A Novel Intragenic Duplication of CREBBP in Rubinstein-Taybi Syndrome: A Case Report Expanding the Genotype-Phenotype Spectrum

Abstract

Introduction

Rubinstein-Taybi syndrome (RSTS) is most often caused by loss-of-function variants in CREBBP; intragenic duplications are rare and extremely under-recognized.

Case Presentation

We describe a 5-year-old girl with global developmental delay, intellectual disability, frontal bossing, upslanted palpebral fissures, broad angulated halluces, and scoliosis. Whole-exome sequencing with copy number analysis revealed a heterozygous de novo duplication of approximately 13 kb encompassing exons 7–16 of CREBBP (NM_004380.3). Multiplex ligation-dependent probe amplification confirmed the duplication in the proband and excluded it in both parents. The event is predicted to introduce a frameshift, leading to premature truncation. No additional pathogenic variants were detected.

Conclusion

This is the first reported CREBBP duplication spanning exons 7–16, expanding the mutational spectrum of RSTS and illustrating that intragenic duplications can manifest with a partially atypical craniofacial profile. The case underscores the value of incorporating high-resolution copy number interrogation into RSTS workflows when single nucleotide variant analysis is uninformative and supports systematic deposition of such variants to refine genotype-phenotype correlations.

Established Facts

• Pathogenic CREBBP loss-of-function variants (nonsense, frameshift, splice-site, deletions) explain around 60% of Rubinstein-Taybi syndrome (RSTS) cases.

• Intragenic deletions and single nucleotide variants are well documented; intragenic duplications are exceptionally rare (only three published to date).

• Duplications predicted to disrupt the reading frame can trigger nonsense-mediated decay or produce truncated CREBBP lacking critical functional domains, leading to the RSTS phenotype.

Novel Insights

• First reported duplication spanning CREBBP exons 7–16 (NM_004380.3) (∼13 kb).

• De novo duplication confirmed by whole-exome sequencing-copy number variant (CNV) analysis and multiplex ligation‐dependent probe amplification, underscoring the utility of copy number interrogation when sequencing is negative.

• Patient shows partial but not full classic craniofacial profile (frontal bossing, upslanted palpebral fissures without low columella, or grimacing smile), broadening the recognized phenotypic spectrum associated with duplications.

• Reinforces the importance of maintaining CNV analysis within routine RSTS diagnostic workflows.

Introduction

Rubinstein-Taybi syndrome (RSTS) is a rare autosomal dominant disorder, with an approximate prevalence of 1 in 125,000 live births [1]. The hallmarks of RSTS include intellectual disability, postnatal growth retardation, broad and angulated first toes and thumbs, and typical craniofacial features such as downslanted palpebral fissures, microcephaly, highly arched eyebrows, a grimacing smile, a hanging columella, a high palate, and talon cusps. Other common features are ocular anomalies, hearing impairment, respiratory problems, cardiac and kidney anomalies, undescended testes (cryptorchidism), feeding difficulties, frequent infections, chronic constipation, and an increased risk of both benign and malignant tumors [2].

RSTS is most frequently (55–60% of cases) caused by pathogenic variants in CREBBP or its paralog EP300 [2]. CREBBP is a ubiquitously expressed gene located on the short arm of chromosome 16 band 13.3 (16p13.3), containing 31 exons and spanning 150 kilobases (kb). It encodes the CREB-binding protein, a 2,442 amino acid protein involved in transcription regulation, as a coactivator for the interaction between the RNA polymerase II complex and various transcription factors [3]. Through its histone acetyltransferase (HAT) activity, CREBBP also plays a role in chromatin remodeling and gene expression [4]. Primarily through these two mechanisms, CREBBP affects the expression of multiple genes related to apoptosis, tumor suppression, cellular differentiation, and cell growth [2].

To date, at least 450 unique pathogenic variants have been publicly submitted for CREBBP [5]. Frameshift, nonsense, missense, and splicing variants account for the majority (30–50%) of CREBBP variants identified in RSTS. Approximately 10% of cases involve disease-causing deletions of varying sizes, which may be intragenic, encompass the entire gene, or extend into adjacent regions. Inversions and translocations also contribute to the allelic heterogeneity of RSTS. However, the molecular basis remains elusive in roughly 25–30% of individuals with clinical signs suggestive of RSTS [6].

In addition to those well-recognized mechanisms, intragenic microduplications, although exceedingly rare with only 3 cases published [6–8], are equally significant in the pathogenesis of RSTS. This report presents a rare case of RSTS with a de novo heterozygous intragenic microduplication of 16p13.3, approximately 13 kb in size, and comprising exons 7–16 of CREBBP (NM_004380.3). Our aim was to enhance the understanding of how various genetic alterations in CREBBP can result in RSTS while emphasizing the importance of investigating intragenic duplications in clinical settings.

Case Report

The patient is a 5‐year‐old female, born at term (birth length 48 cm [25th centile, −0.66 SD], weight 2,450 g [2nd centile, −2.06 SD]) who required a 6‐day neonatal intensive care unit stay for respiratory distress. She had normal cardiac evaluations (normal echocardiogram).

Her developmental milestones have been significantly delayed. She first sat without support at 14 months, walked independently at 3.5 years (with persistent toe walking), and at 5 years of age remains nonverbal (previously used only 2–3 words sporadically). She exhibits bruxism, limited eye contact, repetitive motor behaviors when distressed, and no toilet training to date. She attends special education and receives occupational therapy, with some limited use of sign language. Although she has difficulty following instructions, she can recognize familiar individuals. A Denver Developmental Screening Test indicated approximately 95% developmental impairment, consistent with global developmental delays and intellectual disability. Brain MRI and metabolic assessments have been normal.

At her current age of 5 years, her height is 106 cm (14th centile, −1.1 SD), weight is 15.4 kg (6th centile, −1.54 SD), and BMI is 13.71 (9th centile, −1.37 SD). Head circumference was not recorded at birth or at present. Although somewhat small for weight at birth (−2.06 SD), she does not appear to have ongoing clinically significant growth deficiency.

She has chronic constipation since infancy and continues to have feeding challenges. Physical examination reveals frontal bossing, upslanted palpebral fissures, cup‐shaped anteverted ears, and broad angulated halluces bilaterally; she has scoliosis. No grimacing smile, high palate, or talon cusps are noted. Hearing is normal. There is no history of recurrent infections, genitourinary anomalies, or tumor formation.

Whole-exome sequencing with copy number variant analysis was performed and identified a de novo heterozygous intragenic duplication of approximately 13 kb at 16p13.3, encompassing exons 7–16 of the CREBBP gene (NM_004380.3). This duplication was confirmed by multiplex ligation‐dependent probe amplification and was not detected in either parent, confirming a de novo event.

Discussion

Intragenic duplications are commonly observed in a tandem configuration [9]. Such duplications presumably cause a frameshift, which may cause a premature stop codon, which may lead to nonsense-mediated mRNA decay or the production of a truncated protein. These disruptions may lead to loss of function, which is a well-known pathogenic mechanism in CREBBP [10–12].

Previously, a limited number of similar intragenic duplications in CREBBP have been reported in both the literature and ClinVar. Notably, three previously reported intragenic duplications involved exons 14–19 [6], exon 16 (189 bp) [8], and exon 1 (∼100 bp) [7], respectively. Each of these duplications has been associated with phenotypes characteristic of RSTS. Table 1 compares the clinical features observed in our patient with a previously reported case of CREBBP intragenic duplication [6] and typical RSTS cases [2]. Typical craniofacial traits of RSTS including highly arched eyebrows, slanted palpebral fissures, convex nasal ridge, low hanging columella, and the characteristic grimacing smile are present in >90% of cases [13]. Our patient shows frontal bossing and upslanted palpebral fissures but notably lacks the low columella, highly arched palate, and grimacing smile, exhibiting partial phenotype overlap.

Table 1.

Comparison of clinical features in Rubinstein-Taybi syndrome (RSTS): typical prevalence versus the present patient and a previously published intragenic duplication case by Pérez-Grijalba et al. [6] (2019)

Feature	Typical prevalence in RSTS [2, 13]	Our patient	Pérez-Grijalba et al. [6] (2019)
Growth deficiency	73%	Mild (birth weight −2 SD; height −1 SD; weight −1.5 SD at 5 years)	Yes
Eye findings	80%	Mild myopia (−0.75) and esotropia	Downslanting PF, epicanthus, NLD obstruction, long eyelashes,
Facial dysmorphisms	≥90%	Frontal bossing, upslanted PF, cup-shaped anteverted ears (no low columella/high palate)	Thick arched eyebrows, long eyelashes, microcephaly, downslanting PF, columella below alae, narrow palate and mouth, prominent forehead
Hearing loss	30%	No (audiology normal)	Not reported
Respiratory features	Common	Neonatal respiratory distress, no chronic issues	Not reported
Cardiac features	33%	No (echocardiogram normal)	Not reported
Genitourinary anomalies	27%	No	Urinary-tract anomalies, cryptorchidism, shawl scrotum
Gastrointestinal features	88%	Chronic constipation, long-standing feeding difficulty	Infant feeding problems, constipation
Skeletal abnormalities	Common	Scoliosis, broad, angulated halluces, persistent toe walking	Broad thumbs/halluces, angulated thumbs, pes planus, camptodactyly, syndactyly, polydactyly, hallux duplication
Neurologic issues	21%	Motor delay/early hypotonia, no seizures	Hypotonia
Dental anomalies	73%	None yet (no talon cusps in primary dentition)	Teeth malformations
Skin findings	24%	No keloids or hirsutism	Hirsutism, hemangioma
Recurrent infections	17%	No	Not reported
Tumors	30%	No	Not reported
Developmental delays	98%	Global delays (∼95% impairment on Denver)	Intellectual, psychomotor and language delays
Behavioral issues	41% autism/27–64% anxiety	Autistic-like traits, repetitive motor behaviors, limited eye contact	Not assessed (anxiety/autism N/A)
Brain MRI abnormalities	74%	No (brain MRI normal)	Not available

Prevalence data adapted from GeneReviews [2] and Lacombe et al. [13] (2024). “Not reported/not available” denotes missing source data; “no” means the feature was assessed and absent.

Additionally, 4 pathogenic or likely pathogenic intragenic duplications spanning exons 14–21 (∼21 kb), 16 (∼200 bp), 27–28 (∼800 bp), and 24–27 (4 kb) are present in the ClinVar database. Among these, the duplication involving exon 16 (189 bp) [8] is the only 1 confirmed to cause a frameshift, leading to an early stop codon. The pathogenic mechanism of other duplications remains uncertain. Figure 1 illustrates the structure of the CREBBP gene, showing exon locations, functional domains, and the reported intragenic duplications, including the current case and previously described events.

Fig. 1.

Structure of the CREBBP gene showing exon positions, functional domains, and all reported intragenic duplications. The present duplication (NM_004380.3 exons 7–16, ∼13 kb) is highlighted in blue; previously published events (exons 1, 14–19, 16, 24–27, 27–28) and ClinVar submissions are indicated in green.

Taken together with our case, these findings indicate that further research is needed to elucidate the exact pathogenic mechanisms caused by relatively larger duplications in CREBBP and to determine whether they result from frameshift disruptions or other mechanisms. This case also supports the importance of including copy number variant analysis in genetic testing for RSTS, emphasizing that duplications should not be overlooked.

Acknowledgment

We thank the family for their cooperation.

Statement of Ethics

Written informed consent was obtained from the parent/legal guardian of the patient for publication of the details of their medical case. Ethical approval was not required for this study in accordance with national guidelines. This case report has been prepared in accordance with the CARE Checklist (available at https://doi.org/10.1159/000547120).

Conflict of Interest Statement

The authors have no conflicts of interest to declare.

Funding Sources

This study received no external funding.

Author Contributions

E.D. drafted the manuscript and prepared the figure and table. E.U. collected clinical data and performed and interpreted the genetic testing. S.G. conducted the patient’s clinical evaluation and provided follow-up data. H.M. also contributed to the performance and interpretation of the genetic analyses. A.Y. conceived the study, supervised all stages of the work, and critically revised the manuscript. All authors approved the final version of the manuscript.

Funding Statement

This study received no external funding.

Data Availability Statement

The datasets generated during the current study are available from the corresponding author on reasonable request.