A Witteveen-Kolk Syndrome Patient with Reflux Disease and a de novo Deletion of the SIN3A Gene

Abstract

Introduction

The Witteveen-Kolk syndrome (WITKOS) (OMIM: 613406) is a heterogeneous emerging disorder caused by pathogenic variants or microdeletions encompassing the SIN3A gene (SIN3 Transcription Regulator Family Member A). It is characterized by distinctive facial features, developmental delay, intellectual disability, microcephaly, short stature, and subtle anomalies on brain magnetic resonance imaging (MRI). To date, about 50 patients have been reported in the medical literature.

Patient Presentation

In this article, we reported a patient with classic findings of WITKOS including global developmental delay, microcephaly, hypotonia, vomiting, malnutrition, autistic and dysmorphic facial features, and cardiac abnormalities. Also, a barium esophagogram suggested severe motility disorder and gastroesophageal reflux disease. Affymetrix CytoScan 750K microarray showed a de novo 1.6-Mb deletion at 15q24.1q24.2, including the whole SIN3A gene. We have also summarized the clinical features of WITKOS patients in the medical literature and cardiac abnormalities detected in 4 out of 10 patients in studies that clearly state that cardiac examination was performed in the patients.

Conclusion

Our findings showed that cardiac defects are not uncommon findings in WITKOS. Physicians should also be aware of reflux disease and motility disorder in patients with feeding difficulty together with early cardiac examination in terms of an improved quality of life in WITKOS patients.

Established Facts

• The Witteveen-Kolk syndrome (WITKOS) (OMIM: 613406) is a heterogeneous emerging disorder caused by pathogenic variants or microdeletions encompassing the SIN3A gene.

• It is characterized by distinctive facial features, developmental delay, intellectual disability, microcephaly, short stature, and subtle anomalies on brain magnetic resonance imaging.

• To date, about 50 patients have been reported in the medical literature.

Novel Insights

• We summarized the clinical features of WITKOS patients in the medical literature and cardiac abnormalities detected in 4 out of 10 patients in studies that clearly state that cardiac examination was performed in the patients.

• Our findings showed that cardiac defects are not uncommon findings in WITKOS.

• Physicians should also be aware of early cardiac examination in terms of an improved quality of life in WITKOS patients.

Introduction

Witteveen-Kolk syndrome (WITKOS, OMIM 613406) is an emerging neurodevelopmental disorder caused by heterozygous loss of function variants or microdeletions encompassing the SIN3A gene (SIN3 Transcription Regulator Family Member A). It is characterized by developmental delay, intellectual disability, hypotonia, microcephaly, short stature, distinctive facial features, psychiatric or behavioral disorders, and subtle anomalies on brain magnetic resonance imaging (MRI) [1]. Cardiac abnormalities are not considered a common clinical feature for WITKOS.

WITKOS is due to haploinsufficiency for the SIN3A gene, which results from either heterozygous loss-of-function variants or de novo deletions, as in the present case. This gene encodes a transcriptional regulatory protein, which is associated with scaffolding in the core histone deacetylase complex and mediates transcriptional silencing, DNA and histone methylation, nucleosome remodeling, and cell growth and proliferation [2].

Herein, we described a patient with WITKOS who had cardiac abnormalities and a de novo 1.6 Mb-sized deletion on chromosome 15 (15q24.1q24.2) including the SIN3A. We also reviewed the literature for patients with WITKOS who have well-defined clinical features.

Patient Presentation

Patients and Ethics Statement

We ascertained probands from a nonconsanguineous Turkish family. We obtained written informed consent from the family of the patient for participation in this study and accompanying images. The study was performed according to the Declaration of Helsinki protocols.

Karyotypes Analysis

Karyotype analysis was only performed for the patient. Karyotypes (at standard band resolution of 450–550) were determined by the analysis of 20 Giemsa-stained metaphases each from standard 72-h peripheral blood lymphocyte cultures.

Chromosomal Microarray Analysis

DNA was extracted from peripheral blood lymphocytes for the patient and his parents using QIAamp DNA blood mini kit (Qiagen, Germany) as the manufacturer instructed. The concentration and purity of genomic DNA were measured using a NanoDrop One Microvolume UV-Vis spectrophotometer (Thermo Fisher Scientific, USA). DNA digestion, amplification, purification, fragmentation, labeling, hybridization, washing, staining, scanning, and other steps were carried out according to the manual for an Affymetrix Genome CytoScan 750K gene chip (Affymetrix, Santa Clara, CA, USA). Genotype calling, quality control, and identification of copy-number variation (CNV) were performed using Affymetrix Chromosome Analysis Suite software (ChAS) (version 4.0; Affymetrix; Thermo Fisher Scientific, Inc.), with various databases employed for evaluation of the array data and analysis of genotype-phenotype correlations, including OMIM (http://www.ncbi.nlm.nih.gov/omim), DECIPHER (http://decipher.sanger.ac.uk/), DGV (http://projects.tcag.ca/variation) and ISCA (http://dbsearch.clinicalgenome.org/search/). CNVs >200 kb for gain, and>100 kb for loss with more than 25 deviating probes were accessed with the ChAS. GRCh37 (hg19) was used as the reference sequence. CNVs are described using, respectively, ISCN 2020 and HGVS nomenclature. CNV interpretation was based on guidelines published by the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen) [3].

Patient Report

A 1.5-year-old boy was referred to our clinic for global developmental delay, hypotonia, vomiting, malnutrition, and dysmorphic appearance. He was the third living born to nonconsanguineous marriage at 34^5/7 weeks via cesarean section with a birth weight of 2,200 g (25–50p) and hospitalized at the neonatal intensive care unit due to hypernatremic dehydration and respiratory distress. Family history was unremarkable.

In physical examination, he had microcephaly, high forehead, frontal bossing, long face, hypertelorism, long and smooth philtrum, microretrognathia, large and low-set ears, bilateral epicanthal folds, long eyelashes, depressed nasal bridge, short nose, small and open mouth, thin hair and high anterior hairline, and pectus excavatum (shown in Fig. 1). Anthropometric measurements revealed chronic malnutrition with severe failure to thrive. Detailed neurological examination revealed that he was able to hold his head and sit unassisted; however, his head was lagging on traction and unable to walk. A severe language delay was also detected. His developmental milestones were grossly delayed, and he also had autism findings such as repetitive hand movement. His hearing was normal at 6 months.

Fig. 1.

Appearance of patient from anterior (a) and lateral (b) view.

Since the patient was vomiting and had feeding difficulty for more than 1 year, a barium esophagogram was performed showing delayed gastric emptying suggesting motility disorder and severe reflux disease. During the follow-up, he received a proton pump inhibitor in combination with low-dose prokinetic agent and responded well to the treatment. Echocardiography revealed patent foramen ovale and patent ductus arteriosus in the patient. Electroencephalography showed no epileptic activity. For visual electrical latency assessment, right p100 was delayed and left p100 latency was normal. Brainstem auditory-evoked potentials were normal. A brain MRI revealed mild cortical atrophy.

Genetic Study Results

SMN1 (OMIM: 600354) and BTD (OMIM: 609019) gene analysis and chromosome analysis of the patient are unremarkable. Chromosomal microarray analysis of DNA extracted from peripheral blood revealed a de novo heterozygous 1.6 Mb deletion arr[GRCh37] 15q24.1q24.2(74,395,281_76,053,016)*1 in the patient (shown in Fig. 2). The deleted region encompasses 46 protein-coding genes and 8 morbid genes: STRA6, CYP11A1, SEMA7A, EDC3, MPI, COX5A, MAN2C1, and SIN3A. Except for SIN3A, haploinsufficiency of these genes is tolerated [4]. This deletion encompassing the SIN3A gene explains the phenotype of our patient.

Fig. 2.

a Schematic representation of deleted region in the patient and ClinGen dosage sensitivity map. b Cytogenetic microarray results representing the 15q24.1q24.2 microdeletion of 1.6 Mb arr[hg19] 15q24.1q24.2 (74,395,281–76,053,016), including SIN3A.

Discussion

Here, we describe a patient with WITKOS who had a de novo 1.6 Mb-sized deletion on chromosome 15 (15q24.1q24.2) including the SIN3A. SIN3A is essential for cortical neurogenesis, altered neuronal identity, and aberrant corticocortical projections, and haploinsufficiency of this gene causes WITKOS. To date, about 50 patients with WITKOS have been reported in previous studies.

Echocardiography revealed the presence of patent foramen ovale and patent ductus arteriosus in our patient. To date, cardiac abnormalities in patients with WITKOS have been reported in 4 different studies, which clearly state that cardiac examination was performed in the patients. These findings are atrial septal defect in 3 patients [5, 6], ventricular septal defect in 1 patient [7], and Tetralogy of Fallot in 1 patient [8]. Our study also indicates that cardiac abnormalities could be a more common clinical feature than reported in WITKOS patients.

SIN3A gene plays a regulatory role in the control of various developmental processes, including cortical expansion and maturation. Language and motor delay were previously reported in patients with WITKOS. Brain MRI of the current patient revealed mild cortical atrophy consistent with the previous studies [6].

In the previous literature, reported gastrointestinal findings in patients with WITKOS were failure to thrive, constipation, feeding difficulties due to oro-motor coordination dysfunction, and cow’s milk protein allergy in pediatric age as well as sigmoid adenocarcinoma in adult life [9]. As far as we know motility disorder and severe gastroesophageal reflux disease were not reported, hence physicians should be aware when evaluating feeding difficulties in patients with WITKOS.

We summarize the clinical features of all previously reported patients with WITKOS in Table 1. According to this review, most common clinical manifestations of WITKOS were DD (75%), dysmorphic facial features (97%), microcephaly (55%), short stature (30%), hypotonia (49%), behavioral problems (52%), epilepsy (18%), ectodermal differences (25%), brain abnormalities (38%), and cardiac abnormalities (40%) (Table 1) [1, 5, 6, 9–13]. Consistent with these reports, our patient showed DD, microcephaly, short stature, autistic behavior, and hypotonia but not epilepsy nor ectodermal anomalies.

Table 1.

Phenotypic features of patients with Witteveen-Kolk syndrome

	Our patient	Witteveen 2016 [1]	Ferrer 2019 [10]	Narumi-Kishimoto 2019 [11]	Sleyp 2020 [12]	Ercoskun 2020 [6]	Balasubramanian 2021 [9]	Penon-Portmann 2022 [13]	Coenen-van der Spek 2023 [5]	Total reported patients (n = 49)
Developmental delay	+	9/9	+	+	+	+	16/28	+	6/6	37/49 (75%)
Facial features	+	9/9	+	+	+	+	13/13	+	4/5	32/33 (97%)
Abnormal brain MRI	−	5/5	NR	NR	−	+	6/28	+	2/3	15/39 (38%)
Behavioral problems	+	4/5	+	+	+	+	12/28	−	2/6	23/44 (52%)
Microcephaly	+	3/7	−	−	−	−	14/26	−	4/6	22/40 (55%)
Short stature	+	4/9	+	−	−	+	6/28	−	1/6	14/46 (30%)
Hypotonia	+	2/9	+	NR	+	NR	12/28	+	5/6	23/47 (49%)
Epilepsy	−	2/8	−	−	−	−	4/28	−	1/6	7/38 (18%)
Ectodermal differences	–	1/6	+	−	−	NR	NR	−	2/5	4/16 (25%)
Cardiac finding	+	NR	−	NR	−	+	NR	NR	2/6	4/10 (40%)*

In conclusion, we reported a male patient harboring a de novo 1.6 Mb-sized deletion on chromosome 15 (15q24.1q24.2) including the SIN3A who presented with global developmental delay, microcephaly, hypotonia, malnutrition, autistic features, and dysmorphic facial features consisted with the previous WITKOS patients. Our findings also suggest that cardiac defects are not uncommon findings in WITKOS patients, and they would benefit from early cardiac examination in terms of improved quality of life.

Acknowledgments

We would like to thank the patient and his parents for their cooperation.

Statement of Ethics

The protocols used in this study were in compliance with the Declaration of Helsinki. Written informed consent was obtained from the parent/legal guardian of the patient for publication of the details of their medical case and any accompanying images. Informed consent for genetic analysis was obtained from the family in compliance with national ethics regulations. As so, ethical approval was not required for this study in accordance with local/national guidelines.

Conflict of Interest Statement

The authors declare no conflict of interest.

Funding Sources

The authors have no funding sources to declare.

Author Contributions

All authors read and approved the manuscript. E.U. and N.K. designed and coordinated the study. N.K., A.N.K., and B.K. performed clinical investigations. E.U. performed the visualization of data. E.B.O. and S.T. performed molecular analysis. E.U., N.K., and A.Y. drafted the manuscript. A.Y. provided critical revisions. Review and editing of manuscript: all authors.

Funding Statement

The authors have no funding sources to declare.

Data Availability Statement

All data generated or analyzed during this study are included in this article. Further inquiries can be directed to the corresponding author.