Hum Genet (2015) 134:97–109

DOI 10.1007/s00439-014-1498-1

ORIGINAL INVESTIGATION

De novo mutations in beta-catenin (CTNNB1) appear to be a

frequent cause of intellectual disability: expanding the mutational
and clinical spectrum
Alma Kuechler · Marjolein H. Willemsen · Beate Albrecht · Carlos A. Bacino · Dennis W. Bartholomew ·
Hans van Bokhoven · Marie Jose H. van den Boogaard · Nuria Bramswig · Christian Büttner · Kirsten Cremer ·
Johanna Christina Czeschik · Hartmut Engels · Koen van Gassen · Elisabeth Graf · Mieke van Haelst ·
Weimin He · Jacob S. Hogue · Marlies Kempers · David Koolen · Glen Monroe · Sonja de Munnik ·
Matthew Pastore · André Reis · Miriam S. Reuter · David H. Tegay · Joris Veltman · Gepke Visser ·
Peter van Hasselt · Eric E. J. Smeets · Lisenka Vissers · Thomas Wieland · Willemijn Wissink · Helger Yntema ·
Alexander Michael Zink · Tim M. Strom · Hermann-Josef Lüdecke · Tjitske Kleefstra · Dagmar Wieczorek 

Received: 15 August 2014 / Accepted: 3 October 2014 / Published online: 19 October 2014
© Springer-Verlag Berlin Heidelberg 2014

Abstract  Recently, de novo heterozygous loss-of-function
mutations in beta-catenin (CTNNB1) were described for the
first time in four individuals with intellectual disability (ID),
microcephaly, limited speech and (progressive) spasticity,
and functional consequences of CTNNB1 deficiency were
characterized in a mouse model. Beta-catenin is a key down-
stream component of the canonical Wnt signaling pathway.
Somatic gain-of-function mutations have already been found
in various tumor types, whereas germline loss-of-function
T. Kleefstra and D. Wieczorek contributed equally.
Electronic supplementary material  The online version of this
article (doi:10.1007/s00439-014-1498-1) contains supplementary
material, which is available to authorized users.
mutations in animal models have been shown to influence
neuronal development and maturation. We report on 16
additional individuals from 15 families in whom we newly
identified de novo loss-of-function CTNNB1 mutations (six
nonsense, five frameshift, one missense, two splice muta-
tion, and one whole gene deletion). All patients have ID,
motor delay and speech impairment (both mostly severe) and
abnormal muscle tone (truncal hypotonia and distal hyper-
tonia/spasticity). The craniofacial phenotype comprised
microcephaly (typically −2 to −4 SD) in 12 of 16 and some
overlapping facial features in all individuals (broad nasal tip,
small alae nasi, long and/or flat philtrum, thin upper lip ver-
million). With this detailed phenotypic characterization of 16
additional individuals, we expand and further establish the

A. Kuechler (*) · B. Albrecht · N. Bramswig · J. C. Czeschik · M. J. H. van den Boogaard · K. van Gassen · M. van Haelst ·
H.-J. Lüdecke · D. Wieczorek  G. Monroe 
Institut für Humangenetik, Universitätsklinikum Essen, Department of Medical Genetics, Utrecht Medical Centre,
Universität Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Utrecht, The Netherlands
Germany
e-mail: alma.kuechler@uni-due.de C. Büttner · A. Reis · M. S. Reuter 
Institut für Humangenetik, Friedrich-Alexander-Universität
M. H. Willemsen · H. van Bokhoven · M. Kempers · D. Koolen · Erlangen-Nürnberg, Erlangen, Germany
S. de Munnik · J. Veltman · L. Vissers · W. Wissink · H. Yntema ·
T. Kleefstra  K. Cremer · H. Engels · A. M. Zink 
Department of Human Genetics, Radboud University Medical Institute of Human Genetics, University of Bonn, Bonn, Germany
Centre, Nijmegen, The Netherlands
E. Graf · T. Wieland · T. M. Strom 
C. A. Bacino · W. He  Institut für Humangenetik, Helmholtz Zentrum München,
Department of Molecular and Human Genetics, Baylor College Neuherberg, Germany
of Medicine, Houston, TX, USA
J. S. Hogue 
D. W. Bartholomew · M. Pastore  Department of Pediatrics, Madigan Army Medical Center,
Division of Molecular and Human Genetics, Department Tacoma, WA, USA
of Pediatrics, The Ohio State University/Nationwide Children’s
Hospital, Columbus, OH, USA

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98
clinical and mutational spectrum of inactivating CTNNB1
mutations and thereby clinically delineate this new CTNNB1
haploinsufficiency syndrome.
Introduction
Intellectual disability (ID, IQ < 70) affects up to 2–3 %
of the general population (Ropers 2010; Flore and Milun-
sky 2012). Until recently, the underlying cause of ID was
unclear in about half of the affected individuals. The intro-
duction of whole exome sequencing (WES) techniques has
markedly increased the number of patients in whom the
underlying genetic background can be elucidated. (e.g.,
Rauch et al. 2012; de Ligt et al. 2012).
CTNNB1 loss-of-function mutations were described for the
first time as a cause of unexplained ID by de Ligt et al. (2012).
By WES (trio analysis), a mutation (p.Ser425Thrfs*11) in
one of 100 patients was detected and screening of a replica-
tion cohort of 765 ID patients revealed two further CTNNB1
mutations (p.Arg515* and p.Gln309*). By identification of
these disruptive mutations in three patients with severe ID,
absent or limited speech, microcephaly, and spasticity with
severely impaired walking ability, de Ligt and co-workers
postulated CTNNB1 to be a novel ID gene, subsequently
being introduced to OMIM (*116806) as cause of autosomal
dominant mental retardation type 19, MRD19 (#615075).
Very recently, these three patients were clinically character-
ized by Tucci et al. (2014), along with a fourth affected indi-
vidual. Only these four patients with inactivating CTNNB1
mutations and one individual with a whole gene deletion
(Dubruc et al. 2014) are known so far. Here, we describe and
comprehensively characterize 16 additional individuals from
15 families in whom we identified loss-of-function mutations
in CTNNB1 as the cause of their syndromic ID phenotypes.
Materials and methods
Patients
Written informed consent to the study was obtained from
the legal representatives of each participant and written
D. H. Tegay  (Illumina), targeting 4,813 genes associated with known
Department of Medicine, New York Institute of Technology
College of Osteopathic Medicine, Old Westbury, NY, USA
G. Visser · P. van Hasselt  (Illumina) and generated more than 68.5 million reads
Department of Metabolic Diseases, Wilhelmina Children’s
Hospital, Utrecht Medical Centre, Utrecht, The Netherlands
E. E. J. Smeets 
Department of Clinical Genetics, Maastricht University Medical
Center, Maastricht, The Netherlands
13
Hum Genet (2015) 134:97–109
consents for publication of the clinical photographs were
given. The investigations were performed in accordance
with the Declaration of Helsinki protocols.
Five of the 16 individuals described here (patients 1–5)
were detected in a whole exome sequencing (WES) cohort
of 250 individuals with unexplained ID (Kuechler et al.
2014). Inclusion criteria were developmental delay/ID
(IQ < 70) with or without additional features (e.g., cranio-
facial dysmorphism, organ malformation etc.) which could
not be attributed to a clinically recognizable syndrome by
experienced clinical geneticists. In addition, clinically rel-
evant chromosomal aberrations had to be excluded previ-
ously by chromosomal microarray analysis, and Fragile-X
testing had to be normal.
By clinical cooperation we collected seven further indi-
viduals with newly diagnosed CTNNB1 mutations identi-
fied in different WES and NGS approaches—two siblings
(patients 6 and 7) and eight sporadic patients (patients
8–15)—as well as one further individual with a whole
CTNNB1 gene deletion (patient 16).
Exome sequencing, data analysis
For patients 1–5, exome sequencing was performed as
described in Kuechler et al. (2014). In brief, exomes were
enriched using the SureSelect XT Human All Exon 50 Mb
kit, versions 3 and 5 (Agilent Technologies); sequencing
was performed on HiSeq 2000/2500 systems (Illumina).
Image analysis and base calling were performed using illu-
mina real time analysis. Reads were aligned against the
human assembly hg19 (GRCh37) using Burrows-Wheeler
Aligner (BWA v 0.5.9). We performed variant calling using
SAMtools (v 0.1.18), PINDEL (v 0.2.4t), ExomeDepth (v
1.0.0) and custom scripts. Subsequently the variant qual-
ity was determined using the SAMtools varFilter script. To
discover putative de novo variants, we queried the database
to show only those variants of a child that were not found
in the corresponding parents.
For patients 6 and 7, exome sequencing was performed
at a commercial lab (GeneDx, Gaithersburg, Maryland,
USA) using the Agilent SureSelect XT2 All Exon V4 kit
sequenced with IlluminaHiSeq 2000 (“XomeDx”) accord-
ing to the manufacturers’ standard protocols.
For patient 8, the TruSight One Sequencing Panel Kit
clinical phenotypes, was used for enrichment. Paired-end
sequencing was carried out on a HiSeq 2500 instrument
passing filters. After quality trimming, 99.6 % could be
mapped to the hg19 reference genome (BWA-MEM; Li
and Durbin 2009). Average target coverage was 170×,
while 98.4 % of the target sequence was covered at least
20 times. Following local realignment, single-nucleotide
Hum Genet (2015) 134:97–109 99
variants and small indels were called with GATK´s unified
genotyper (version 3.1; McKenna et al. 2010). Data were
compiled from a variety of public databases and variant
annotation was performed with ANNOVAR (Wang et al.
2010). Variants were filtered against common (minor allele
frequency of >0.1 % in the NHLBI Exome Sequencing
Project or the 1000 Genomes Project) and synonymously
coding variants, and were prioritized according to their
phenotypic plausibility.
Patients 9, 13, and 15 were ascertained through family-
based WES as previously described (de Ligt et al. 2012).
In short, exome sequencing was performed on the Illumina
HiSeq 2000 TM machine after enrichment with the Agi-
lent SureSelectXT Human All Exon 50 Mb Kit. After read
alignment with BWA and variant calling with GATK, vari-
ants were annotated.
For patients 10 and 11, WES was done using Illu-
mina HiSeq platform with a mean coverage of target
bases >100×. Data analysis and interpretation were per-
formed using Mercury 1.0, SIFT and PolyPhen-2.
For patients 12 and 14, enrichment was performed using
Agilent Sureselect XT All Exon V5 kit and sequenced on
an Illumina HiSeq 2500 instrument at the Utrecht DNA
Sequencing Facility (Utrecht, Netherlands). Reads were
aligned using BWA and data were processed with GATK
v3.1.1 (McKenna et al. 2010), according to best practice
guidelines (Van der Auwera et al. 2013). Obtained cover-
age was 107× with 92.9 % covered >20×. Variant analysis
was performed using the commercially available tool Cart-
agenia Bench Lab, filtering upon Mendelian violations to
find de novo variants and prioritizing the variants using a
classification tree, according to presence in public and clin-
ical relevant variant databases, location, coding effect, and
corresponding literature.
We used PolyPhen-2 (http://genetics.bwh.harvard.edu/
pph2/), SIFT (http://sift.bii.a-star.edu.sg) and Mutation-
Taster (http://www.mutationtaster.org/) to predict the pos-
sible impact of a missense mutation on the structure and
function of the protein.
Sanger sequencing
Sanger sequencing of CTNNB1 was performed on whole
blood genomic DNA in the patients and their parents
to verify the mutations and their de novo status. Primer
sequences are available upon request. CTNNB1 reference
sequence was NM_001904.3.
For patient 16, a whole genome array analysis was per-
formed at a commercial laboratory (Quest Diagnostics,
Nichols Institute, Chantilly, Virginia, USA) using an Affy-
metrix 6.0 array according to standard protocols. De novo
occurrence of the detected aberration was investigated by
parental array analysis.
Results
Clinical reports and identification of CTNNB1 mutations
The main clinical findings of the 13 novel patients are sum-
marized in the following case reports; additional detailed
information and comparison with so far published patients
(de Ligt et al. 2012; Tucci et al. 2014; Dubruc et al. 2014)
are provided in Supplementary Table S1. Mutational data
are summarized in Table 2.
Patient 1 (see Fig. 1a, b) is the second son of healthy
non-consanguineous parents. During pregnancy, a single
umbilical artery was diagnosed by ultrasonography. He was
born by primary Cesarean section with normal weight and
length but primary microcephaly (−2.79 SD, see Supple-
mentary Table S1). After a normal neonatal period, hypoto-
nia and delayed psychomotor development became obvious
(unsupported walking from approximately 8 years on). At
6 months of age, he was diagnosed with strabismus and later
on with hyperopia (+7/+6.5 dpt). He suffered from frequent
respiratory infections. Brain MRI was normal. Because of
hypertonia of the legs, an MRI scan of the spine was per-
formed at age 3¾ years that revealed a syringomyelia (TH8-
L1). Upon clinical examination at age 4 years, height and
weight were normal; but OFC had decreased to −4.0 SD.
Apart from microcephaly, he presented with some crani-
ofacial dysmorphism (hypotelorism, long and flat philtrum,
thin upper lip vermillion and strabismus). His hands were
broad with short distal phalanges; his feet displayed a pes
cavus with a discrete 2–4 soft tissue syndactyly. At re-eval-
uation at age 8½ years he was able to walk without support
(broad-based gait) and was toilet trained during the day. He
could speak only few single words but had better speech
comprehension and communicated using gestures.
WES detected a de novo frameshift mutation in exon 12
[c.1923dupA, p.(Glu642Argfs*6)].
Patient 2 (see Fig. 1c, d) is a 5-year-old girl, first child
of healthy non-consanguineous parents from Bangladesh
with unremarkable family history. She was born sponta-
neously with normal birth weight and length but small
OFC (−2.1 SD; see Supplementary Table S1). Postnatal
course was normal. Neonatal jaundice required photo-
therapy for 2 days. She developed hypotonia and feeding
difficulties (poor sucking, no breast feeding possible),
and a severe psychomotor delay soon became obvious.
She gained head control at age 8–10 months, started sit-
ting at 18 months, crawling at 23 months and pulling her-
self to stand at 33 months. Upon several clinical follow-
up examinations her length and weight remained in the
low normal range but her OFC dropped down further to
about −3 SD. She had no obvious craniofacial dysmor-
phism (see Fig. 1c, d) apart from a broad nasal tip and a
flat occiput. Fingers were tapered. At age 53/12 years, she
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100
Fig. 1  Facial phenotypes of individuals with CTNNB1 mutation.
Patient 1 at the age of 9 months (a) and 8½ years (b), patient 2 at
1 year (c) and at 3 years (d), patient 3 at 2½ years (e), patient 4 at
6 years (f) and at 14 years (g), patient 5 at 5 years (h), patients 6 and
7 (siblings) at 4 and 2 years (i, j), patient 9 at 14 months (k) and at
2 years (l), patient 10 at 4 years (m), patient 11 at 4 years (n), patient
12 at 13 years (o), patient 13 at 6 years (p), patient 14 at 14 months
still could not walk without support, had hypotonia of the
trunk and hypertonia of the legs. She showed some ste-
reotypic movements (smacking her lips, protruding her
tongue), had lost the ability to speak few single words or
syllables, and had poor speech comprehension. Feeding
problems had remained; she hardly felt hungry, did not
chew or drink properly, had frequent vomiting and suf-
fered from constipation. She had no contact to other chil-
dren and no interest in toys. She suffered from intermit-
tent sleep disturbances. Her mood was generally friendly
but she had occasional outbursts of temper tantrums and
crying that were difficult to interrupt. She had no seizures;
EEGs were normal as well as a brain MRI (at age 3 years),
visual-evoked potentials (VEP), echocardiography, and
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Hum Genet (2015) 134:97–109
(q) and 3 years (r), patient 15 at 2 years (s), and patient 16 at 3 years
of age (t). Photographs of patients 8 were unavailable for publication.
All individuals share some craniofacial features—a broad nasal tip
with small alae nasi, a long or flat philtrum and a thin upper lip ver-
million. In older individuals, the nose appeared longer and the colu-
mella more prominent
otoacoustic emissions (OAEs). She wears glasses because
of a hyperopia (+7/+6 dpt).
WES identified a de novo heterozygous CTNNB1 non-
sense mutation c.1420C>T, p.(Arg474*) in Exon 9.
Patient 3 (see Fig. 1e) is the second child of healthy
non-consanguineous Turkish parents. During pregnancy,
a cardiac “white spot” was detected by ultrasonography.
The girl was born with normal measurements (see Supple-
mentary Table S1); postnatal course was normal. Normal
breastfeeding was possible in spite of hypotonia. Starting
at age 2 months she suffered from skin problems (diaper
rash and later eczema). At age 5–6 months, a motor delay
became obvious and physiotherapy was started. She was
able to turn over at 1½ years but could not sit or walk
Hum Genet (2015) 134:97–109 101
without support at age 25/12 years. Speech development
was also delayed (no words, only syllables). She showed
behavioral abnormalities with outburst of temper tantrums
or crying and self-biting. A hip dysplasia and peripheral
hypertonia with a spastic component especially in the legs
were diagnosed. MRI scans of the brain and the spine (at
age 1½ years) were normal apart from a lumbosacral epi-
dural lipoma as an additional finding. EEG, EMG, NCV,
ECG, echocardiography and metabolic screening gave nor-
mal results. Clinical examination at age 25/12 years revealed
microcephaly (−2.2 SD), but normal length and weight
(see Supplementary Table S1). She had a slender build and
a pectus excavatum. There was little eye contact. Craniofa-
cial findings were small alae nasi, a broad nasal tip, a long
philtrum, small upper lip vermillion, deep-set ears, and
micrognathia (see Fig. 1e).
WES identified a de novo heterozygous CTNNB1 splice
mutation (c.1683+1G>A, Intron 10).
Patient 4 (see Fig. 1f, g) is the third child of healthy non-
consanguineous Vietnamese parents. She was born after an
uneventful pregnancy with normal birth measurements (see
Supplementary Table S1). At 3 months of age, motor delay
and at 1 year, speech delay were noticed. She had hypo-
tonia of the trunk and hypertonia and dystonic movements
of the extremities. Talipes deformities were treated with
orthopedic shoes. She learned to walk independently at age
10 years, but could only walk short distances on her tip-
toes. She used 2 words and no signs. She developed auto-
aggressive behavior with self-injuries (biting her hands),
showed some stereotypic movements and held only short
eye contact. Sleep disturbances were treated with Risperi-
done. Clinical examination at the age of 28/12 years showed
mild microcephaly (−2.1 SD) that was no longer present at
reevaluations at the age of 15 years. The patient had stra-
bismus, a flat midface, small alae and broad tip of the nose,
a long, flat philtrum (see Fig. 1f, g), a high arched palate
and small, low set ears. Metabolic screenings, neurotrans-
mitters, EEG, MRI and CDG investigations were normal.
WES revealed a heterozygous de novo CTNNB1 non-
sense mutation c.755T>AAC, p.(Leu251*) in Exon 6.
Patient 5 (see Fig. 1h) is the third child of healthy, non-
consanguineous German parents. Pregnancy and birth
were normal (see Supplementary Table S1). Microcephaly
developed within the first year of life. Motor delay was
diagnosed at 1 month and speech impairment at 1 year of
age. Assisted walking and first words were achieved at age
4 years. She performed repetitive movements and had sleep
disturbances in early childhood. Clinical examination at the
age of 57/12 years showed microcephaly (−2.94 SD), a long
face, small alae nasi, a broad nasal tip, long and smooth
philtrum, a thin upper lip (see Fig. 1h) and diastema. She
was hypotonic, had an ataxic gait, wore orthopedic shoes
and ambulated with assistance of a walker frame. She
communicated by sign language and used about 30 words.
MRI of the brain and spinal cord (at age 4 years), EEGs
and metabolic screening were normal.
WES showed a de novo frameshift mutation
c.423_424insG, p.(Tyr142Valfs*4).
Patient 6 (see Fig. 1i, sister of patient 7), a 13-year-old
girl, is the first child of healthy non-consanguineous par-
ents of mixed European (Italian/Irish) and Puerto Rican
ancestry. The family history was unremarkable. She was
born by Caesarian section with normal measurements by
report (length and OFC not exactly documented). There
were no significant perinatal or neonatal issues. She was
sitting independently by 12 months, walking but not using
any words by 18 months at which time she was diagnosed
with global developmental delay, and speech, physical and
occupational therapies were initiated. At the age of 3 years
she was diagnosed with cerebral palsy due to mixed central
hypotonia and peripheral hypertonia with heel cord tight-
ness and toe walking and was referred for initial Genetics
evaluation. Her height, weight and OFC were all normal.
She had mild dysmorphic features including upslanting
palpebral fissures, a boxy nasal tip, thin upper lip, long
philtrum, narrow palate, small chin and prominent fingertip
pads. At 6 years of age she was diagnosed with ADHD and
anxiety and placed on a number of stimulant medications
and serotonin-reuptake inhibitors with minimal improve-
ment. At 7 years of age she was diagnosed with scoliosis
and a tethered spinal cord and underwent a dorsal spine rhi-
zotomy with some improvement of spasticity in her lower
extremities. At last evaluation she was 13-year-old and car-
ried diagnoses of mild ID (with full-scale IQ scores ranging
from 46 to 66), autism, ADHD, anxiety, strabismus, myo-
pia and tics. She had initiated normal menarche at 12 years
of age and had normal pubertal development. Her parents
noted increased behavioral difficulties including frustra-
tion, aggression, opposition and occasional self-injury but
she was communicative and social. Her facial phenotype
remained essentially unchanged. Her height and OFC were
in the normal range and BMI above the 97th percentile (see
Supplementary Table S1). Metabolic testing (lactic acid,
ammonia, acylcarnitine profile and VLCFAs) and brain
imaging by CT and MRI were normal.
Patient 7 (see Fig. 1j), a 10-year-old boy, is the full sib-
ling of patient 6 and the second and only other child of
these parents. He was born by vacuum-assisted vaginal
delivery with normal measurements (exact birth length and
OFC not documented). He remained in the NICU for one
day for respiratory distress which resolved spontaneously.
He was diagnosed shortly after birth with a PDA. A bilat-
eral esotropia was treated surgically at 7 months of age. He
was sitting independently and using words by 12 months,
crawling at 17 months, but not walking until 24 months and
carried a diagnosis of cerebral palsy since 12 months of
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102
age due to mixed central hypotonia and peripheral hyper-
tonia with tight heel cords at which time he began receiv-
ing physical therapy. He was referred for initial genetics
evaluation at the age of 13 months along with his sister. His
height and weight were normal and his OFC mildly micro-
cephalic (−2.2 SD). He had mild dysmorphic features
including dolichocephaly, upslanting palpebral fissures, a
boxy nasal tip, thin upper lip, long philtrum, and a small
chin (see Fig. 1j). Subsequently at the age of 3 years he was
diagnosed with ADHD and placed on a number of stimu-
lant medications with some improvement. He was also
diagnosed with tethered spinal cord and underwent dorsal
spine rhizotomy at 3 years of age but had little improve-
ment of his lower extremity spasticity. At last evaluation,
he was 10 years of age and carried diagnoses of borderline
ID, cerebral palsy, ADHD, microcephaly and hypo-/oli-
godontia. His parents noted increased difficulty with pro-
gressive lower extremity spasticity despite treatment with
Botox, bracing and an intrathecal Baclofen pump. He was
communicative and social. His weight and height remained
normal and his OFC microcephalic (−3.2 SD, see Supple-
mentary Table S1). CPK and cholesterol levels, metabolic
testing (lactic acid, ammonia, acylcarnitine profile, uric
acid level, glycosylated transferrin levels and VLCFAs) and
brain imaging by MRI were normal.
Both siblings, clearly borderline to mildly mentally
impaired, were able to speak in sentences enjoying social/
verbal interaction with somewhat simple speech display but
good receptive understanding.
WES revealed that both siblings carried a heterozy-
gous CTNNB1 nonsense mutation c.2038_2041dupAGCT,
p.(Ser681*). Neither parent was found to carry this muta-
tion (in blood), suggesting parental germline mosai-
cism. In addition, Patient 7 was found to carry a mater-
nally inherited, heterozygous non-synonymous WNT10A
mutation, known to cause ectodermal dysplasia and
believed to account for this patient’s hypo-/oligodontia
(OMIM*606268).
Patient 8 (no photograph shown) is a 15-month-old
male, first child of healthy non-consanguineous parents,
originating from Italy and the Philippines, respectively.
In the 5th month of pregnancy, reduced head growth and
enlarged ventricles were detected by ultrasound. Amnio-
centesis revealed a normal male karyotype. The boy was
born spontaneously with normal weight and length but
mild microcephaly (−2.23 SD, see Supplementary Table
S1). In the neonatal period, feeding difficulties and hypo-
tonia emerged. At age 2 months, neonatal seizures were
noted, but postictal EEG examinations were normal.
He was evaluated at age 3.5 months because of devel-
opmental delay, progressive microcephaly (OFC −3.3
SD), hypotonia of the trunk, hypertonia of the arms and
legs, and convergent strabismus. Hearing was normal. A
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Hum Genet (2015) 134:97–109
brain MRI (shown in Supplementary Figure S1) revealed
enlarged lateral ventricles, dysgenesis of the corpus cal-
losum, abnormal gyration of the temporal lobe, absence
of the right fornix and a hypoplastic brain stem. When
last seen at age 15 months, his OFC had dropped to −4.8
SD. He vocalized only a few syllables, did not show suffi-
cient head control, nor could he grasp objects or sit freely.
Mild craniofacial dysmorphisms (hypotelorism, upslant-
ing palpebral fissures, epicanthus, long, flat philtrum, thin
upper lip, and prominent occiput) were noted. Metabolic
screening was normal. Molecular panel analysis resulted
in the identification of a single mutation in a gene match-
ing the patient’s phenotype, a c.1251_1252insACGTG,
p.(Cys419*) de novo nonsense mutation in Exon 9 of the
CTNNB1 gene.
Patient 9 (see Fig. 1k, l) was born as the fourth child
of healthy non-consanguineous parents with normal birth
weight and length; OFC was not reported. Since birth he
showed a high muscle tone in his arms and legs. Upon neu-
rological examination at the age of 13 months he had a sig-
nificant hypertonia of his upper and lower extremities and
axial hypotonia. Deep tendon reflexes were increased. He
cried a lot and the parents noticed that his development was
delayed as compared to his three healthy sisters. During the
first year of life, he had mild feeding problems, including
difficulties to swallow, chew and eat solid food. At the age
of 8 months he started to roll over from his abdomen to his
back. He did not crawl. Until the age of 18 months he was
not able to sit independently. Since the age of 19/12 years
he was able to walk a few steps with a walking aid. His
comprehensive language developed much better than his
expressive language. He mainly used non-verbal commu-
nication. At the age of 2 years, he was able to use a few
simple words. Social interaction and eye contact were ade-
quate. He had sleeping problems, mainly including difficul-
ties to fall asleep. His general medical condition was good.
During a period of fever he possibly had one seizure. Brain
MRI showed delayed myelination in the frontal lobes. At
the age of 2 years he had normal height, weight and head
circumference (see Supplementary Table S1). He had mild
facial dysmorphism including a prominent metopic ridge,
upslanting palpebral fissures, full nasal tip, long philtrum,
thin upper lip, high palate and pointed chin. In addition, he
had deep palmar creases, a mild clinodactyly of the fifth
fingers and a medial fatpad on his feet. A metabolic screen
in blood and urine revealed mild unspecific abnormalities.
These findings could not be related to his phenotype and
he was included in family-based whole exome sequencing
studies, which revealed a de novo nonsense mutation in
CTNNB1: c.1420C>T; p.(Arg474*).
Patient 10 (see Fig. 1m) was first seen at 11 months
of age. At delivery, a single umbilical artery was noted.
Birth measurements were normal. At 6 months of age, a
Hum Genet (2015) 134:97–109 103
low head circumference was reported. At age 12 months,
she could army crawl but not sit up, and had no language.
Parents described her as being “stiff”. She showed early
fisting, right esotropia, cutis marmorata and a somewhat
hoarse voice. She began walking with a walker device at
about 20 months of age, but always on her toes with ankles
almost fixed in extension. She started unsupported walk-
ing at age 4 years but falls a lot and has a very abnormal
toe-walking gait. Eventually, tizanidine was tried but was
withdrawn due to a seizure. She is not particularly dysmor-
phic but remains speech delayed (~20 words). There was a
history of some self-destructive behavior (poking with fin-
gers, biting, head-banging) that has now improved. EEGs
were normal as were two cranial MRI scans (a subtle area
of abnormal signal in the inferior right basal ganglia/medial
right temporal lobe was of unknown significance and
finally interpreted as normal). Biochemical studies were
normal.
WES revealed a nonsense mutation c.283C>T
p.(Arg95*) in CTNNB1.
Patient 11 (see Fig. 1n) is an 8-year-old male who pre-
sented initially to the genetics consult at 28 months of
age. He has a long-standing history of global develop-
mental retardation with delayed acquisition of speech
and delayed motor development involving fine and gross
motor areas. He sat up at 13 months, crawled at 18 months
and walked at 30 months. He also had a history of swal-
lowing issues probably due to texture aversions. His food
needed to be blended early on although it improved with
time and therapy. At the time of the first exam his head was
microcephalic (−3.6 SD). A follow-up at 4 years contin-
ued to show microcephaly (−3.3 SD). On exam, his ears
appeared prominent and protuberant but measured at the
50th centile for length so likely due to the microcephaly.
He had a triangular face appearance, deep-set eyes, small
nares and prominent columella. He never had seizures but
an EEG at age 7 years was abnormal (with normal alpha
waves but presence of high voltage slow waves in clumps
over the right hemisphere with tendency to paroxysms of
1–2 s) which was interpreted as epileptiform activity with
tendency to spread.
WES detected a de novo missense mutation in CTNNB1,
c.1163T>C, p.(Leu388Pro), which was predicted to be
“disease causing” with a score of 1 (MutationTaster),
“probably damaging” with a score of 1.000 (PolyPhen-2),
and to affect protein function with a score of 0.00 (SIFT).
Patient 12 (see Fig. 1o) is a now 13 year-old girl, first
child of healthy, non-consanguineous Dutch parents. Fam-
ily history is unremarkable and a younger sister is healthy.
Pregnancy and birth were normal. Her motor and intel-
lectual development is delayed since birth. At the age of
1 year she had generalized pyramidal symptoms which
were most prominent on the distal legs, and strabismus
alternans. Assisted walking, first words and toilet train-
ing were achieved at around 6 years. She spoke first words
at age 6 years and now speaks in sentences with a rather
hoarse voice. She never had seizures and generally sleeps
well, but has sometimes laughing periods at night. From
the age of 8 years she had behavioral problems with rages/
tantrums. Clinical examination at the age of 118/12 years
showed a normal head circumference. She had amblyopia
of her right eye (probably due to congenital strabismus), a
short philtrum and widely spaced teeth. She had long, slen-
der fingers, long toes with a sandal gap, showed pyramidal
symptoms of her legs, wore orthopedic shoes and used a
walker frame. She had a very friendly personality, a very
short attention span and made poor eye contact. She was
recently diagnosed with autism by a psychiatrist. Cra-
nial MRIs (at 13 months and 12 years) showed no abnor-
malities. Metabolic investigations were all normal, apart
from a transient elevation of phytanic acid at the age of
4–5 years (22.3 µmol/l, normal reference <10 µmol/l). Per-
oxisomal investigations in cultured fibroblasts revealed no
abnormalities.
A de novo frameshift mutation c.1925_1926delAG,
p.(Glu642Valfs*5) in CTNNB1 was detected by WES.
Patient 13 (see Fig. 1p), a 6-year-old boy, was born after
an uneventful pregnancy to healthy unrelated parents with
normal length and weight; OFC was not reported. The
neonatal period was uneventful. However, his motor devel-
opment was delayed from the start. He started to laugh at
8 weeks, rolled from back to stomach at 11–13 months,
crawled at 25 months and pulled to stand at 26 months. At
14 months of age, he had persisting head-lag when pulled
to a sitting position and was not able to sustain his weight
when supported under the arms (slipping through). Neu-
rologic examination at 2½ years showed axial hypertonia
and exaggerated deep tendon reflexes of the legs, Babins-
ki’s sign and talipes equinus. His general development was
estimated at 20 months (BSID-II-NL). MRI and magnetic
resonance spectroscopy (MRS) of the brain were normal.
At the last clinical examination (5½ years), his length and
weight were normal, but head circumference was micro-
cephalic (−2.81 SD). At the current age of 6 years he can
walk short distances without a walker, but cannot stand
without support. Urine incontinence and drooling are still
a problem. He speaks short sentences of 5–6 words, but his
understanding of language is much better. He is a social
and friendly boy without behavioral problems. His concen-
tration, however, is limited and he is sensitive to noises.
WES revealed a de novo frameshift mutation in
CTNNB1: c.99_100delTG, p.(Gly34Asnfs*15).
Patient 14 (see Fig. 1q, r) is the second child of healthy
non-consanguineous Dutch parents. Family history is unre-
markable; he has a healthy older brother. Routine intrauter-
ine ultrasound at 20 weeks of gestation revealed 2 umbilical
13

104
vessels. He was born at 38 weeks with normal weight and
length, but has been microcephalic from birth onwards.
At the age of 6 weeks he presented with feeding problems
and required nasal tube feeding. Delayed development was
noted from 6 months of age and rolling over first occurred
at 6 months. Parents noted a striking muscle tone, rapidly
changing between normal, low and strongly elevated. For
his failure to thrive he received a gastrostoma and prokinet-
ics. Hearing and vision are normal, although parents report
photophobia. He is a very happy and social boy. At the age
3.5 years, he could not sit or stand unsupported, mainly due
to insufficient control of muscle tone, but he was able to
steer a wheel chair. Formal testing of cognitive develop-
ment was hampered by his motor impairments. He could
however control electronic devices, and attained a broad
vocabulary in two languages. On clinical examination at
the age of 19/12 years he was a very alert boy with a slightly
asymmetric face (right side bigger than left), sparse hair,
deep-set eyes, upslanted palpebral fissures, broad nasal
tip, long philtrum, thin upper lip vermillion, small teeth,
a small chin and large ears. There was a slight asymmetry
of the legs (circumference of the right upper leg is 1.5 cm
larger than the left). He had a small penis with only one
descended testis. Neurological evaluation revealed motor
restlessness, no evident extra pyramidal dyskinetic move-
ment disorder. Axial muscle tone was reduced and periph-
eral muscle tone elevated, particularly in lower extremities,
with brisk tendon reflexes. There was a pronounced startle
response on both auditory and visual stimuli, provoking a
breath holding spell. Metabolic analyses (including plasma,
urine and CSF) were normal. Muscle biopsy showed no
evidence of mitochondriopathy.
WES revealed a de novo splice mutation c.1081+1G>C
in Intron7 of the CTNNB1.
Patient 15 (see Fig. 1s) is the first child of healthy par-
ents with unremarkable family history. During pregnancy,
an intrauterine growth retardation and breech position
were diagnosed. She was born by Caesarian section with
low birth weight and normal length; OFC was not reported.
Development was initially normal, but from 2 to 3 months
of age, she showed a motor delay and later on a stagnation
and regression including loss of words and few two-word
sentences. She was not hypotonic and never crawled. She
had truncal ataxia, dysmetric eye–hand coordination and
hypertonia and spasticity of the lower limbs with abnormal
postural development but slowly progressing at her own
pace until now. At 2 years of age she had a social adapta-
tion of 1 year and a motor developmental level of 7 months.
She was microcephalic (−2.5 SD), had thin hair, a square
face, deep-set eyes, a stubby nose with broad nasal tip, and
a thin upper lip vermillion Her eye movements were not
always well coordinated with intermittent strabismus. She
babbles now (aged 33/12 years) constantly and some words
13
Hum Genet (2015) 134:97–109
are understandable. She is very happy and friendly, but
can show a low frustration tolerance. Extensive metabolic
screening of urine and plasma was normal.
WES analysis revealed a de novo frameshift mutation in
CTNNB1:c.1272_1275delTTCT, p.(Ser425Thrfs*11).
Patient 16 (see Fig. 1t) was born after complicated
pregnancy (chronic hypertension and recognition of
intrauterine growth retardation during the third trimester)
with normal length but low weight and OFC (see Sup-
plementary Table S1). At about 3 months he was noted
to have persistently clenched hands and poor head con-
trol. Around 1 year of life he was first identified as having
increased tone in all extremities. This has not worsened
since that time but he has been noted to have dystonic
posturing of the upper extremities as well. He started
rolling over around 2 years and standing with assistance
shortly thereafter. He did not sit on his own, but walked
with assistance up on his toes at 2½ years. He started to
babble and say “mama” and “dada” specifically shortly
before age 3 years. He had no other intelligible words but
could follow simple commands and point to a few body
parts. He had a generally happy demeanor. His general
health was otherwise good without any history of major
illnesses, hospitalizations, or surgeries. On physical exam
at 3 years, he was mildly short and had a significant
microcephaly (−4.09 SD, see Supplementary Table S1).
He made good eye contact and smiled responsively. He
had right esotropia, a right frontal hair upsweep and a
double posterior hair whorl. His ears were low set, pos-
teriorly rotated, and had a hypoplastic upper crus of the
inner helix. His philtrum was mildly/slightly flat and his
upper vermillion was thin. His thumbs were adducted at
rest and he occasionally displayed dystonic posturing of
the arms with attempts to reach for objects. He had mildly
decreased tone in the trunk and increased tone that is
more notable in the lower extremities with scissoring of
the legs. Previous studies included plasma amino acids,
acylcarnitine profile, uric acid, and alpha-fetoprotein.
Brain MRI showed mild thinning of the corpus callosum
and was otherwise normal.
Chromosome microarray analysis revealed a 505 kb dele-
tion at 3p22.1 (arr[hg19] 3p22.1(41,209,868-41,714,118)×1)
including the entire CTNNB1 and part of ULK4 genes. Paren-
tal array analysis was normal confirming that the deletion was
de novo.
Discussion
Clinical characterization of CTNNB1-related syndromic ID
With the availability of next generation sequencing tech-
niques, inactivating de novo CTNNB1 (beta-catenin 1,
Hum Genet (2015) 134:97–109 105
OMIM *116806) mutations have been recognized for the
first time as cause of syndromic ID (de Ligt et al. 2012).
In this study, we present 16 additional individuals (eight
males, eight females) from 15 families with previously
unexplained ID plus additional findings, in whom we
identified heterozygous de novo inactivating CTNNB1
mutations. When comparing the clinical findings of all
21 patients with CTNNB1 mutations (19 with mutations,
2 with deletions) known so far, consistent phenotypic
features emerge (see Table 1 and Supplementary Table
S1).
The neurological phenotype was the most striking con-
sistent finding in all 21 patients. Hypotonia and delayed
motor milestones were observed from early infancy. While
hypotonia of the trunk remained, a distal hypertonia (arms
and legs) with spasticity especially of the legs developed,
leading to an impaired walking capability. Eight out of
20 patients (one is still too young) achieved the ability to
walk independently, but often severely delayed (at about
4–5 years or even at 10 years of age); only one patient
started unsupported walking at age 18 months. Gait was
frequently described as unsteady, ataxic or spastic.
Another consistent finding was severe speech impair-
ment (no or only single words) in eleven out of 20 patients
(55 %); nine patients (45 %) had a delayed but mild-to-
moderately affected speech being able to communicate
in sentences. ID was present in all patients, ranging from
mild to severe. Some kind of regression (e.g., loss of some
already acquired words or fine motor skills) was noticed in
about one-third of individuals.
Seven out of 14 patients (50 %) had a primary micro-
cephaly (ranging from −2.1 to −4.1 SD). Postnatal micro-
cephaly was a frequent finding (present in about 81 % (17
of 21), ranging from −2.2 to −4.8 SD).
In addition, all 21 affected individuals had some overlap-
ping craniofacial features, including a broad nasal tip with
small alae nasi, a long or flat philtrum and a thin upper lip
vermillion. In older individuals, the nose appeared longer
and the columella more prominent.
It is of note that no seizures were observed so far (apart
from neonatal seizure in patient 8) although beta-catenin
has been implicated in epilepsy (Campos et al. 2004). The
majority of patients (15/20; 75 %) had some abnormalities
of vision—strabismus and/or hyperopia or myopia.
Twelve out of 21 patients (57 %) showed behavioral
abnormalities; temper tantrums, autistic features, aggres-
sive or auto-aggressive behavior or sleep disturbances were
the most frequent findings.
Cranial MRI scans were performed in 18 out of 21
patients showing normal results in 13 individuals (72 %).
Minor changes such as corpus callosum thinning or
mildly enlarged ventricles were observed in three (17 %),
delayed myelination of frontal lobes in one and structural
abnormalities in another patient (patient 8, see text, Supple-
mentary Table S1 and Figure S1). In three patients, spinal
MRI abnormalities (syringomyelia or tethered cord) were
described.
Mutational spectrum
All 18 intragenic mutations (our study, de Ligt et al. 2012,
Tucci et al. 2014, summarized in Table 2) were inactivat-
ing mutations—including eight nonsense mutations, seven
frameshift mutations, two splice mutation, and one mis-
sense mutation predicted to be probably damaging. For two
of the initial patients, Tucci et al. could show that the muta-
tions lead to nonsense-mediated mRNA decay.
The finding that CTNNB1 haploinsufficiency is respon-
sible for the phenotype is supported by two individuals
with different overlapping deletions affecting the entire
CTNNB1 gene (our patient 16 and the patient published
by Dubruc et al. 2014), representing a clinically similar
phenotype to patients with intragenic mutations. A third
deletion of 437 kb in size, affecting the entire CTNNB1
gene, is listed in the DECIPHER database (Firth et al.
2009; Decipher ID #275677), and was identified in a
patient with abnormalities of higher mental function,
behavioral/psychiatric abnormalities, and muscular dys-
trophy. In all three individuals, the deletions (see Fig. 2a)
also comprised parts of the neighboring gene ULK4 (unc-
51 like kinase 4), one of five members of the unc-51-like
serine/threonine kinase (STK) family. Little is known so
far about ULK4 function and there is no OMIM entry
until now. Null mice with targeted deletion of Ulk4 were
recently described to develop congenital hydrocephalus,
and their respiratory epithelia and ependymal cells had
shorter cilia than normal, indicating ciliopathies (Vogel et
al. 2012). Neither our patient 16 nor the patient described
by Dubruc et al. (2014), have clinical manifestations
consistent with a ciliopathy. In a recent study, ULK4
was reported as a rare susceptibility gene for schizo-
phrenia, based on the finding of recurrent rare intragenic
ULK4 deletions in patients with schizophrenia and other
psychiatric disorders (Lang et al. 2014). Since Ulk4−/−
mice were found to have partial agenesis of the corpus
callosum, this gene might be crucial to brain develop-
ment (Lang et al. 2014). It remains unclear whether the
heterozygous partial ULK4 deletions contribute to the
clinical phenotype which is dominated by CTNNB1
haploinsufficiency.
The characteristic structural components of CTNNB1
are 12 armadillo repeats (ARMs 1–12) facilitating interac-
tions with multiple protein partners such as cadherin (Xing
et al. 2008). The mutations identified so far are scattered
throughout the entire coding region of CTNNB1, most of
them localized in ARM 1–ARM 12 (see Fig. 2b).
13

106 Hum Genet (2015) 134:97–109

Table 1  Summary of the main clinical features in patients with CTNNB1 mutation

Clinical features in patients with 16 Novel patients 5 Previously published Summary Frequency
CTNNB1 mutations (not every feature (from 15 families) patients (de Ligt et al., (n = 21)
is documented for all patients) Tucci et al., Dubruc et al.)

Gender 8 females 4 females 12 females

8 males 1 males 9 males
Age range (years) 13/12–154/12 4½–51
Birth weight 14 normal 2 normal 16/19 normal 84 % normal
2 < −2 SD 1 < −2 SD 3/19 low
Birth length 16/16 normal 1/1 normal 17/17 normal 100 % normal
Primary microcephaly 6 < −2 SD 1 < −2 SD 7/14 50 %
6 normal 1 normal
Height 13 normal 5/5 normal 18/21 normal 86 % normal
3 < −2 SD
Weight/BMI 14 normal 3/3 normal 17/20 normal 85 % normal
1 > 97th percentile 1 < 3rd percentile
1 < 3rd percentile
Microcephaly 12 < −2 SD 5/5 < −2 SD 17/21 81 %
4 normal
Craniofacial dysmorphism 16/16 5/5 21/21 100 %
Truncal hypotonia 14/16 5/5 19/21 90 %
Peripheral hypertonia/spasticity 15/16 5/5 20/21 95 %
Motor delay 9 severe 4 severe 21/21 100 %
4 moderate 1 moderate
3 mild
Free walking ability 6/15 2/5 8/20 40 %
Speech impairment 8/15 severe 3/5 severe 20/20 100 %
7/15 mild–moderate 2/5 mild–moderate
Basic speech comprehension 14/15 4/4 18/19 95 %
Intellectual disability 15/15 5/5 20/20 100 %
Regression 4/14 2/2 6/16 38 %
Behavioral anomalies 9/16 3/5 12/21 57 %
Seizures 0/16 0/5 0/21 None
Brain MRI anomalies 3/16 2/2 5/18 28 %
Hearing loss 0/16 Not reported 0/16 None
Visual defects 11/16 4/4 15/20 75 %
CTNNB1 mutation 6 nonsense 2 nonsense
5 frameshift 2 frameshift
2 splice 1 whole gene deletion
1 missense
1 whole gene deletion

Not every feature was documented for all patients; therefore, the total number of patients can differ

Before the implication of CTNNB1 in a novel ID syn-
drome (de Ligt et al. 2012), CTNNB1 and upstream inter-
acting genes of the beta-catenin pathway had already been
suspected to be fundamental developmental regulators in
previous studies among cohorts of individuals with autism
spectrum disorder (ASD). O’Roak and colleagues identi-
fied two CTNNB1 mutations (Trp504* and Thr551Met) in
two individuals with ASD (O’Roak et al. 2012a, b). The
latter missense mutation Thr551Met is predicted to be
“possibly damaging” with a score of 0.804 (PolyPhen-2)
and “disease causing” with a score of 0.9999 (Mutation-
Taster). Since the only available additional information on
these two individuals was a non-verbal IQ of 57 and 58,
respectively, it is not possible to judge whether these indi-
viduals clinically also fit in the condition “CTNNB1 related
syndromic ID”. However, this might be well possible since

13
Hum Genet (2015) 134:97–109 107

Table 2  Overview of all CTNNB1 mutations identified in individuals with syndromic intellectual disability
Genomic position cDNA position Protein position Exon

Pat 1 chr3:g.41,277,959dupA c.1923dupA p.(Glu642Argfs*6) 12

Pat 2 chr3:g.41,275,254C>T c.1420C>T p.(Arg474*) 9
Pat 3 chr3:g.41,275,789G>A c.1683+1G>A splice mutation Intron 10
Pat 4 chr3:g.41,267,170_41,267,172insAAC 41,267,171delT c.755T>AAC p.(Leu251*) 6
Pat 5 chr3:g.41,266,626_41,266,627insG c.423_424insG p.(Tyr142Valfs*4) 4
Pat 6 and 7 (siblings) chr3:g.41,278,162_41,278,165dupAGCT c.2038_2041dupAGCT p.(Ser681*) 13
Pat 8 chr3:g.41,275,085_41,275,090insACGTG c.1251_1252insACGTG p.(Cys419*) 9
Pat 9 chr3:g.41,275,254C>T c.1420C>T p.(Arg474*) 9
Pat 10 chr3:g.41,266,486C>T c.283C>T p.(Arg95*) 4
Pat 11 chr3:g.41,274,913T>C c.1163T>C p.(Leu388Pro) 8
Pat 12 chr3:g.41,277,961_41,277,962delAG c.1925_1926delAG p.(Glu642Valfs*5) 12
Pat 13 chr3:g.41,266,102_41,266,103delTG c.99_100delTG p.(Gly34Asnfs*15) 3
Pat 14 chr3:g.41,268,844G>C c.1081+1G>C splice mutation Intron 7
Pat 15 chr3:d.41,275,106_41,275,109del c.1272_1275delTTCT p.(Ser425Thrfs*11) 9
Pat 16 chr3:g.41,209,868_41,714,118del whole gene deletion
Publ. pat. 1 (“3rd p”)a, b chr3:g.41,275,648C>T c.1543C>T p.(Arg515*) 10
Publ. pat. 2 (P70)a, b chr3:g.41,275,106_41,275,109delTTCT c.1272_1275delTTCT p.(Ser425Thrfs*11) 9
Publ. pat. 3 (“2nd p”)a, b chr3:g.41,267,341C>T c.925C>T p.(Gln309*) 6
Publ. pat. 4b chr3:g.41,267,034dupA c.705dupA p.(Gly236Argfs*35) 5
Publ. pat. 5c chr3:g.41,104,508_41,437,397del whole gene deletion

Genomic, cDNA and protein positions are given as well as affected exons. All genomic positions are based on GRCh37/hg19; CTNNB1 refer-
ence sequence is NM_001904.3
a
  Published by de Ligt et al. (2012)
b
  Published by Tucci et al. (2014)
c
  Published by Dubruc et al. (2014)

seven out of 21 individuals also show some autistic features
(see Supplementary Table S1).
Further functional characterization of a CTNNB1 muta-
tion was performed by Tucci et al. (2014) who used a
mouse mutant (‘batface’, Bfc) carrying a heterozygous
Thr653Lys mutation in the C-terminal armadillo repeat of
the protein (see Fig. 2). They carried out morphological,
behavioral, molecular and physiological investigations and
compared the murine with the human phenotype. Mutant
mice showed craniofacial abnormalities (shortened antero-
posterior axis, broad face, and shortened nasal length), as
well as morphologic brain changes, such as reduced cer-
ebellar and olfactory bulb size and underdeveloped corpus
callosum which was also observed in some of the affected
human individuals. Mutant mice also demonstrated behav-
ioral and cognitive abnormalities, motor deficits, and
decreased vocalization complexity, the latter possibly being
comparable to impaired speech ability in affected humans.
Beta-catenin was also found to be critical for dendritic
morphogenesis. Yu and Malenka (2003) showed that
increasing intracellular levels of beta-catenin and other
members of the cadherin/catenin complex enhance den-
dritic arborization in rat hippocampal neurons.
Beta-catenin is a key downstream component of the
canonical Wnt signaling pathway. Somatic gain-of-
function mutations in CTNNB1 have already been iden-
tified in various tumor types (e.g., colorectal cancer,
hepatocellular carcinoma, ovarian cancer and pilomatri-
coma). In none of the patients with inactivating muta-
tions, tumor manifestations have been observed and are
unlikely to be expected due to the converse mechanism
of haploinsufficiency.
Conclusion
The clinical features of individuals with inactivating
CTNNB1 mutations constitute a distinct syndromic phe-
notype that is characterized by ID, significant motor delay
with hypotonia of the trunk and (progressive) distal hyper-
tonia/spasticity of the legs, speech impairment, behavioral
anomalies, frequent microcephaly and overlapping facial
features. With this detailed clinical characterization of 16
newly identified individuals we delineated and further char-
acterized the clinical features of the novel CTNNB1-related
ID syndrome, thereby quadrupling the number of reported

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108
Fig. 2  Localization of deletions and mutations affecting CTNNB1.
a Localization of the CTNNB1 deletion detected in our patient 16
compared to the deletions in the patient published by Dubruc et al.
(2014), and the DECIPHER patient 275677. All three deletions affect
the entire CTNNB1 gene. b Schematic structure of CTNNB1 showing
the approximate positions of the mutations in relation to the 12 arma-
patients. Based on the number of patients that we identi-
fied in our cohorts we assume that this new CTNNB1 hap-
loinsufficiency syndrome might actually be a relatively fre-
quent cause of ID.
Acknowledgments  We are grateful to the patients and their families
for participating in this study and for giving consent to publish data
and photographs. We thank Sabine Kaya and Daniela Falkenstein for
excellent technical assistance. This work was supported by grants of
The Netherlands Organization for Health Research and Development
(ZonMw grant 907-00-365 to TK) and the European Union under the
7th framework program (Gencodys HEALTH-F4-2010-241995 to
HvB and TK).
Conflict of interest  The authors declare that they have no compet-
ing interests. The views expressed are those of the author and do not
reflect the official policy of the Department of the Army, the Depart-
ment of Defense or the U. S. Government.
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13
Hum Genet (2015) 134:97–109
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