From weeks to hours: rapid whole-genome sequencing reduces diagnostic odyssey in Menke–Hennekam syndrome—a case report

Abstract

Background

Menke–Hennekam syndrome (MKHK) is a rare autosomal dominant disorder caused by mutations in the CREBBP and EP300 genes. The absence of established diagnostic criteria and non-specific clinical manifestations complicate timely diagnosis and management. This report presents a case of MKHK in which early diagnosis and intervention were achieved through the application of rapid whole-genome sequencing (rWGS), a tool that offers superior speed and genomic coverage compared to whole-exome sequencing (WES).

Case presentation

This case report describes a male Han Chinese neonate who presented at birth (0 days) with intrauterine growth restriction, respiratory distress, and feeding difficulties. During follow-up, he developed hearing loss and demonstrated global developmental delay. Clinical examination revealed craniofacial dysmorphism. Trio rWGS was performed in the neonatal period, with results returned within 72 h of sample submission at 23 days of age. Trio rWGS identified a de novo missense variant in the CREBBP gene (c.5570A > C, p.His1857Pro). Sanger sequencing confirmed its absence in both parents, and the variant was classified as likely pathogenic despite no prior documented cases. Based on integrated genetic and clinical findings, a neonatal diagnosis of MKHK-ID4 was established. Following this diagnosis, early targeted interventions were initiated, including hearing aid fitting, enrollment in a comprehensive rehabilitation program, and planning for necessary surgical corrections. Significant developmental improvement was observed at the 15-month follow-up assessment.

Conclusion

In this case, rWGS facilitated a neonatal diagnosis of MKHK-ID4 and enabled early multidisciplinary intervention during a critical neurodevelopmental window. This experience suggests that such an approach may contribute to improved developmental outcomes in this rare disorder, though further studies are required to confirm its broader applicability and long-term benefits.

Introduction

Menke–Hennekam syndrome (MKHK) is a rare autosomal dominant disorder caused by pathogenic variants in CREBBP (MKHK1; OMIM: 618,332) or EP300 (MKHK2; OMIM: 618,333) [1, 2]. Distinguished from Rubinstein–Taybi syndrome (RSTS) by the absence of its hallmark broad digits, MKHK1—associated with CREBBP exons 30–31 variants—typically presents more severe features than MKHK2 [1, 3–9]. Recent domain-based classifications (ZZ/TAZ2/ID4) have refined genotype–phenotype correlations [10].

Whole-exome sequencing (WES) is the primary diagnostic tool for MKHK [1–4, 10–12]. Its standard turnaround time, however, is 4–8 weeks due to procedures such as hybrid capture and bioinformatic analysis, which critically delays intervention. Notably, most cases are diagnosed after 24 months of age [1–4, 10], and neonatal diagnoses are exceedingly rare. This delay often results in missed opportunities to initiate interventions within the critical neurodevelopmental window (0–24 months), thereby risking irreversible impairment of cognitive and motor development.

We report a neonatal diagnosis of MKHK-ID4 established via trio rapid whole-genome sequencing (rWGS) within approximately 3 days post-sample submission—significantly shorter than the conventional multi-week timeframe. A de novo missense variant in exon 31 of CREBBP (c.5570A > C, p.His1857Pro; ClinVar: VCV000422204.2) was identified, and its potential pathogenicity was supported by phenotype correlation.

Case presentation

A male neonate (G1P1) of Han Chinese ethnicity with healthy parents, on day 0 of life, admitted to the NICU for dyspnea and weak crying, had antenatal findings of oligohydramnios, intrauterine growth retardation, and mild left posterior horn ventriculomegaly (10.2 mm). Amniocentesis with karyotype and copy number variation sequencing (CNV-seq) was unremarkable. The infant was delivered via cesarean section at 37³/⁷ weeks’ gestation due to oligohydramnios, with a birth weight of 2100 g, length of 45 cm, head circumference of 30 cm, and Apgar scores of 8, 10, and 10 at 1, 5, and 10 minutes, respectively. Physical examination during this period revealed poor nutritional status, weak cry, and decreased response to stimuli. Dysmorphic features included micrognathia, hypertelorism, blepharophimosis, a long philtrum, sparse hair, low-set left ear, bilateral undescended testes, and a gradually appearing egg-sized mass in the right inguinal region. Additional findings included a small penis, diminished primitive reflexes, hypertonia, and dorsiflexion with eversion of the ankles. Broad thumbs or toes were not observed (Fig. 1).

Fig. 1.

Physical Characteristics of the Patient. a, b Broad thumbs or toes were not observed. c Bilateral undescended testes, egg-sized mass in the right inguinal region and a small penis

Postnatal auxiliary examinations revealed the following: echocardiography raised suspicion of a small atrial septal defect (ASD), although the findings were inconclusive. Additionally, complete blood count indicated mild anemia, and biochemical tests showed hypoalbuminemia and hyperbilirubinemia. Amplitude-integrated electroencephalography (aEEG) at 23 days of age showed normal background activity for the corrected gestational age. Brain magnetic resonance imaging (MRI) demonstrated thinning of the corpus callosum, bilateral ventricular dilation, presence of the cavum septum pellucidum, and widened extracerebral spaces in the temporal and cerebellar hemispheres. Screening for inborn errors of metabolism was unremarkable. Genomic DNA from the proband and parents underwent trio rWGS on an MGI DNBSEQ-T7 platform (mean coverage: 30 ×) at 20 days of age. Sequencing reads were aligned to the human reference genome (GRCh37/hg19) using the Burrows–Wheeler Aligner (BWA). Variant calling was conducted using the Genome Analysis Toolkit (GATK). The pathogenicity of identified variants was assessed according to the guidelines of the American College of Medical Genetics and Genomics (ACMG). Results were available within 72 h (at 23 days of age) and identified a de novo missense variant in the CREBBP gene (NM_004380.3): c.5570A > C (p.His1857Pro). This variant was classified as likely pathogenic in ClinVar and had no previously documented pathogenic cases. Sanger sequencing confirmed the variant and its de novo origin by excluding its presence in both parents (Fig. 2). Based on the above findings, we established the clinical diagnosis of MKHK-ID4. After diagnosis, the parents declined the offer of genome-wide methylation profiling. On day 24, the Test of Infant Motor Performance (TIMP) score was 51, equivalent to 35–36 weeks corrected gestational age (P5–16), while the Neonatal Behavioral Neurological Assessment (NBNA) scored 28.

Fig. 2.

Sanger sequencing analysis of the patient and parents. The proband exhibited a heterozygous missense mutation in the CREBBP gene (c.5570A > C, p.H1857P), while both parents displayed the wild-type genotype, confirming the mutation as de novo

During the neonatal period, the patient was managed with 8 days of non-invasive ventilation for respiratory distress and empirical ceftazidime for suspected pneumonia. Feeding intolerance, manifested by abdominal distension and vomiting, necessitated partial parenteral nutrition for 10 days and the use of an extensively hydrolyzed formula, with subsequent transition to nasogastric tube feeding. An improvement in swallowing and sucking function was observed alongside the administration of targeted therapy and kangaroo care. The infant achieved full oral feeding by 1 month of age. The infant was discharged in stable condition at 1 month of age. Post-discharge follow-up until 15 months of age is summarized in Table 1. Neurodevelopmental assessments initially indicated severe global delay, which showed improvement during the course of rehabilitation. By 15 months, the child could crawl, stand alone, and vocalize words like “mama” and “baba,” although the Gesell assessment still indicated moderate delay.

Fig. 3.

Fundus examination at 1 month and 14 days of age. a, b Optic disc pallor, peripapillary retinal hyperpigmentation, ill-defined macula, diffuse retinal hypopigmentation

Table 1.

Chronological summary of clinical follow-up, interventions, and outcomes

Age	Clinical event/assessment	Intervention/investigation	Outcome/findings
From 1 mo (ongoing)	Rehabilitation	Home-based training (rehabilitative therapy)	Promote development
1 mo 14 d	Ocular findings	Funduscopy	See Fig. 3
2 mo 24 d	Hearing screening	Otoacoustic emissions/AABR	Failed
From 2 mo 24 d (ongoing)	Rehabilitation	Structured rehabilitation program (rehabilitative therapy)	Improve motor/cognitive function
2.8 mo	Neurodevelopmental assessment	INFANIB, DDST, Gesell	INFANIB: 48; DDST: Abnormal; DQs: -/52/27/23/25†
2, 4, 5 mo	Acute upper respiratory infection	Supportive care	Resolved
5 mo	Acute pneumonia	Hospitalization (6 days)	Full recovery
5.3 mo	neurodevelopmental assessment	Gesell	DQs: 38/51/42/38/30†
5.9 mo	Neurodevelopmental assessment	Gesell	DQs: 37/47/43/34/39†
6 mo 15 d	Hearing diagnosis	Auditory brainstem response	Bilateral moderate sensorineural hearing loss
6 mo 15 d	Hearing intervention	Bilateral hearing aids (assistive device)	Correct hearing loss
7.4 mo	Neurodevelopmental assessment	Gesell	DQs: 51/54/54/54/49†
10 mo	Oral development	Dental consultation	Lingual ankyloglossia diagnosed
10 mo	Ankle deformity management	Custom orthopedic shoes (assistive device)	Correct ankle deformity
11.1 mo	Neurodevelopmental assessment	Gesell	DQs: 68/54/48/39/48†
13 mo	Hernia and cryptorchidism (diagnosed in the neonatal period)	Right Herniorrhaphy + bilateral orchidopexy (surgical)	Correct hernia and cryptorchidism
13.9 mo	Neurodevelopmental assessment	Gesell	DQs: 43/44/44/39/48†
15 mo	Influenza A	Hospitalization (3 days)	Resolved without sequelae
15 mo	Neurodevelopmental assessment	Gesell	DQs: 67/48/48/44/50†
15 mo	Anthropometry	Measurement	Weight: 8 kg (< 3rd), Length: 75 cm (3rd–10th), HC: 45 cm (3rd–15th)

DQs developmental quotients, † DQ scores values are presented as gross motor DQ/fine motor DQ/adaptive DQ/personal-social DQ/language DQ, AABR automated auditory brainstem response, INFANIB infant neurological international battery, DDST Denver developmental screening test, mo months, TIMP test of infant motor performance, NBNA neonatal behavioral; neurological assessment, HC head circumference

Discussion

This case report demonstrates the efficient application of rWGS in diagnosing neonatal MKHK and offers new insights into its genotype–phenotype correlations. Its key contributions include (1) achieving one of the fastest reported neonatal diagnoses of MKHK-ID4 to date; (2) conducting an in-depth, ACMG guideline-based evaluation of a specific CREBBP variant (c.5570A > C (p.His1857Pro)), supporting its reclassification; (3) documenting a clinical course where early development in a patient with the MKHK-ID4 subtype was faster than typical cohort averages; and (4) providing evidence for the dual value of rWGS in shortening diagnostic time and reducing healthcare costs.

In-depth genotypic analysis: supporting variant reclassification. This variant is currently listed as “Likely Pathogenic” in the ClinVar database. Our formal reassessment according to current ACMG guidelines supports its reclassification to “Pathogenic,” based on the following evidence: (1) pathogenic strong (PS) 2: confirmed de novo origin in the affected proband; (2) pathogenic moderate (PM) 1: location within a critical functional domain—the core α-helix of the ID4 domain (CBP:1852–1875)—specifically linked to the MKHK-ID4 subtype [10]; (3) PM2_Supporting: absence in a homozygous state and an extremely low population frequency (< 0.0005) in databases such as gnomAD; (4) pathogenic supporting (PP) 2: occurrence in CREBBP, a gene highly intolerant to missense variation (missense Z-score ≥ 3.09); and (5) PP3: consistently deleterious predictions from multiple computational tools (for example, Provean, SIFT). The patient’s classic MKHK phenotype further strengthens the clinical correlation (PP4). Together, these criteria (PS2 + PM1 + PM2_Supporting + PP2 + PP3) satisfy the evidence requirements for a “Pathogenic” classification under current guidelines. Therefore, the observed genotype–phenotype concordance supports considering an upgrade in this variant’s classification. It should be noted that a proposed methylation signature analysis—which can serve as a functional assay for the characteristic epigenetic profile associated with this disorder—was not performed due to parental refusal. While not essential for diagnosis in this specific context, such data could have provided an additional layer of confirmatory evidence.

Phenotypic heterogeneity, prognosis, and the potential impact of early intervention: The prognosis of MKHK is subtype-dependent. The MKHK-ID4 subtype is often associated with multi-organ malformations, with outcomes critically influenced by the severity of congenital anomalies [10]. In the present case, follow-up evaluations revealed no critical structural anomalies in the cardiac, renal, or laryngopharyngeal systems, suggesting a potentially more favorable prognosis. Notably, the patient achieved independent standing and first words by 15 months of age, which is markedly earlier than the average developmental milestones reported in larger MKHK cohorts (for example, independent walking at ~ 28.8 months; first words at ~ 39.6 months) [10, 13]. This accelerated developmental progress may be attributable to the early multidisciplinary interventions enabled by rWGS, although the influence of variant-specific effects or natural phenotypic variability cannot be ruled out. Innovation in diagnostic paradigm: speed, breadth, and clinical utility. A significant challenge in MKHK management is the typical diagnostic delay, often extending beyond the critical window of neuroplasticity. While conventional diagnosis relies on WES, which identifies causal variants in ~ 90% of cases [1, 2], it typically requires 4–8 weeks [10–12, 14]. In this case, the need for the fastest possible comprehensive analysis led to the choice of trio rWGS over WES. rWGS delivered a definitive diagnosis within 72 h of sample submission. As a comprehensive first-tier test, rWGS can detect a wider range of pathogenic variations (including structural and non-coding variants) that may be missed by WES, which is particularly advantageous for time-critical diagnoses in critically ill neonates [12, 15]. This rapid result allowed for the immediate initiation of targeted interventions, including swallowing therapy, rehabilitation, audiological assessment, and surgical planning for hernias. The speed and breadth of rWGS also highlight its potential utility in prenatal settings, where it could provide results within legal gestational limits for reproductive decision-making [12, 15].

Demonstration of health economic benefits: Furthermore, this case demonstrates the economic benefits of rWGS. Evidence shows that rWGS reduces the diagnostic time for inherited metabolic disorders from a median of 623 days to 3–5 days [16]. This approach demonstrates cost-effectiveness, generating net savings of $12,041–$15,786 per case and avoiding 457–592 inpatient days through its 3-day turnaround time [17]. In the present case, the diagnosis achieved within 3 days enabled targeted interventions and facilitated discharge planning within 1 week, thereby potentially preventing prolonged hospitalization. These findings support the value of rWGS as an effective tool for optimizing clinical decision-making and reducing hospital stays. Context for successful implementation and future directions: The smooth diagnostic process in this case was facilitated by the family’s supportive socioeconomic background, a proficient clinical team, and a coordinated multidisciplinary approach. This experience underscores that the full clinical potential of advanced genomic testing is best realized within a supportive ecosystem. Future initiatives should aim to address persistent challenges related to cost and accessibility to promote more equitable implementation.

Limitations

As a single case report, the findings cannot establish definitive causation or be generalized. Furthermore, although the identified variant is classified within the MKHK-ID4 subtype, which is defined by a highly specific epigenetic signature [10], we could not perform genome-wide methylation profiling (for example, EpiSign analysis) to confirm this signature in the patient. The absence of this correlative data is a recognized shortcoming. Future studies should aim to include such analyses to strengthen diagnostic confirmation and provide insights into the underlying epigenetic mechanisms.

Conclusion

This case contributes valuable diagnostic and clinical insights into MKHK, suggesting that rWGS-driven neonatal diagnosis of the ID4 subtype can facilitate proactive management during a critical neurodevelopmental window. The key contributions of this report are (1) the earliest neonatal diagnosis of MKHK via rWGS, (2) characterization of the CREBBP variant c.5570A > C (p.His1857Pro) supporting its pathogenicity, (3) classification as MKHK-ID4 subtype per recent criteria, and (4) documentation of favorable early outcomes potentially linked to rapid diagnosis. The case further demonstrates the economic benefits of rWGS through shortened diagnosis and avoided hospitalization. These findings support further investigation into this diagnostic paradigm’s potential to improve long-term outcomes.

Abbreviations

MKHK

Menke–Hennekam syndrome

rWGS

Rapid whole-genome sequencing

WES

Whole-exome sequencing

RSTS

Rubinstein–Taybi syndrome

CNV-seq

Copy number variation sequencing

ASD

Atrial septal defect

aEEG

Amplitude-integrated electroencephalography

MRI

Magnetic resonance imaging

BWA

Burrows–Wheeler aligner

GATK

Genome analysis toolkit

ACMG

American College of Medical Genetics and Genomics

TIMP

Test of infant motor performance

NBNA

Neonatal Behavioral Neurological Assessment

PS

Pathogenic strong

PM

Pathogenic moderate

PP

Pathogenic supporting

Author contributions

Huang.Q conceived the idea and designed the study, collected the clinical data and patient information, analyzed the data and interpreted the results, wrote the initial draft of the manuscript, edited the manuscript for clarity and accuracy. Fan.W reviewed and edited the manuscript for clarity and accuracy. Hu.Y conceived the idea, designed the study analyzed the data and interpreted the results, wrote the initial draft of the manuscript. Chen.S supervised the project, provided guidance throughout the research process and secured funding for the study. All the authors read and approved the final manuscript.

Funding

This study was supported by the National Natural Science Foundation of China (Grant No. 82170565) and the Chongqing Medical Research Fund (Grant No. 2024NSCQ-KJFZZDX0018).

Declarations

Ethics approval and consent to participate

This study was approved by the Ethics Committee of The First Affiliated Hospital of Army Medical University (approval no. (B2)2024KY061). All patient data have been de-identified to protect confidentiality.

Consent for publication

Written informed consent was obtained from the patient’s legal guardian for publication of this case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.

Availability of data and material

All data generated or analyzed during this study are included in this published article.

Competing interests

The authors declare no conflicts of interest related to this study.