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Expanding The Genotype Phenotype Correlation of de Novo Heterozygous Missense Variants in YWHAG
Expanding The Genotype Phenotype Correlation of de Novo Heterozygous Missense Variants in YWHAG
DOI: 10.1002/ajmg.a.61483
ORIGINAL ARTICLE
1
Sheffield Clinical Genetics Service, Sheffield
Children's NHS Foundation Trust, Abstract
Sheffield, UK Developmental and Epileptic encephalopathies (DEE) describe heterogeneous epi-
2
Clinical Genetics, Birmingham Women's and
lepsy syndromes, characterized by early-onset, refractory seizures and developmental
Children's NHS Foundation Trust,
Birmingham, UK delay (DD). Several DEE associated genes have been reported. With increased access
3
South West Thames Regional Genetics to whole exome sequencing (WES), new candidate genes are being identified
Service, St George's, University of London, UK
4
although there are fewer large cohort papers describing the clinical phenotype in
North East Regional Genetics Service, Great
Ormond Street Hospital, London, UK such patients. We describe 6 unreported individuals and provide updated information
5
Clinical Genomics and Research Programs, on an additional previously reported individual with heterozygous de novo missense
Gaithersburg, Maryland
6
variants in YWHAG. We describe a syndromal phenotype, report 5 novel, and a recur-
Human Genetics & Genomics, Northwell
Health System, New York, USA rent p.Arg132Cys YWHAG variant and compare developmental trajectory and treat-
7
Assistance Publique–Hôpitaux de Paris, ment strategies in this cohort. We provide further evidence of causality in YWHAG
Département de Génétique and Centre de
variants. WES was performed in five patients via Deciphering Developmental Disor-
Référence Déficiences Intellectuelles de
Causes Rares, Groupe Hospitalier ders Study and the remaining two were identified via Genematcher and AnnEX data-
Pitié-Salpêtrière, France
bases. De novo variants identified from exome data were validated using Sanger
8
Assistance Publique–Hôpitaux de Paris,
Service de Neuropédiatrie, Hôpital Armand sequencing. Seven out of seven patients in the cohort have de novo, heterozygous
Trousseau missense variants in YWHAG including 2/7 patients with a recurrent c.394C > T, p.
9
Département de génétique, hôpital Pitié-
Arg132Cys variant; 1/7 has a second, pathogenic variant in STAG1. Characteristic
Salpêtrière, Assistance publique-Hôpitaux de
Paris, France features included: early-onset seizures, predominantly generalized tonic–clonic and
10
Wessex Clinical Genetics Service, Princess absence type (7/7) with good response to standard anti-epileptic medications; mod-
Anne Hospital, Southampton, UK
11
erate DD; Intellectual Disability (ID) (5/7) and Autism Spectrum Disorder (3/7). De
Wellcome Trust Sanger Institute,
Cambridge, UK novo YWHAG missense variants cause EE, characterized by early-onset epilepsy, ID
12
Academic Unit of Child Health, University of and DD, supporting the hypothesis that YWHAG loss-of-function causes a neurologi-
Sheffield, Sheffield, UK
cal phenotype. Although the exact mechanism of disease resulting from alterations in
Correspondence YWHAG is not fully known, it is possible that haploinsufficiency of YWHAG in devel-
Meena Balasubramanian and Farah Kanani,
oping cerebral cortex may lead to abnormal neuronal migration resulting in DEE.
Sheffield Clinical Genetics Service, Sheffield
Children's Hospital NHS Foundation Trust,
Western Bank, Sheffield S10 2TH. KEYWORDS
Email: meena.balasubramanian@nhs.net (M. B.) developmental delay, early-onset seizures, epileptic encephalopathy, intellectual disability,
and farah.kanani@nhs.net (F. K)
YWHAG
Developmental and Epileptic Encephalopathies (DEE) are a group of Patient Predicted protein
severe childhood epilepsy disorders; genetics is believed to play an number YWHAG variant change
important role in epilepsy syndromes with an increasing number of 1 c.169C > G p.Arg57Gly
candidate genes being identified via whole genome and exome 2 c.398A > C p.Tyr133Ser
sequencing. Specific genes are still only discovered in a small propor- 3 c.532A > G p.Asn178Asp
tion of cases. 4 c.394C > T p.Arg132Cys
YWHAG is one such gene that has been implicated in DEE.
5 c.394C > T p.Arg132Cys
YWHAG (*605356) on Chr 7q11.23 encodes for YWHAG, a member
6 c.169C > T p.Arg57Cys
of 14–3-3 protein family, which are involved in intracellular signaling
7 c.529C > A p.Leu177Ile
pathways, playing an important role in signal transduction leading to
mitosis and cellular proliferation. Given their role, they are prevalent
in several human diseases (Aghazadeh & Papadopoulos, 2016). 3.2 | Patient 2: NM_012479 YWHAG: c.398A > C
YWHAG is highly expressed in brain, skeletal muscle and heart; (p.Tyr133Ser) Decipher ID- 276784
mouse models suggest an alteration in Ywhag level lead to delayed
neuronal migration in developing brain (Cornell, Wachi, Zhukarev, & A 16-year-old male with a history of a single generalized tonic–clonic
Toyo-Oka, 2016). ywhag1 knockdown in zebrafish show reduced seizure recently. He had global developmental delay, intellectual dis-
brain size, cardiomegaly and increased cardiac arrhythmia. Interstitial ability, and ASD. Neuroimaging was unremarkable. Dysmorphic facial
deletions at Chr 7q11.23 have led to infantile seizures and cardio- features included: downslanting palpebral fissures, downturned cor-
myopathy in patients with Williams-Beuren syndrome, suggesting ners of mouth, ptosis, and a bulbous nose.
haploinsufficiency of YWHAG as likely explanation (Komoike
et al., 2010).
3.3 | Patient 3: NM_012479 YWHAG: c.532A > G
(p.Asn178Asp) Decipher ID- 299681
2 | METHOD
A 7-year-old male in whom a de novo variant has also been identified
We present six previously unreported patients with de novo missense in STAG1. He was diagnosed with absence seizures at the age of
variants in YWHAG and provide updated information on one previ- 2 years. There had been no particular developmental concerns prior
ously reported individual to expand further on this patient's clinical to that time. He was initially treated with sodium valproate, but this
phenotype. WES was performed in five patients via Deciphering had little effect. The addition of Lamotrigine resulted in a change of
Developmental Disorders Study. Recruitment to this study was via personality and was ceased, and Ethosuximide then added. This
UK regional Clinical Genetics centers after routine referral. Two resulted in some improvement in seizure control. Since the sodium
patients were identified via Genematcher and AnnEX databases. valproate was stopped, seizure control improved further, and he has
De novo variants identified from exome data were validated using remained seizure-free on Ethosuximide, with a plan to wean this. He
Sanger sequencing. was also reported to have moderate global developmental delay, and
a diagnosis of autism was made at the age of 6 years; he has a number
of sensory issues. Neuroimaging was unremarkable.
3 | CLINICAL REPORTS
3.1 | Patient 1: NM_012479 YWHAG: c.169C > G 3.4 | Patient 4: NM_012479 YWHAG: c.394C > T
(p.Arg57Gly) Decipher ID- 280332 (p.Arg132Cys) Decipher ID- 269359
A 15-year-old female who presented with absence, focal, and This patient was previously reported by Guella et al. (Subject E) but is
generalized tonic–clonic seizure activity with onset at 10 months- included here as further phenotypic information has become available
of-age (Tables 1 and 2). Seizure control had been established with since the time of last reporting. A 23-year-old female with moderate–
Levetiracetam and Ethosuximide. She also had moderate global severe developmental delay, significant speech delay, moderate ID
developmental delay, intellectual disability, and a diagnosis of and ASD. Characteristic facial features included: hypertelorism, down-
autism spectrum disorder (ASD). Neuroimaging was unremarkable. slanting palpebral fissures and small ears. She has experienced gener-
With regards to facial dysmorphism, she had downslanting alized tonic–clonic, myoclonic, and absence seizures. Age of onset
palpebral fissures, an upturned nose, absent Cupid's bow and was reported to be less than six months-of-age. She has had a partial
small ears. response to Stiripentol and Sodium Valproate. Electroencephalogram
KANANI ET AL.
TABLE 2 Genotype and phenotypic features of patients within our cohort
3
TABLE 2
4
(Continued)
Note: One patient previously reported by Guella et al. 2017 (Patient 4) is included here, as further phenotypic information has been obtained since time of last reporting.
KANANI ET AL.
KANANI ET AL. 5
3.6 | Patient 6: NM_012479 YWHAG: c.169C > T Four patients are female. Five are currently under the age of 16; and
(p.Arg57Cys) Decipher ID-283758 two are 16 years or above.
F I G U R E 1 YWHAG gene (transcript ENST00000307630). Boxes indicate exons, lines introns. First amino acid of each exon shown above.
Predicted protein change from variants from patients in this series shown below gene. Functional domain shown below gene [Color figure can be
viewed at wileyonlinelibrary.com]
6 KANANI ET AL.
epileptics required was not available for one patient. One patient between those with the recurrent c.394C > T, p.Arg132Cys variant
(patient 4) achieved only partial response to anti-epileptic medication and the remainder cohort.
and there were no other reports of treatment refractory seizures. Neu-
roimaging was unremarkable in five of the seven patients. Patients
5 and 6 had frontal lobe hyperintensity and subtle signal changes in 5 | DI SCU SSION
frontal subcortical white matter on cranial MRI, respectively.
Many causal variants in developmental and epileptic encephalopathies
arise de novo with increasing numbers of candidate genes being iden-
4.4 | Neurodevelopment and cognition tified through WES. Allen et al., 2013 explored the impact of de novo
variants on neuropsychiatric disease risk, specifically on those associ-
Developmental delay was widely reported amongst our cohort with ated with infantile spasms and Lennox–Gastaut Syndrome via the Epi-
7/7 patients having global delay ranging from mild to severe. Del- lepsy Phenome/Genome Project (Allen et al., 2013). In this study,
ayed milestones were a frequent presentation with the average age Sanger sequencing confirmed 329 de novo variants in 264 trios that
of walking being 20 months (range 15 to 30 months) and age at first were analyzed. Each trio had on average 1.25 confirmed de novo vari-
words, 15 months (range 9 to 24 months). Many patients subse- ants in several genes that have also been linked to ID and ASD.
quently went on to experience further speech and language delay. In 2016, Vissers et al. subsequently reported that de novo point
Intellectual disability was present in six patients with additional edu- mutations, insertions or deletions, or structural genomic variation
cational support required. Autism Spectrum Disorder was reported accounted for most cases of severe ID and that this was likely to be the
in three patients including the patient who additionally carried a de case for other related neurodevelopmental disorders (Vissers, Gilissen, &
novo STAG1 mutation. Other behavioral anomalies were only Veltman, 2016).
reported in one patient, who had short attention span and challeng- YWHAG, a member of the 14–3-3 protein family, is involved in
ing behavior. modulating cell survival and control of apoptosis (Morrison, 2009;
Porter, Khuri, & Fu, 2006) and inhibition of 14-3-3 and ligand protein
binding causes apoptosis (Masters & Fu, 2001).
4.5 | Facial gestalt YWHAG was identified as a candidate gene for epilepsy by
Komoike et al., 2010 (Komoike et al., 2010). Here, they reported two
The most commonly noted features in our cohort included a promi- patients with Williams-Beuren Syndrome (WBS) who presented with
nent forehead, long palpebral fissures, bulbous nose, and absent infantile spasms, a rare presentation in WBS. Subsequent arrayCGH
Cupid's bow (Figure 2). and FISH analysis identified atypical deletions of 7q11. In one patient,
the deletion extended to the distal telomeric region, containing
YWHAG, amongst other genes. Reduced expression of YWHAG was
4.6 | Additional features seen in lymphocytes derived from the patient. Further analysis was
performed using gene knockdown of zebrafish. Knockdown of ywhag1
Other reported features included ataxia (1/7), thoracolumbar scoliosis (zebrafish homolog of human YWHAG) resulted in reduced brain size
(1/7), and tremors (1/7); though no firm correlation can be made. as well as ventricular enlargement and arrhythmia. The function of
There were no apparent dissimilarities in the overall phenotype YWHAG in cerebral and neural growth, required for normal
F I G U R E 2 Clinical photographs showing characteristic facial features including prominent forehead, long palpebral fissures, bulbous nose,
and absent Cupid's bow [Color figure can be viewed at wileyonlinelibrary.com]
KANANI ET AL. 7
development of brain and heart, was described and thus, YWHAG c.148A > C p.Lys50Gln through WES when exploring the interplay of
haploinsufficiency was proposed as a cause of infantile spasms and common and rare genetic variation in ASD (De Rubeis et al., 2014).
cardiomegaly, as seen in the subject with WBS. In the only YWHAG series to-date, Guella et al., 2017 described
Wachi et al., 2017 described the important role of 14-3-3 proteins in four patients with de novo variants in YWHAG and suggested it as a
neuronal migration. They identified that 14-3-3epsilon and 14-3-3zeta cause of early-onset epilepsy, DEE and ID (Guella et al., 2017). In this
are important for brain development and radial migration of pyramidal series, the de novo variants were predicted to impair dimerization and
neurons in the developing cerebral cortex. It was also reported that phosphopeptide binding. Age at seizure onset was typically under
14-3-3gamma-deficiency resulted in delayed neuronal migration as well 12 months; myoclonic seizure type being the most common with focal
as morphological defects. Therefore, disruption of 14-3-3 proteins is motor, the absence and eyelid myoclonia also reported.
known to be associated with pathological brain development and neuro- As demonstrated in our cohort, interestingly, seizure control was
nal migration defects (Wachi, Cornell, & Toyo-Oka, 2017). generally established with anti-epileptic medication, monotherapy
Previous to this, in 2013, Allen et al. described a patient with a de (most often sodium valproate) though each patient did require more
novo missense variant in YWHAG c.387C > G p.Asp129Glu in associa- than one medication at various stages in their treatment pathway, in
tion with epileptic encephalopathy (Allen et al., 2013) and De Rubeis order to maintain seizure control. ID was a common finding in this
et al. reported a patient with a de novo missense variant in YWHAG cohort, ranging from mild to severe and each of the patients had
TABLE 3 Genotype and phenotypic features of previously published patients (Guella et al., 2017)
T A B L E 4 Comparison of features in individuals with YWHAG patient 4. ML provided clinical information for patient 3. JJ, LP, and
variants compared with those reported in the literature CMcK provided clinical information for patient 5. CM, SV, and BK pro-
This study Guella Total reported vided clinical information for patient 7. KL provided clinical informa-
Clinical features cohort et al. 2017 features tion for patient 6. MB provided clinical information for patient 1 and
Seizures 7/7 3/3 10/10 was the senior supervisor of the project.
Seizure onset prior to 4/7 3/3 7/10
five years-of-age DATA AVAILABILITY STAT EMEN T
Treatment refractory 1/7 0/3 1/10 Data sharing is not applicable to this article as no new data were cre-
seizures ated or analysed in this study.
Facial dysmorphism 5/7 0/3 5/10
Developmental delay 7/7 3/3 10/10 OR CID
ID 6/7 2/3 8/10 Farah Kanani https://orcid.org/0000-0003-4388-0290
Speech impairment 4/7 1/3 5/10
Abnormal MRI brain 2/7 1/3 3/10 RE FE RE NCE S
Aghazadeh, Y., & Papadopoulos, V. (2016). The role of the 14-3-3 protein
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developmental delay. Neuroimaging was unremarkable in most cases,
Allen, A. S., Berkovic, S. F., Cossette, P., Delanty, N., Dlugos, D.,
with one patient found to have generalized atrophy with diffuse loss Eichler, E. E., … Winawer, M. R. (2013). De novo mutations in epileptic
of white matter. Facial dysmorphism was not commented upon in this encephalopathies. Nature, 501(7466), 217–221.
series. (Tables 3 and 4). Cornell, B., Wachi, T., Zhukarev, V., & Toyo-Oka, K. (2016). Regulation of
neuronal morphogenesis by 14-3-3epsilon (Ywhae) via the microtu-
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4405–4418.
6 | C O N CL U S I O N S De Rubeis, S., He, X., Goldberg, A. P., Poultney, C. S., Samocha, K.,
Cicek, A. E., et al. (2014). DDD study, homozygosity mapping col-
laborative for autism, UK10K consortium. Synaptic, transcrip-
The phenotypic data from our cohort supports YWHAG as a DEE can-
tional and chromatin genes disrupted in autism. Nature, 515,
didate gene. Our series indicates that de novo YWHAG missense vari-
209–215.
ants cause DEE, characterized by early-onset epilepsy, ID and DD, Guella, I., McKenzie, M. B., Evans, D. M., Buerki, S. E., Toyota, E. B., Van
supporting the possible hypothesis that YWHAG loss-of-function cau- Allen, M. I., … Epilepsy Genomics Study. (2017). Deciphering develop-
ses a neurological phenotype. We report an extended phenotype and mental disorders study. De Novo mutations in YWHAG cause early-
onset epilepsy. American Journal of Human Genetics, 2, 300–310.
propose that there are similar seizure phenotypes. While multiple
Komoike, Y., Fujii, K., Nishimura, A., Hiraki, Y., Hayashidani, M.,
antiepileptic medications may be needed to establish seizure control, Shimojima, K., … Saitsu, H. (2010). Zebrafish gene knockdowns imply
treatment resistant epilepsy appears to be rare. There appears to be a roles for human YWHAG in infantile spasms and cardiomegaly. Gene-
strong association between de novo YWHAG variants, global develop- sis, 4, 233–243.
Masters, S. C., & Fu, H. (2001). 14-3-3 proteins mediate an essential anti-
mental delay, and mild–moderate ID.
apoptotic signal. The Journal of Biological Chemistry, 276,
There also appears to certain variant hotspots in YWHAG as 45193–45200.
described here, further case reports of patients with this recurrent Morrison, D. K. (2009). The 14-3-3 proteins: Integrators of diverse signal-
variant are needed to determine if these patients have a discernible, ing cues that impact cell fate and cancer development. Trends in Cell
Biology, 19, 16–23.
more specific phenotype but from our cohort, this does not appear to
Porter, G. W., Khuri, F. R., & Fu, H. (2006). Dynamic 14-3-3/client protein
the case from the data collected so far. interactions integrate survival and apoptotic pathways. Seminars in
We propose that haploinsufficiency of YWHAG in developing cere- Cancer Biology, 16, 193–202.
bral cortex leads to abnormal neuronal migration resulting in EE. Further Vissers, L. E., Gilissen, C., & Veltman, J. A. (2016). Genetic studies in intellec-
tual disability and related disorders. Nature Reviews. Genetics, 17(1), 9–18.
patients and functional studies will help determine this hypothesis.
Wachi, T., Cornell, B., & Toyo-Oka, K. (2017). Complete ablation of the
14-3-3epsilon protein results in multiple defects in neuropsychiatric
ACKNOWLEDGMENTS behaviors. Behavioural Brain Research, 319, 31–36.
Deciphering Developmental Disorders Study, Wellcome Trust Sanger
Institute, Cambridge, UK.