KBG syndrome underdiagnosed and a DDD “hit” · PDF fileDr Kay Metcalfe DD,...

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KBG syndrome

underdiagnosed and a DDD “hit” UKGTN service

Dr Alison Hills1,

Maggie Williams1,

Karen Low2,

Sarah Smithson2

DDD Study Group 1) Bristol Genetics Laboratory

2) Clinical Genetics, St Michael’s Hospital, Bristol


• OMIM 148050 AD rare

• Est. incidence <1/1,000,000

• likely underdiagnosed

• phenotypic variability

• subtle features

• lack of clinical familiarity

• frequent DDD diagnosis

• ? 100KG

• Characterized by

• Developmental delay

• Specific dentition

• Craniofacial features

• Skeletal anomalies

• Additional symptoms

Introduction- KBG syndrome

From Ockeloen et al. Eur J Hum Genet (2014), 1–10 All patients have an upturned nose with a broad base to the nose and full nasal tip. Other characteristic

features are broad or bushy eyebrows with synophrys, strikingly prominent eyelashes (g, h, k, n, o), a low posterior hairline, brachy/turricephaly, a long

philtrum, hypertelorism and prominent or protruding ears with dysplastic helices. Some patients have an exaggerated cupid’s bow-shaped mouth (a, i, k, m,

n, o) but other patients have a thin upper lip (e, h, l, p, s). The hair can be coarse (a, b, d, l, q).


History 1975 Herrmann et al Birth Defects Orig

Artic Ser 11:7-18

KBG - syndrome of short

stature, characteristic facies,

mental retardation,

macrodontia and skeletal

anomalies

First described in 7 patients

from 3 unrelated families

Families had the surname

initials K, B and G

2010 Willemsen et al

Netherlands

USA

Canada

Eur J Hum Genet

18:429-435

aCGH 4 male patients de-

novo microdeletions 16q24.3

SRO contains

Ankyrin Repeat Domain 11

(ANKRD11) and Zinc Finger

778 (ZNF778)

? haploinsufficiency

2011 Sirmaci et al

USA

Italy

Turkey

Am J Hum Genet

89:289-294

Exome sequencing

Sanger sequencing

ANKRD11

5 heterozygous patients

c.7570-1G>C ( familial )

c.2305del

c.5953_5954del

c.6071_6094del

c.7189C>T p.(Gln2397*)

2012 Isrie et al

Belgium

Netherlands

Eur J Hum Genet

20,131-133

High resolution aCGH

2 patients

220kb and 138kb deletion in

16q24.3 ( ANKRD11 partial

deletion )

2013 Khalifa et al

USA

Am J Med Genet

161A:835-840

aCGH

2.5yr old male KBG patient

and mildly affected mother

154kb deletion in ANKRD11

mother mosaic

2015 Crippa et al

Italy

Mol Cytogenetics

8:20

aCGH, microsatelite, i-FISH,

gene expression

2 patients and mildly

affected mother

89kb microduplication in

ANKRD11

Mother mosaic


Clinical phenotype

Ockeloen et al. Eur J Hum Genet (2014) 20 patients from 13 families

Netherlands led multicentre collaboration

Walz et al. Hum. Genet 2015 11 patients

Miami -USA, Malaysia, Italy.

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The ANKRD11 gene

• Encodes the 2663 amino acid ANKRD11 (Ankyrin Repeating Domain-Containing

protein 11) protein, a cofactor that interacts with p160 nuclear receptor coactivators to

repress transcriptional activation of nuclear receptor target genes.

• ANKRD11 has been shown to interact with TP53 and indirectly with CDKN1A, these

proteins have important roles in cell cycle progression (Walz et al 2015)

• ANKRD11 is GC rich and polymorphic

• exon 9 (NM_013275.5) is 6.5kb (~75% of coding sequence) 17 fragments

• 27 amplicon gene screen

• 100% predicted coverage Sure Select (Agilent)

• 85% coverage TS1 (Illumina) – poor for 33% exon 9


• The majority of published pathogenic variants are novel truncating variants

• Predominantly in the largest exon (9)

• Truncated ANKRD11 proteins lack the C-terminus D-box critical for protein

degradation, this is tightly regulated through the cell cycle (Walz et al 2015)

• 1 missense and 1 splice site mutation also affect the C-terminus D-box (exon 10)

• Majority cases are de-novo, a few familial cases have been reported.

• Intragenic deletions and one intragenic duplication reported.

• Larger 16q24.3 deletions cause a similar phenotype with autism and additional

facial features. Variability of clinical features makes it difficult to elucidate which are

attributable to haploinsufficiency of ANKRD11 and which to surrounding genes

• Crippa et al 2015 70 cases of KBG syndrome described to date

Spectrum of published mutations

Non-coding

exon 9 c.893-7470


• Accurate diagnosis

• Reproductive risks

• Clinical management

• Cardiac clinical

investigation and

screening

• Specialist dentition

assessment

• Appropriate support

for learning difficulties

UKGTN gene dossier April 2015


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16

Reported referrals from April 2015

30 patients

5 validations 4 DDD

1 research study

25 ANKRD11 gene screen

9 novel truncating mutations

16 negative


• Clinical variability has likely led to under-diagnosis of KBG syndrome.

• Clinicians of both mutation positive and mutation negative cases have

been contacted and asked to complete a proforma with the aim of

further delineating the phenotype of KBG syndrome.

Refinement of phenotype

Dental anomalies

Macrodontia upper central incisors

Other – please specify

Characteristic facial appearance

Broad forehead

Triangular face

Anteverted nostrils

Long palpebral fissures

Skeletal abnormalities -specify

Learning difficulties mild/mod/severe

Postnatal short stature Centile:

Other – please specify


Mutations detected at BGL

Manchester Dr Kay Metcalfe DD, scoliosis, Hearing loss, Exon 4

c.160C>T, p.(Arg54*)

Auckland New Zealand Dr Juliet Taylor

DD, broad central incisors Exon 9 c.1381_1384del, p.(Glu461Glnfs*48)

Bristol Prof Ruth Newbury-Ecob

Speech and language delay, mild dysmorphic features, short stature,

Exon 9 c.1977C>G, p.(Tyr659*)

Wessex Dr Katherine Lachlan

DD, PDA, finger contractures, seizures, keratoconus Exon 9 c.3208_3209del, p.(His1070Trpfs*31)

Auckland New Zealand Dr Ian Hayes

“clinical diagnosis of KBG syndrome”. Exon 9 c.3255_3256del, p.(Lys1086Glufs*15)

Bristol Prof Ruth Newbury-Ecob

DD, mild speech delay, short hand tubular bones, bracyclinodactyly 5th finger, macrodontia, characteristic facies, short stature, orchidopexy 18mths

Exon 9 c.5199_5227del, p.(Asp1734Alafs*53)

Bristol Prof Ruth Newbury-Ecob “clinical diagnosis of KBG syndrome ”

Exon9 c.5274dup, p.(Ser1759Leufs*38)

Manchester Prof Jill-Clayton Smith Case 2

Exon 9 c.7362del, p.(Leu2455Cysfs*36)

Newcastle Dr Ian Wilson

“clinical features of KBG” Exon 9 c.7183C>T, p.(Gln2395*)

Non-coding

exon 9 c.893-7470

Published mutations


G18687

• Macrodontia with oligodontia

• Prominent/high nasal bridge

• Thin upper lip

• Brachycephaly

• Mild hypertelorism

• Wide characteristic eyebrows

• Prominent/anteverted ears

Case 1 – research validation

11 yr old male

Dr Sarah Smithson

Clinical Genetics

Bristol

Referred age 9

ANKRD11 variant

Dr Melita Irving Guys

Research study

c.[2398_2401del];[(=)],

p.[(Glu800Asnfs*62)];[(=)]

• Moderate delay – special needs school

• Brachy-clinodactyly 5th finger

• Short stature

• Seizures

• Hearing loss and recurrent infections – grommets

• Abnormal arm shoulder pigmentation

• No congenital heart defect

• Mother likely affected not as yet confirmed


Case 2 – new diagnosis

21 yr old male

Prof Jill Clayton-Smith Manchester

c.[7362del];[(=)],

p.[(Leu2455Cysfs*36)];[(=)]

• No Macrodontia

• inward sloping incisors, malocclusion

• Prominent/high nasal bridge

• Brachycephaly

• Hypertelorism

• Wide characteristic eyebrows

• Prominent/anteverted ears

• Mild delay

• behavioural difficulties, very introverted

• Short hand tubular bones

• Short stature

• Seizures

• Hearing loss

• No congenital heart defect


Birmingham Dr Trevor Cole

Global DD, anisocoria, irregularly spaced teeth, delayed S&L, clinodactyly, abnormal facial shape

Exon 6 c.538delG, p.(Asp180Thrfs*48)

Manchester Dr Kay Metcalfe

TBC Exon 9 c. 1935_1944del, p.(Cys646Alafs*4)

Exeter Dr Emma Kivuva

Global DD; mild short stature; hypertelorism; anteverted nares; large fontanelles; proportionate short stature; tapered finger; wide anterior fontanelle; persistent open anterior fontanelle; delayed cranial suture closure; unilateral ptosis.

Exon 9 c.2408_2412del, p.(Lys803Argfs*5)

Manchester Dr Kay Metcalfe

moderate ID, Aplasia/hypoplasia of the 5th finger; predominantly lower limb lymphodema; abnormality of the soft palate; hypernasal speech; generalised ichthyosis; anterior creases of earlobe; congenital Horner syndrome.

Exon 9 c.4177_4189del, p.(Glu1393Trpfs*12)

DDD mutations confirmed

Mutations in ANKRD11 are common hit from the DDD project.

Non-coding

exon 9 c.893-7470

c.538delG, p.(Asp180Thrfs*48)

c. 1935_1944del, p.(Cys646Alafs*4)

c.2408_2412del, p.(Lys803Argfs*5)

c.4177_4189del, p.(Glu1393Trpfs*12)

6

Published mutations

BGL mutations


DDD study 1133 trios Lancet 2014 Nature 2015

ARID1B 11

SCN2A 9

ANKRD11 8

June 2015

DECIPHER

26 ANKRD11

truncating DNV


KBG syndrome: a series of 26 French patients

T. Busa1, A. Tessier2, F. Riccardi3, A. Jacquette4, D. Genevieve5, V. Gatinois6, D.

Lacombe7, V. Michaud8, M. Rossi9, C. Lebreton9, B. Leheup10, C. Vincent-Delorme11,

A. Delahaye12, L. Van Maldergem13, P. Cacciagli1,14, H. Scheffer15, P. Saugier-Weber16,

A. Goldenberg17, N. Philip1,18;

According to diagnosis criteria de fined

by Skjei & al (2)

% Comments

Macrodontia 71 %

(14/19)

Macrodontia is not any more a mandatory criteria

1st degree relative with KBG 32 %

Other manifestations % Comments

Congenital heart defects 38 % Valvular insufficiency, VSD, AVSD

Behavioural disorders 38 % Autism spectrum disorder, attention-deficit/hyperactivity disorder, non specific

Palatal anomalies 19 % Velopharyngeal insufficiency and/or submucous cleft

Sleep disorders 28 %

Deafness 26 % Sensorineural = 50%, Conductive = 33%, Mixed = 17%

Caudal anomalies 11% 2 patients had a caudal appendage, a one a sacral dimple.

11 patients (10 families) with ANKRD11 mutations splicing mutation (n=1) and missense mutation (n=1)

3 recurrent mutations: c.1903_1907del (p.Lys635fs*26) 6 families

c.1381_1384del (p.Glu461Glnfs*48) 2 families

c.2398_2401del (p.Glu800Asnfs*62) 2 families 15 patients from 11 families with deletions involving ANKRD11 ranging from 118Kb to 1.6 Mb.

The two largest deletions (35 and 39 genes) associated with more severe phenotype (severe intellectual

disability and associated malformations).

In the vast majority of cases, the breakpoints were located within ANKRD11.


Future directions

Genetic Testing • Sure Select Panel assay – for CNV analysis

• Re-design of our aCGH to include more probes within and around ANKRD11.

Current probe density does not allow reliable detection of smaller CNVs in the

region

Clinical Phenotype • Collaboration with the DDD complimentary analysis project to further refine the

phenotype of KBG patients with the aim of improving diagnosis and making

recommendations regarding the long term treatment of patients e.g. dental,

cardiac follow-up

• Crippa et al 2015 -70 KBG cases reported

• DDD -26 cases Marseille 26 cases BGL 9 cases Total 61 cases

Negative Referrals (16) • Questionnaire to ascertain phenotype

• Search for additional genes –exome or 100KG


Acknowledgments

Bristol Genetics Laboratory

www.nbt.nhs.uk/genetics

[email protected]

[email protected]

Clinicians Bristol Dr Sarah Smithson Dr Karen Low Prof Ruth Newbury-Ecob Manchester Prof Jill Clayton-Smith Guys Dr Tazneem Ashraf DDD study Dr Caroline Wright Marseille KBG study Dr T Busa

BGL Scientific

Alison Hills

Laura Yarram

Bioinformatics

Geoff Woodward

Chris Buxton

Technical

Gemma Dennis

Thais Simmons

Richard Wells

Jo Davies

Jenny Glauert

mailto:[email protected]

mailto:[email protected]


Info for ANKRD coverage assessment slide

• Not all ANKRD ROIS included in TS1 design are relevant

• Presented coverage reflects only those regions currently included in

Sanger test

• A coverage issues in the last 3rd of exon 9 (cov under 30x), mostly

covered >15x though. No complete gaps.

• I’ve added the best covered on above if you need a picture (sample NM)

KBG syndrome underdiagnosed and a DDD “hit” · PDF fileDr Kay Metcalfe DD,...

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