A 3-year-old boy was brought to the hospital in December 2021 for an evaluation of developmental delay and multiple anomalies. He had no known family history of genetic diseases. His parents, who were nonconsanguineous and healthy, provided informed consent for trio-based WGS and the research use of biological and related clinical data (Institutional Review Board [IRB] No.: SMC 2020-10-042).

We analyzed data from three Korean patients newly diagnosed with 1p36DS who underwent CMA at Samsung Medical Center between 2020 and 2021. Our goal was to compare and analyze their clinical features with those associated with RTS. These patients were evaluated through a review of medical records, which included various parameters such as growth, craniofacial features, cognition and behavior, neurological features, brain anomalies, cardiac features, gastrointestinal features, ocular involvement, and musculoskeletal anomalies. A retrospective analysis of these 1p36DS cases received approval from the IRB of Samsung Medical Center and was exempted from the requirement of informed consent (IRB No.: SMC 2024-02-087).

We further investigated the clinical and molecular features of 1p36DS cases as reported in previous publications. A literature search was conducted in March 2024 using the keyword ‘chromosome 1p36 deletion’ on PubMed (https://scholar.google.com/) and KoreaMed (https://koreamed.org/). We included studies that met the following criteria: (1) research involving Korean patients, and (2) studies that provided a clear description of the 1p36 deletion breakpoint. Additionally, we gathered data on copy number variants, including SPEN, from the public repository Database of Genomic Variation and Phenotype in Humans Using Ensembl Resources (DECIPHER) v.11.23 (https://www.deciphergenomics.org/) [9], and analyzed the clinical features documented in the database.

Genomic DNA was extracted from peripheral blood for WGS. The DNA was fragmented and then used to prepare a library without amplification. This library underwent paired-end sequencing on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA) achieving a mean depth of 35×. Sequence reads were aligned to the human reference genome GRCh38 (hg38) using the Burrows-Wheeler Alignment software (BWA-MEM) version 0.7.17. Preprocessing and variant calling were subsequently carried out using the Genome Analysis Toolkit (GATK) version 4.2.0. Variant annotation was conducted using ANNOtate VARiation (ANNOVAR) and SnpEff across all genomic sequences, including introns. Information on the pathogenicity of the variants was sourced from disease databases such as Online Mendelian Inheritance in Man (OMIM) (http://omim.org), ClinVar (https://ncbi.nlm.nih.gov/clinvar), and various in silico tools that predict the functional effects of each variant. The pathogenicity of each identified variant was assessed based on the 2015 American College of Medical Genetics and Genomics (ACMG) sequence variant interpretation guidelines [10].

DNA was analyzed using the Affymetrix CytoScan Dx platform (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s recommendations. This platform features approximately 1,950,000 copy number variation (CNV) markers and 750,000 single nucleotide polymorphism markers, achieving a resolution between 25 and 50 kB. Data analysis was conducted using the Chromosome Analysis Suite Dx software package from Affymetrix. The reference sequence used was the human reference genome GRCh37 (hg19). All detected CNVs were categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign, in accordance with the ACMG’s CNV interpretation guidelines [11].

The presenting boy was born at a gestational age of 39 weeks and 3 days, weighing 2,760 g. At 2 months old, he exhibited congenital stridor due to epiglottic malacia and demonstrated poor sucking power. During infancy, he presented with axial hypotonia and primary microcephaly, with a head circumference of 35.3 cm at 2 months (3rd to 5th percentile) and 45.1 cm at 2 years (<3rd percentile). There was no history of delayed development or genetic disorders in his immediate family, including his older brother and parents. He displayed distinct facial dysmorphisms, including a small anterior fontanelle, prominent vertex, retrognathia, and hypertelorism. An echocardiogram revealed a moderate secondum atrial septal defect measuring 7.3×5.4×6.1 mm. In addition, horseshoe kidney and communicating hydrocele were found on abdominal ultrasonography (Fig. 1A). Due to poor weight gain and recurrent aspiration, he underwent fundoplication and gastrostomy at 4 months of age and continued tube feeding until the age of 3. He achieved head control at 10 months, rolled over at 13 months, and sat with support at 28 months. He showed global developmental delays according to the Korean Bayley Scales of Infant Development-III. At 28 months, his scores were as follows: cognitive scale, 7 months; receptive communication scale, 14 months; expressive communication scale, 13 months; fine motor scale, 9 months; and gross motor scale, 6 months. By the age of 5, he was able to walk with support and combine two words when speaking. Currently, at 6 years old, he exhibits no abnormal behaviors or psychiatric features. His brain magnetic resonance imaging showed ventriculomegaly and a dysmorphic cranium (brachycephaly) without any brain parenchymal abnormalities (Fig. 1B). Cytogenetic analysis confirmed a normal karyotype (46,XY). WGS identified a heterozygous variant in SPEN, NM_015001.3:c.5806C>T (Fig. 1C), predicted to cause premature termination of the SPEN protein (p.Arg1936*). This SPEN variant was classified as pathogenic based on the following evidence: (1) absence in the gnomAD dataset, (2) prediction of a stop-gained variant leading to loss of normal protein function through nonsense-mediated decay, and (3) previous pathogenic classification in ClinVar. Furthermore, the SPEN variant was not found in his parents, confirming its de novo occurrence (Fig. 1C). No other significant candidate variants were identified in the WGS results.

The molecular and clinical characteristics of cases with 1p36DS are summarized in Table 1 and Fig. 2. We retrieved a total of 159 publications using the search term ‘chromosome 1p36 deletion’ from PubMed and KoreaMed, covering the period from 2015 to March 2024. Out of these, three publications were selected based on specific criteria [12-14]. Among them, the study by Shim et al. [12] explored the detailed phenotypes of 15 patients with 1p36DS. This study was utilized to compare the clinical features of patients identified at our institution with those reported in the DECIPHER database, as illustrated in Table 1.

All three Korean patients with 1p36DS at our institution exhibited pathogenic or likely pathogenic CNVs located in the distal critical region, none of which included SPEN. The patients fell into different age categories at diagnosis: one was a neonate, another was an infant aged 10 months, and the third was a preschool-aged child of 6 years. The neonate, who underwent CMA due to neonatal seizures and distinct facial features, had a 1.3 MB deletion at 1p36.33, affecting approximately 50 genes. Among these, the deletion of gamma-aminobutyric acid type A receptor subunit delta (GABRD) was believed to be responsible for his seizures. In the cases of the infant and the preschooler, both of whom exhibited delayed development, deletions measured 900 kB and 5.2 MB at 1p36.33, respectively. All patients displayed consistent phenotypes associated with 1p36DS, including delayed development, impaired cognition, and distinctive facial features.

The clinical features of the patient with RTS identified in this study were compared with those of previously reported cases involving truncating mutations of SPEN, as detailed in Table 2. Although the neurodevelopmental characteristics of our patient closely resembled those reported previously, no behavioral or psychiatric disorders have been observed to date (Table 2). Notably, the presence of genitourinary anomalies, such as a horseshoe kidney and a communicating hydrocele, sets our findings apart from previous reports [1]. To assess the genotype-phenotype correlation in patients with 1p36DS based on the presence of SPEN, we analyzed the clinical features of the patients in this study and compared them with those documented in earlier cases, as presented in Table 1. The analysis revealed common clinical features between RTS and 1p36DS, including developmental delay/intellectual disability, facial dysmorphisms, and cardiac anomalies.