A Diagnostic Dilemma: Concurrent Diagnosis of Cystic Fibrosis and Definitive Kabuki Syndrome Type 1

Abstract

The article presents a clinical case involving a patient with presumptive coexistence of two hereditary disorders, confirmed by molecular genetic analyses. Clinical evaluation of the proband, a 9-year-old girl, revealed features characteristic of Kabuki syndrome, including a typical “Kabuki makeup” facial phenotype, short stature, intracranial hypertension, and diffuse muscular hypotonia. Additional clinical findings included chronic right-sided otitis media, conjunctivitis, recurrent pneumonia, bilateral conductive hearing loss, astigmatism, and primary adenitis. Clinical assessment and molecular genetic testing were performed. High-throughput sequencing identified a previously reported pathogenic heterozygous variant in the KMT2D gene, NM_003482.4:c.15142C>T p.Arg5048Cys, and two known heterozygous variants in the CFTR gene: NM_000492.4:c.1521_1523delCTT p.Phe508del and c.3454G>C p.Asp1152His, classified as pathogenic and of variable clinical significance, respectively. Segregation analysis demonstrated that the KMT2D variant most likely arose in the proband de novo, whereas the CFTR variants were inherited from each of the parents. Notably, the proband’s clinically unaffected elder sister carried the same CFTR genotype. Based on the clinical presentation and molecular genetic findings, the diagnosis of Kabuki syndrome type 1 was conclusively established in the patient. Functional assessment of CFTR demonstrated its preserved function, which did not support a diagnosis of CF or CFTR-related disorders.

1. Introduction

The identification of multiple hereditary disorders in a single patient has become increasingly common in the era of high-throughput sequencing (next-generation sequencing, NGS). On the one hand, NGS facilitates adherence to the fundamental medical principle “primum non nocere” by enabling the recognition of coexisting inherited conditions that may interact or exacerbate one another, thereby improving risk stratification and patient management. In addition, comprehensive genomic analysis contributes to a more accurate elucidation of the etiopathogenesis underlying complex and atypical phenotypes. On the other hand, the widespread use of NGS carries the risk of overdiagnosis, including the detection of pathogenic or potentially pathogenic variants associated with conditions that may never manifest clinically during a patient’s lifetime. Carrier genetic testing, based on NGS multi-gene panels, not only identifies frequent pathogenic variants in well-known genes but also uncovers a wide spectrum of allelic heterogeneity in less common conditions [1].

Kabuki syndrome (KS), also known as Niikawa–Kuroki syndrome (ORPHAcode: ORPHA2322, OMIM phenotypic series PS147920), is a rare multisystem syndromic disorder characterized by delayed psychomotor development, generalized hypotonia, and distinctive facial dysmorphisms. The characteristic craniofacial features include elongated palpebral fissures, eversion of the lateral third of the lower eyelid, large and low-set ears, a short philtrum, a thin upper lip, and a short, broad nasal tip. Additional clinical manifestations may include postnatal growth retardation, congenital heart defects, malformations of the gastrointestinal tract and kidneys, neurobehavioral abnormalities, hearing and visual impairment, and immunodeficiency. The clinical phenotype of KS is notably heterogeneous, with considerable interfamilial variability [2]. Approximately 95% of molecularly confirmed KS cases are caused by heterozygous loss-of-function pathogenic variants in the KMT2D gene, corresponding to KS type 1 with autosomal dominant inheritance, whereas about 5% of cases result from pathogenic variants in the KDM6A gene, leading to KS type 2 with X-linked dominant inheritance [3,4]. Notably, in up to 20% of patients with a clinical diagnosis of KS, the underlying molecular cause could remain unidentified [5,6]. The estimated prevalence of KS is approximately 1:32,000 [5]. The KMT2D and KDM6A genes encode proteins with key regulatory roles in chromatin remodeling through histone methyltransferase and demethylase activity, respectively, thereby influencing chromatin accessibility and gene expression [6]. Consequently, KS is classified among the chromatinopathies [7,8].

Cystic fibrosis (CF, OMIM# 219700) is a multisystem autosomal recessive disorder characterized by chronic involvement of the respiratory, digestive, and reproductive systems and accompanied by persistent inflammation [9]. CF is caused by biallelic pathogenic variants in the CFTR gene, which is primarily expressed in the apical membrane of epithelial cells, where the encoded protein functions as an ion channel transporting chloride, bicarbonate, and water. Impaired CFTR function leads to electrolyte imbalance, increased viscosity of epithelial secretions, and obstruction of exocrine gland ducts [9]. Pathogenic variants in CFTR are associated with a phenotypic spectrum ranging from classical CF to CFTR-related disorders, which encompass clinical conditions linked to partial CFTR dysfunction that do not fulfill diagnostic criteria for CF [10]. These disorders include congenital bilateral absence of the vas deferens, recurrent acute or chronic pancreatitis, disseminated bronchiectasis, episodic electrolyte imbalance, metabolic alkalosis, and impaired fertility [11]. The clinical variability and incomplete penetrance observed in CF and CFTR-related disorders are largely determined by the type and combination of underlying CFTR pathogenic variants [11].

Here, we present a case of a patient in whom genetic variants causative of two hereditary disorders—Kabuki syndrome type 1 and cystic fibrosis—were identified. The probability of observing both disorders in one individual can be approximated as the product of their independent frequencies. Using an estimated KS frequency of 1:32,000 and a CF frequency ranging from 1 to 5 per 10,000, the expected co-occurrence ranges from approximately 1:64,000,000 to 1:320,000,000 (https://www.orpha.net/en/disease/detail/586?name=Cystic%20fibrosis&mode=name, accessed on 16 February 2026). The occurrence should be assessed as an extremely rare event.

2. Results

A family with a 9-year-old female proband (II.2) was referred by an endocrinologist for diagnostic clarification due to short stature, delayed physical development (bone age corresponding to 7 years), characteristic dysmorphic facial features (“Kabuki makeup”), and multiple congenital anomalies. The family history was unremarkable. The proband’s mother and three siblings (aged 7, 13, and 16 years) (II.1, II.3, II.4) were clinically healthy. The father was deceased, and his biological material was unavailable for genetic testing (Figure 1).

2.1. Prenatal and Perinatal History

The proband was born from the fourth pregnancy, which was complicated by two episodes of threatened miscarriage and resulted in the third preterm delivery. Gestational age at birth was 33 weeks. Birth weight was 2100 g, length was 47 cm, and head circumference was 29 cm. The Apgar score was 6. The neonatal period was complicated by pneumonia with multiple areas of atelectasis. Additionally, cerebral ischemia, hypertensive syndrome, diffuse muscular hypotonia, and moderate neonatal jaundice were diagnosed.

The results of neonatal screening for cystic fibrosis could not be clarified.

2.2. Medical History

During early childhood, the patient experienced recurrent upper respiratory tract infections, requiring multiple hospitalizations.

The child had been under the care of a pediatric endocrinologist since the age of two years old due to her short stature (at 6 years—height <5th percentile). The bone age assessment conducted at the age of 8 years and 3 months indicated a bone age of 6 years and 10 months. A delay in early physical development was observed: held head up at 2–3 months, sat up at 8–9 months, crawled at 1 year, and walked without support at 2 years and 4 months. Speech development was as follows: first words appeared at 1.5–2 years of age, and phrase speech developed from 2.5 years.

2.3. Clinical Examination

At the age of 9 years, the proband underwent a comprehensive multidisciplinary evaluation for diagnostic clarification and medical genetic counseling. Her general condition was assessed as moderately severe due to the underlying disease and comorbidities but clinically stable. Psychomotor and speech developmental delays were observed. Residual encephalopathy manifested by intracranial hypertension and diffuse muscular hypotonia was noted.

Distinctive phenotypic features included a broad nasal bridge, antimongoloid palpebral fissures, a typical “Kabuki makeup” facial appearance, and primary adentia. Anthropometric measurements revealed a height of 117 cm (<5th percentile), weight of 19.3 kg (<5th percentile), and body mass index (BMI) of 14.1 kg/m² (BMI SDS—1.4). A melanocytic nevus of the trunk was observed.

Signs of connective tissue dysplasia were present, including foot deformities, kyphosis, generalized hypotonia, umbilical hernia, and joint hypermobility without structural joint abnormalities. Cardiac evaluation revealed minor congenital anomalies, including grade 1 mitral valve prolapse with mild regurgitation, valvular myxomatosis, grade 1 tricuspid regurgitation, patent foramen ovale, and false tendons of the left ventricle. Cardiac auscultation demonstrated rhythmic, muffled heart sounds without murmurs.

Sensory impairments included conductive hearing loss (grade 1–2) with Eustachian tube dysfunction and visual abnormalities, including astigmatism and mild amblyopia.

Based on the constellation of findings, Kabuki syndrome was clinically suspected.

2.4. Investigations

Thyroid ultrasonography and hormone levels were within age-specific reference ranges, excluding thyroid dysfunction.

Renal evaluation revealed an L-shaped kidney with hypoplasia of the left segment and stage 1 chronic kidney disease, without arterial hypertension. Ultrasonography demonstrated horizontal kidney positioning, normal on the right, and lumbar dystopia on the left. Duplex ultrasonography of the renal arteries identified multiple right renal arteries.

Hand radiographs showed shortening and deformity of the 4th and 5th metacarpals of the right hand, the 3rd–5th metacarpals of the left hand, and the middle phalanges of the 5th digits bilaterally. Bone age corresponded to 9 years, with a predicted adult height of 139.12 cm.

Computed tomography of the temporal bones revealed right-sided otitis media and sphenoiditis. Brain MRI and echoencephalography showed no pathological changes. Doppler ultrasonography demonstrated increased cerebral blood flow. Electroencephalography showed no epileptiform activity. No peripheral lymphadenopathy was detected.

2.5. Laboratory Test Results

Routine blood and urine analyses were within normal limits. Biochemical testing showed an isolated elevation of alkaline phosphatase (205 U/L); other parameters were normal. Thyroid function tests were normal (TSH 2.89 µIU/mL; T4 1.53 ng/mL; T3 4.34 pg/mL). IGF-1 level was 101.2 ng/mL (reference range 87.3–324.0).

Flow cytometry demonstrated mild T-cell lymphopenia and a borderline reduction in B-cell counts (CD4⁺ 0.799 cells/µL, CD8⁺ 0.823 cells/µL, NK cells 0.259 cells/µL, B cells 0.212 cells/µL). TREC (550 copies/10⁵ cells) and KREC (3400 copies/10⁵ cells) levels were within normal ranges. Immunoglobulin profiling revealed selective IgA deficiency (IgA < 0.01 g/L), with normal levels of IgM (1.39 g/L) and IgG (9.39 g/L). Adequate post-vaccination titers to measles and tetanus were detected.

2.6. The Results of DNA Diagnostics

Conventional cytogenetic analysis demonstrated a normal female karyotype (46, XX).

NGS analysis identified a heterozygous pathogenic variant in the KMT2D gene, NM_003482.4:c.15142C>T p.Arg5048Cys (CM114909), resulting in a missense substitution at a highly conserved residue. The variant was extremely rare in population databases (1/1,613,328 alleles in gnomAD v4.1.0; frequency 0.00006%), consistent with autosomal dominant inheritance, and had not been observed in the homozygous state. In silico prediction tools indicated a damaging effect. This variant has previously been reported in patients with Kabuki syndrome type 1 [6,12]. Segregation analysis showed the absence of the variant in the mother and healthy siblings (II.1, II.3, II.4). That supported a presumably de novo origin, taking into account that the father’s biological material was unavailable. (Figure 1). Though we could not exclude the possibility that the variant was inherited from the father, especially since familial cases of Kabuki syndrome and its significant clinical heterogeneity had been described [13].

Additionally, two known heterozygous variants were detected in the CFTR gene NM_000492.4:c.1521_1523delCTT, p.Phe508del (F508del legacy name), (CD890142), and c.3454G>C, p.Asp1152His (D1152H legacy name) (CM950256) [14,15]. The pathogenicity of p.Phe508del was well established. The p.Asp1152His variant was identified in population databases at a frequency of 0.04% (641/1,610,026 alleles, once in the homozygous state; gnomAD v4.1.0), compatible with autosomal recessive inheritance, and was predicted to impair CFTR function. This variant demonstrates variable expressivity and incomplete penetrance [16,17] and has been reported in patients with mild CF, CFTR-related disorders, and asymptomatic individuals when present in compound heterozygosity [15,18,19].

The p.Asp1152His variant was detected in the mother and proband’s elder sister (II.4), whereas p.Phe508del was identified in the proband (II.2) and her elder sister (II.4) only, suggesting paternal inheritance. Thus, both sisters (II.2 and II.4) carried the two CFTR variants in trans (Figure 1).

Further analysis of the other two siblings (II.1 and II.3) within the family revealed the absence of both variants in the CFTR gene as well as a pathogenic variant in the KMT2D gene (Figure 1).

2.7. Pulmonological Assessment

Given the presence of two CFTR variants in trans, the proband and her sister (II.2 and II.4) were evaluated by a pulmonologist. Physical examination of the respiratory system was unremarkable. Spirometry demonstrated normal pulmonary function (FEV₁, FVC, FEV₁/FVC). Chest CT revealed normal lung parenchyma without bronchiectasis or infiltrates and normal mediastinal and hilar structures (Figure 2). In the anamnesis of the proband (II.2), pleuropulmonary adhesion in the middle lobe of the right lung was mentioned on one of the CTs. Sweat chloride testing showed normal values (38 mmol/L in both sisters; normal < 50 mmol/L). The results of neonatal screening for cystic fibrosis could not be clarified in either sister.

2.8. CFTR Functional Assessment

Intestinal current measurement (ICM) was performed as an ex vivo functional assay of CFTR activity [20]. Both sisters (II.2 and II.4) demonstrated normal electrophysiological responses to all stimuli, including amiloride, forskolin/IBMX, carbachol, and histamine, indicating preserved CFTR channel function (Figure 3).

2.9. CFTR Modifier Analysis

Genotyping of polymorphic poly-T and poly-TG repeats in intron 9 of CFTR revealed identical genotypes in both sisters (II.2 and II.4), lacking the 5T allele: c.[1210-34TG [10]T [5]];[1210-34TG [9]T [8]] (Figure 1). This configuration is not associated with exacerbation of CFTR-related phenotypes [21]. Analysis of the poly-T and poly-TG repeat markers in the other two siblings (II.1 and II.3) indicated that they inherited alternative alleles from both parents (Figure 1).

2.10. Final Diagnosis

The proband was diagnosed with Kabuki syndrome type 1, confirmed clinically and molecularly. A diagnosis of cystic fibrosis or a CFTR-related disorder was not supported due to preserved CFTR function, normal sweat chloride levels, negative cystic fibrosis newborn screening results, absence of CF-specific clinical manifestations, and the presence of identical CFTR genotypes in the proband (II.2) and her healthy sibling (II.4).

3. Discussion

Kabuki syndrome was first delineated in 1981 by two independent groups led by Niikawa N. and Kuroki Y., who reported ten unrelated Japanese children with a characteristic pattern of multiple congenital anomalies and intellectual disability [22]. KS is characterized by a great heterogeneity of clinical manifestations [23]. The differential diagnosis of KS could be, for example, CHARGE syndrome, 2q11 deletion syndrome, IRF6-related disorders, hypermobile Ehlers–Danlos and Larsen syndromes, and Hardikar syndrome [24]. Current diagnostic criteria include a history of childhood hypotonia, developmental delay, and/or intellectual disability, and at least one of the following: (i) a distinctive facial phenotype (“Kabuki makeup”) and/or (ii) a pathogenic variant in KMT2D or KDM6A [7]. In the present case, the clinical phenotype and DNA analysis supported and confirmed the diagnosis of Kabuki syndrome type 1 (KS1).

The heterozygous KMT2D variant NM_003482.4:c.15142C>T results in the missense substitution p.Arg5048Cys and was presumed to have arisen de novo in the patient. In addition to the core KS features—hypotonia, developmental delay, the characteristic “Kabuki makeup” facial phenotype, and a pathogenic KMT2D variant—the patient exhibited several common KS manifestations that have been reported particularly in individuals with missense variants in KMT2D. These included selective IgA deficiency [25], congenital heart defects [2,26], recurrent infections, renal malformations, skeletal abnormalities (including kyphoscoliosis and deformities of the hand bones) [2], delayed physical development, and visual and hearing impairment [27,28]. Epilepsy and endocrine disorders were not observed, which is also consistent with the spectrum reported in patients with KMT2D missense variants [2]. The NM_003482.4(KMT2D):c.15142C>T (p.Arg5048Cys) variant in exon 49 has been repeatedly described in individuals with Kabuki syndrome type 1 (CM114909) [12,29]. A summary of published clinical descriptions of patients carrying this variant is provided in

Table 1. Clinical features in patients with the c.15142C>T (p.Arg5048Cys) variant in the KMT2D gene.

KS Features	[30]	[2]	[31]	[32]	[26]	Current Study
Abnormal immune profile	yes	n/t	n/t	n/t	n/t	yes
Dysmorphism	typical facial dysmorphism	Noticeable coloboma, lower eyelid eversion, prominent ears, short stature	n/t	n/t	n/t	Wide nose bridge, anti-mongoloid eye incision, short stature
Prenatal and postnatal history	n/t	Term, no complications, birth weight 2750 g, 3–15 WHO percentile	n/t	n/t	n/t	Prematurity at 33 weeks, grade 2 cerebral ischemia, pneumonia, moderate neonatal jaundice, transient cardiopathy
Physical assessment	n/t	Abnormal emotionality, stereotypy, wide-based gait, kyphoscoliosis, muscle hypotonia, joint hypermobility	n/t	n/t	congenital cardiac left-sided lesion	L-shaped kidney, chronic kidney disease 1, diffuse muscle hypotonia, headache, joint hypermobility, grade 1–2 bilateral conductive hearing loss, chronic right-sided otitis media, mixed astigmatism, flat-valgus deformity of the feet, primary adentia, congenital cardiac left-sided lesion, kyphoscoliosis
Intellectual disability/neurodevelopmental disorders	n/t	Yes	yes	yes	n/t	Mild speech delay

Note. n/t—not tested.

.

The clinical spectrum of KS is broad. Although robust genotype–phenotype correlations have not been established, it has been suggested that missense variants affecting the C-terminus of the protein may be associated with comparatively milder phenotypes [2]. In this context, a “milder” clinical manifestation may include the absence of epilepsy and other severe neurological complications or a later manifestation of neurological symptoms. Our patient, at the age of the assessment, represents a detailed clinical characterization of such a presentation, including mild immune abnormalities, headaches, hearing and visual impairment, and short stature.

As secondary findings, NGS identified two CFTR variants in compound heterozygosity: NM_000492.4:c.1521_1523delCTT (p.Phe508del) and c.3454G>C (p.Asp1152His). Variant interpretation was performed in the context of complete/incomplete penetrance and the CFTR2 classification system (https://cftr2.org). CFTR2 defines: (1) CF-causing variants (two variants in trans reliably causing CF); (2) variants with varying clinical consequences (VVCC), where some individuals with the variant in trans with a CF-causing allele develop CF, whereas others do not, and some may develop CFTR-related disease (CFTR-RD); (3) variants not causing CF, which do not cause CF even in trans with a CF-causing allele, although CFTR-RD may rarely occur; and (4) variants of unknown significance (VUS), for which available data are insufficient to define associated phenotypic patterns. In the present case, c.3454G>C (p.Asp1152His) corresponds to the VVCC category with incomplete penetrance and variable expressivity, creating substantial interpretive challenges in the setting of a concomitant monogenic disorder [33].

Data from 715 patients and asymptomatic carriers in whom c.3454G>C (p.Asp1152His) constituted one of two CFTR alleles indicating that this genotype does not invariably result in CF; however, when CF develops, it often presents as nonclassical CF [34]. This is consistent with the classification of c.3454G>C (p.Asp1152His) as a missense variant with variable clinical consequences (https://cftr2.org/mutation/general/D1152H/F508del, accessed on 16 February 2026). Nonclassical CF phenotypes and CFTR-related conditions may include recurrent pneumonia and bronchitis and/or electrolyte disturbances, reduced fertility, and congenital bilateral aplasia of vas deferens (CBAVD); sweat chloride concentrations may be normal or only mildly elevated [34]. The NM_000492.4(CFTR):c.3454G>C (p.Asp1152His) variant has indeed been reported in individuals with mild CF and CFTR-related conditions [15,35].

We also determined genotypes at the polymorphic microsatellite repeat locus in intron 9 of CFTR in the patient (II.2) and her healthy sister (II.4), who also carried the same CFTR genotype. The 5T allele has been shown to be associated with incomplete penetrance of CF and CBAVD, with risk modified in part by the adjacent poly-TG tract. The poly-TG tract typically comprises 11, 12, or 13 repeats (c.1210-34TG [10], c.1210-34TG [11], c.1210-34TG [12]). In cis, 5T with 11TG rarely increases the risk of CBAVD in males, whereas 5T in cis with 12TG or 13TG increases the risk of CBAVD and, more rarely, nonclassical CF. Given the relatively high prevalence of the 5T allele (approximately 10% carrier frequency), its clinical contribution is interpreted in conjunction with the number of associated TG repeats [21]. In our family, both sisters (II.2 and II.4) had identical intron 9 repeat genotypes without 5T: c.[1210-34TG [10]T [5]];[1210-34TG [9]T [8]]. The p.Phe508del variant is known to be linked to the TG [9]T [8] allele, as demonstrated in 85 p.Phe508del chromosomes in German patients with cystic fibrosis [36]. The other two healthy siblings (II.1 and II.3) were defined to have an identical genotype at the locus c.[1210-34TG [10]T [5]];[1210-34TG [10]T [8]] also without the 5T allele (Figure 1).

Our patient’s phenotype includes recurrent respiratory infections, which could raise the question of an additional CFTR-related diagnosis. However, laboratory findings (normal results of two functional CFTR assays) and the absence of characteristic CF manifestations do not support a diagnosis of CF or CFTR-related disease/disorder [10]. The first episode of pneumonia may be attributable to prematurity, whereas subsequent acute respiratory infections may be related to immune vulnerability. Notably, the immunologic evaluation, apart from selective IgA deficiency, was otherwise unremarkable.

Despite the absence of a current CF diagnosis, ongoing monitoring for potential CFTR-related manifestations is warranted. Over the past two decades, substantial progress has been made in the evaluation and management of infants and children with ambiguous CF diagnostic outcomes, particularly in the context of newborn screening. A globally recognized designation has been adopted for this population: CRMS/CFSPID (CFTR-related metabolic syndrome/Cystic Fibrosis Screen Positive Inconclusive Diagnosis) [37]. The Cystic Fibrosis Foundation defines key criteria for CRMS/CFSPID in individuals with atypical newborn screening outcomes, including (1) sweat chloride concentrations of 30–59 mmol/L and (2) identification of two CFTR variants with at least one variant of uncertain clinical significance and phenotypic implications or the absence of CF-causing mutations [Annual Data Report 2023]. Cystic Fibrosis Foundation Patient Registry. (https://usrds-adr.niddk.nih.gov/2023, accessed on 16 February 2026). Most individuals (up to 90%) with CRMS/CFSPID remain healthy; however, approximately 10% develop CF-typical clinical features such as pulmonary disease or Pseudomonas aeruginosa in respiratory cultures, underscoring the importance of early recognition and follow-up. Importantly, some individuals not reclassified as CF in childhood may develop clinically significant disease later [33]. Accordingly, management consistent with CRMS/CFSPID clinical guidance is advisable [37].

The reported efficiency of CF newborn screening in the Russian Federation is 93% [38]. However, in certain regions of Russia, performance may be as low as 67% [39], potentially due to mild variants producing minimal or no abnormalities on screening. Therefore, a false-negative neonatal screening result in this patient cannot be excluded and should be considered in clinical interpretation. Although current CFTR functional testing is reassuring, it cannot fully exclude the possibility of later clinical expression. Consequently, even if the patient is not currently classified as CRMS/CFSPID, periodic follow-up in the context of medical genetic counseling remains justified. This approach is supported by the study by Terlizzi et al., who evaluated 43 CFSPID subjects with at least one D1152H (p.Asp1152His) variant and found that most remained without a definitive diagnosis after several years of follow-up, whereas a minority developed CF-related symptoms, more frequently among individuals with a CF-causing variant in trans (as in our patient (II.2) and her sister (II.4) carrying F508del (p.Phe508del) in trans with D1152H (p.Asp1152His) [17].

In conclusion, although the co-occurrence of KS and CF would be expected to be extremely rare, at least one patient with KS and presumed CF has been described previously, albeit without genetic confirmation [40].

In the previously reported patient, CF was presumed based on elevated sweat chloride concentrations and pancreatic insufficiency without genetic testing [40].

Table 2. Clinical manifestations in two patients with a suspected combination of KS and CF.

Pt Age at Examination (Year), Gender	Prenatal and Postnatal History	Dysmorphism	Significant Medical Problems	Sweat Chloride	Pancreatic Insufficiency	Other CF Features
20-year-old female [40]	born after an uncomplicated 40-week gestation with Apgar scores of 8, birth weight of 3.7 kg, length of 52 cm, hypotonic and delayed development, talked at age 5 y.o. (less than 20 words)	flat nasal root, depressed nasal tip, flattened midface with long palpebral fissure, ectropion of the outer third of the inferior palpebrum, high-arched palate, large ears, simple helix, low posterior hairline, Tanner Stage IV sexual development, mild scoliosis, short fourth metacarpals	bilateral hip dislocation was diagnosed at birth, recurrent otitis media, 12 abnormal primary teeth, obstructed nasolacrimal ducts, an atonic seizure disorder at 2.5 y.o., dense cataracts at 18 y.o.	elevated (71 mEq/L)	present	no cough, no sputum production, no nasal polyps or an increased chest diameter, normal chest radiograph, and examination
9-year-old female (this study)	prematurity of 33 weeks, grade 2 cerebral ischemia in the form of hypertensive syndrome, diffuse muscular hypotonia, pneumonia on the background of multiple atelectasis with acute course, grade 2 respiratory failure, moderate neonatal jaundice, transient cardiopathy, at 2.5 months focal-draining pneumonia, on the right, acute course. respiratory failure of the 1st degree	Kabuki makeup face, wide bridge of nose, anti-mongoloid eye incision, short stature	primary immunodeficiency, L-shaped kidney, grade 1 chronic kidney disease, residual encephalopathy in the form of intracranial hypertension, oculomotor disorders, diffuse hypotonia, grade 1–2 bilateral conductive hearing loss, chronic right-sided otitis media, mixed astigmatism, mild amblyopia, flat-valgus deformity of the feet, positional kyphosis, primary dental adentia, melanoform nevus torso, small anomalies of heart development in the form of grade 1 mitral valve prolapse with mild regurgitation on the background of myxomatosis of the valves, grade 1 tricuspid valve insufficiency, open oval window, false chords of the left ventricle, delayed physical development	Normal (conductivity testing—38 mmol/L)	Not present	Low BMI of 14.1 kg/m2 (BMI SDS −1.4). No cough, no sputum production, no nasal polyps, chest CT—normal lung parenchyma without bronchiectasis or infiltrates, and normal mediastinal and hilar structures.

compares clinical manifestations in that patient with suspected dual pathology and in our patient, who has genetically confirmed KS and a genetically plausible but clinically unconfirmed CFTR-related diagnosis.

If this comparison is valid, it suggests a more severe phenotype in the previously described case, whereas our patient’s phenotype is comparatively less consistent with classical CF. Nonetheless, the presence of the same CFTR genotype in the proband’s clinically unaffected sister (II.4) cannot be considered definitive evidence against a CFTR-related contribution in the proband, given the possibility of epistatic interactions between KMT2D dysfunction and CFTR variation. Even if c.3454G>C p.Asp1152His does not measurably reduce CFTR channel conductance, it could affect other CFTR functions, including the regulation of inflammatory cascades [41]. However, the normal results of CFTR functional testing remain a major argument supporting a single primary diagnosis—Kabuki syndrome type 1—confirmed by molecular genetic findings.

Recommendations

Given the relatively high carrier frequency of pathogenic CFTR variants in the general population (https://www.orpha.net/en/disease/detail/586?name=Cystic%20fibrosis&mode=name, accessed on 16 February 2026), preconception genetic counseling is recommended for the patient’s mother. This should include carrier screening for pathogenic CFTR variants in a future partner and consideration of prenatal diagnostic testing for Kabuki syndrome, as the possibility of parental gonadal mosaicism for the pathogenic KMT2D variant, as well as its paternal origin, cannot be excluded.

In males carrying the CFTR variants NM_000492.4:c.1521_1523delCTT (p.Phe508del) and c.3454G>C (p.Asp1152His) in compound heterozygosity, congenital bilateral absence or obstruction of the vas deferens may develop [34]. Genetic testing of the patient’s brother for the identified CFTR variants was negative, and his genotype at the intron 9 repeat locus did not contain the 5T allele, suggesting for him a population risk of CBAVD development.

For the proband, longitudinal clinical follow-up is advised in accordance with current CRMS/CFSPID management guidelines [37].

4. Materials and Methods

4.1. Patient

The proband was a 9-year-old female presenting with dysmorphic facial features, delayed physical development, and multiple congenital anomalies involving several organ systems. She represented a sporadic case in the family (Figure 1). The proband’s mother and three siblings (two females aged 7 and 16 years (II.1 and II.4) and one male aged 13 years (II.3)) were clinically unaffected. Her father died earlier from trauma.

Clinical evaluation was performed by specialists in multiple disciplines, including pediatrics, orthopedics, gastroenterology, pulmonology, cardiology, clinical genetics, otolaryngology, audiology, neurology, ophthalmology, and immunology.

Instrumental investigations included ultrasonography of the abdominal cavity and thyroid gland, radiographic examination of the lungs, skull, and hand skeleton, magnetic resonance imaging (MRI) of the brain, computed tomography (CT) of the temporal bones, electroencephalography, spirometry, and electrocardiography.

Newborn screening for 5 diseases (cystic fibrosis, phenylketonuria, galactosemia, congenital adrenal hyperplasia, and congenital hypothyroidism) was performed as described previously [42]. Laboratory assessments comprised a complete blood count, routine urinalysis, biochemical blood tests, evaluation of lymphocyte subsets (performed at the age of 9 years 11 months), microbiological cultures of pharyngeal and nasal swabs, and sweat testing using pilocarpine iontophoresis. In addition, ex vivo measurement of intestinal electrical potentials in rectal biopsy specimens was conducted as previously described [20]. Quantification of T-cell receptor excision circles (TREC) and kappa-deleting recombination excision circles (KREC) in dried blood spots was performed by real-time polymerase chain reaction according to a previously published protocol [43].

4.2. Molecular Diagnostics

Genomic DNA was extracted using a salting-out procedure with Wizard^® Genomic DNA Purification Kit (Promega Corporation, Madison, WI, USA). High-throughput sequencing (NGS) was performed on an Illumina MiSeq platform (USA) using paired-end sequencing. Library preparation involved selective capture of the coding regions of 1466 genes included in a comprehensive neurological gene panel associated with hereditary neurological disorders and curated in the OMIM database. The mean coverage of target regions across the analyzed genes was at least 70×.

Sanger sequencing was used to validate variants identified by NGS and to perform segregation analysis within the family. Previously published primer pairs were used for the CFTR gene [44], while primers KMT2D_49F (5′-GCGGAGGCTCCAATAGATG-3′) and KMT2D_49R (5′-GAATCAGCCCGACCCAAG-3′) were designed for exon 49 of the KMT2D gene.

Genotyping of the poly-T/TG repeat tract in intron 9 of the CFTR gene was performed using the CFTR-TIPS tool in accordance with the published protocol [45] with manual review of the results.

4.3. Assessment of Cystic Fibrosis–Related Phenotype

The patient’s phenotype was evaluated in the context of a possible diagnosis of cystic fibrosis (CF). Diagnostic assessment followed established criteria, which include the presence of two pathogenic CFTR variants in trans in combination with either a clinical phenotype consistent with CF, elevated sweat chloride concentrations, or positive results of neonatal CF screening based on increased immunoreactive trypsinogen (IRT) levels [46].

Clinical manifestations potentially associated with CF were assessed using body mass index (BMI), pulmonary function parameters (percent predicted FEV₁, FVC, and FEV₁/FVC ratio), sputum microbiology (standard culture and phenotypic identification of Gram-positive and Gram-negative bacteria), and fecal pancreatic elastase-1 concentration (normal > 200 µg/g of feces) as a marker of exocrine pancreatic function [47].

4.4. Evaluation of CFTR Functional Activity

Screening sweat conductivity testing was performed using the Nanoduct system (Wescor, South Logan, Utah, UT, USA) [48]. Intestinal current measurement (ICM) was conducted as previously described [49] in accordance with the European standard operating procedure V2.7_26.10.11 [20]. Briefly, the functional activity of epithelial ion channels in rectal biopsy specimens was evaluated by measuring electrophysiological responses to amiloride, forskolin/IBMX, carbachol, and histamine. Amiloride inhibits epithelial sodium channels (ENaC), forskolin/IBMX (3-isobutyl-1-methylxanthine) activates cAMP-dependent chloride transport via CFTR, carbachol stimulates calcium-dependent chloride secretion, and histamine reactivates the Ca²⁺-dependent secretory pathway.

4.5. Evaluation of Immunological Profile

Peripheral blood lymphocyte subsets were assessed by multicolor flow cytometry (CytoFLEX, Beckman Coulter, Indianapolis, IN, USA). Major lymphocyte populations were quantified, including CD3⁺ T cells with CD4⁺ and CD8⁺ subsets, CD19⁺ B cells, and CD3⁻CD16⁺/CD56⁺ NK cells, using the DuraClone IM Phenotyping BASIC tube (Beckman Coulter) according to the manufacturer’s instructions. Results were interpreted using age-adjusted reference ranges. Serum immunoglobulins (IgG, IgA, IgM) were measured as part of routine humoral immunology assessment using a standardized immunochemical method (e.g., nephelometry or turbidimetry) on an automated clinical analyzer.

5. Conclusions

The patient was diagnosed with Kabuki syndrome type 1 based on concordant clinical features and molecular genetic findings. Given the normal results of CFTR functional testing—including a normal sweat test and preserved intestinal current measurements—CFTR channel activity appears intact, most likely reflecting the variable clinical significance of the c.3454G>C (p.Asp1152His) variant. Therefore, neither cystic fibrosis nor a CFTR-related disorder can be diagnosed at present.

Nevertheless, regular clinical monitoring remains warranted, consistent with recommendations for individuals meeting CRMS/CFSPID surveillance criteria, to enable timely identification of potential late-onset CFTR-related manifestations.