikel EVal.Analysiset ofprotein-coding genetic variationin 60,706 285-291. 536: 2016: humans. Nature 12. Sobreira F,ValleDetal. N,Schiettecatte interest withan in sa the investigators 11. 19: 1194-1196. 2016: Nat Neurosci disability. intellectual for new genes 10 r biology 2015: 35: 928-938. 928-938. 35: 2015: r biology undt R et al. undt Ret Meta-analysis of2, me gene. HumMutat 2015:36: 928-930. GeneMatcher: a matching tool for atool matching connecting GeneMatcher: . Heterozygous mutations affecting the protein affecting the mutations Heterozygous . by exome sequencing. Nature genetics 2016: 48: 48: 2016: Naturegenetics sequencing. exome by spectrum of obesity andinthe ofmutations obesity spectrum pression. Experimental neurology 2014: 261: 10- 261: 2014: neurology Experimental pression. phosphorylation, gene transcription, and RNA RNA and transcription, gene phosphorylation, ce and architecture of de novo mutations in in mutations novo de of architecture ce and 104 trios provides support for for triosprovides support 104 (a) 1 Fig.

1

This articleisprotected bycopyright.Allrightsreserved. Accepted(2x)p. Gly717Arg p.Gly714Arg Article p.Ala162fs (3x) p.Val719Gly 697

p.Gly714Asp ATPsite binding

p.Lys734Arg p.Lys734Glu

p.Arg737Cys p.Arg751Gln

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p.Asn842Asp (2x) p.Asn842Ser (12x) p.Asn842Ser (5x) Active site CDK13protein variants

c.2601-

p.Arg860Gln Kinase

p.Val874Leu p.Arg880Cys

2A>G (2x) p.Asn896Asp

domain

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p.Arg999*

p.Arg1025*

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1512 1 Fig.

AcceptedThis articleisprotected bycopyright.Allrightsreserved. Article (b) Exonic

transcripts Detected

structure

7 7 7 7

CDK13 - c.2601 8 10 * 8

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AcceptedThis articleisprotected bycopyright.Allrightsreserved. Article Individual 9 Individual Individual 1 Individual Splice variantSplice p.Asn842Ser

Individual 11 Individual Individual 3 Individual p.Asn842Ser p.Ala162fs

Individual 12 Individual Individual 5 Individual p.Asn842Ser p.Ala162fs

Individual 14 Individual Individual 7 7 Individual p.Arg737Cys Arg999*

Individual 15 Individual Individual 8 Individual p.Arg880Cys Arg1025*

This articleisprotected bycopyright.Allrightsreserved. Accepted Article ‡ † Abbreviations y, male; areM, as F, year; female; follows: month; m, +, present; -, absent; NR, not reported; NA, not applicable Pes planus pathologyJoint Gynaecomastia (males) Sloping shoulders Others Small mouth Thin lips (narrow mouth) Philtrum abnormalities Broad nose/nasal bridge Ear abnormalities Eye anomalies (strabismus) Hypertelorism Blepharophimosis Flat midface Facial Structural brain abnormalities Congenital heart defects Congenital malformations Sleeping problems Speech problems Hypotonia Behavioural problems (SD)Head circumference Feeding problems ID/DD Neurological behaviour and CDK13 Age at examination Gender Individual Table 1. SummaryTable major of clinical features individuals of with variants in CDK13 Monozygotic twins Extensive data are given clinical Suppl in Table 1 variant + (moderate ID) (p.Asn842Ser) c.2525A>G 6 y, 3m +1 SD +1 NR + M + + + 1 + + + + + + + + + ------+ (moderate ID) (p.Asn842Ser) c.2525A>G -1 SD -1 NA 8 y + + + + F 2 + + + ------(borderline ID) (p.Asn842Ser) c.2525A>G + 1 SD 1 + NA 9 y + + + + + + + + F 3 + + + + + + + - - - - (p.Asn842Ser) c.2525A>G + (mild ID) (mild + + 0.75 SD 10 y, 1m NR NA + + + + F 4 + + + + + + ------+ (moderate ID) (p.Asn842Ser) + (until 12y) c.2525A>G +0.39 SD † 22 y + M + + + + + 5 + + + + + + + + + + - - - + (moderate ID) (p.Gly714Asp) c.2141G>A > 2.5 SD 11 y NR NR NR NR NR NR NA + + + F 6 + + + ------(p.Arg737Cys) c.2209C>T + (DD/ID) + + 1 SD 1 + 13 y NR NA + + + + F + 7 + ------+ (borderline ID) (p.Arg880Cys) c.2638C>T 9 y , 10m 0 SD 0 NR NR M + + + + + + + + + 8 + + + ------c.2601-2A>G (splice site) + (mild ID) < -2.5 SD -2.5 < 13 y NR NR NA + 9 + + + F + + + + + ------‡ c.2601-2A>G (splice site) + (mild ID) < -2.5 SD -2.5 < 13 y NR NR 10 NR NA + + F + + + + + + + + ------‡ (p.Ala162fs) + (mild ID) c.484dup c.484dup > 2.5 SD 11 y NR NR NR NR NA + 11 + + F + + + + ------+ (moderate ID) (p.Ala162fs) c.484dup c.484dup + 0.7 SD 13 y 12 + M + + + + + + + + ------(p.Ala162fs) + (as child) + (mild ID) c.484dup c.484dup +0.5 SD 54 y NR NR NR NR NR NR 13 + M + + + + + + + - - - - - + (borderline ID) (p.Arg999*) c.2995C>T + 3 SD 3 + NR NR NR 9 y 14 + M + + + + + + + ------(p.Arg1025*) c.3073C>T +1.53 SD + (DD) + 3 y, 4m NR NA + 15 + + + F + + ------3/15 macrocephaly; 2/15 microcephaly Cumulative 9 F, 6M 15/15 10/12 15/15 10/15 11/15 10/15 5/13 9/15 7/15 6/10 6/15 7/15 6/15 9/13 6/14 7/15 2/13 4/15 7/8 3/5 3/7 Clinical information from later published studies on certain individuals is included in this overview. this in included is individuals certain on studies published later from information Clinical ‡ † not reported ; NR, M, male; F, female; arefollows: as Abbreviations planus Pes pathology Joint (males) Gynaecomastia shoulders Sloping Others (narrow lips Thin mouth) abnormalities Philtrum bridge nose/nasal Broad abnormalities Ear Eye anomalies Hypertelorism Blepharophimosis midface Flat Facial abnormalities brain Structural heart defects Congenital malformations Congenital problems Sleeping problems Speech Hypotonia problems Behavioural Macrocephaly Microcephaly problems Feeding ID/DD behaviour and Neurological individuals novel of Number individuals described of Number Study Table 2. Overview of main clinical features of individuals variants with in Since some individuals have been reported multiple times over different reports, only the firstly published study is indicated here. studyindicated is published only reports, the firstly different over times been reported multiple have individuals some Since 3. Table Suppl in given is reported individuals all of overview An This articleisprotected bycopyright.Allrightsreserved. Accepted Article ‡ Sifrim Sifrim 5 F, 2 M et al NR NR NR NR 1/7 6/7 3/7 5/7 4/7 4/7 4/7 2/5 4/6 7/7 7/7 3/7 3/3 0/7 4/7 7/7 7/7 2/2 7 ., 2016 ., DDD Study, 2017 DDD NR 6 F NR NR NR 1/6 4/6 3/6 4/6 5/6 4/6 2/6 6/6 1/1 1/5 0/6 2/4 4/4 0/7 1/6 5/6 6/6 1/1 13 Bostwick Bostwick 4 F, 5 M NR NR NR NR NR NR NR NR NR NR 9/9 9/9 0/8 1/8 9/9 5/8 6/8 8/9 6/9 6/8 5/6 6/9 16 et al ., 2017 ., CDK13 Hamilton Hamilton † NR NR NR NR NR 3 F 1/3 1/3 2/3 0/3 2/3 2/3 1/3 1/3 1/3 1/1 1/3 1/2 1/1 0/7 1/3 3/3 3/3 16 et al ., 2017 ., Current study Current 9 F, 6 M 10/15 10/15 15/15 15/15 11/15 10/12 2/13 3/15 2/15 9/13 6/10 6/14 7/15 9/15 7/15 6/15 7/15 6/15 5/13 3/5 3/7 7/8 15 10/16 24/39 15/31 28/39 27/40 25/40 19/39 16/29 19/25 16/38 23/24 25/34 18/31 40/40 23/23 9/26 6/14 7/16 3/25 9/25 8/16 3/5 Cumulative 27 F, 13 M (100%) (100%) (36%) (63%) (35%) (62%) (48%) (50%) (12%) (58%) (60%) (43%) (72%) (68%) (63%) (49%) (55%) (44%) (76%) (96%) (75%) (42%)