Microcephaly, primary lymphedema, and chorioretinopathy dysplasia (MLCRD) is a rare autosomal dominant disorder with variable expressivity [1, 2]. Since the first description of MLCRD in 1992, kinesin family member 11 (KIF11) mutations have been linked to autosomal dominant forms of microcephaly with or without lymphedema and chorioretinopathy [3, 4]. KIF11, a gene encoding the spindle motor protein EG5, is essential for spindle separation in mitosis. Studies have highlighted the critical roles of EG5 in cell proliferation, chromosome stability, and organogenesis during development [5]. Genetic diagnosis of MLCRD is challenging and often delayed due to the overlapping, variable, and incomplete penetrance of the clinical presentation. Familial members with the same KIF11 mutation can exhibit significant variability in the presence and severity of clinical manifestations [4]. Here, we present the case of a 14-year-old boy diagnosed with MLCRD following the discovery of a pathogenic variant in KIF11. To our knowledge, this is the first case in Korea to demonstrate all major clinical features of MLCRD.

He was the only child of healthy, unrelated parents. He was born at 39 weeks’ gestation with a birth weight of 2,410 grams (<3rd percentile for age and gender) and a head circumference of 30.5 cm (<2 SD). He presented with bilateral foot swelling and bluish discoloration at birth. Ultrasonographic examination revealed a well-defined, homogeneous, hypervascular lesion in the subcutaneous fat layer of the dorsa on both feet, suggesting lymphatic malformation. The edema in both feet gradually improved with compression bandage therapy. He exhibited microcephaly and facial dysmorphic features, including hypertelorism, upslanting palpebral fissures, a rounded nasal tip, a thin upper lip, and prominent ears. Ophthalmologic evaluation revealed widespread diffuse bilateral retinitis pigmentosa (RP) with normal optic nerves (Table 1). A next-generation sequencing-based gene panel study for RP revealed no pathogenic variants associated with the disease. The patient has mild intellectual disability with a full-scale intelligence quotient score of 50, as assessed by the Korean Wechsler Intelligence Scale (K-WISC)-V. Brain magnetic resonance imaging revealed microcephaly with a simplified gyral pattern, but no additional cortical abnormalities were observed. Neurologic examination revealed normal muscle strength, deep tendon reflexes, sensory responses, and intact cranial nerves. He is currently 14 years old, and the edema in his foot has mostly resolved. He is under observation without medication, despite suspected symptoms related to attention deficit/hyperactivity disorder. To identify disease-associated variants, genomic DNA from peripheral blood was collected for whole genome sequencing (WGS). The library was paired-end sequenced on a NovaSeq 6000 platform (Illumina) at a mean depth of 35x. Sequence reads were aligned to human reference genome GRCh38 (hg38) using Burrows-Wheeler Alignment Aligner (v0.7.17). Subsequent preprocessing and variant calling were performed using GATK (v4.2.0). Variant annotation was conducted using ANNOVAR and SnpEff for all genome sequences, including introns.

Using WGS, a heterozygous de novo variant in KIF11 was identified as NM_004523.4:c.308+1G>A and validated through Sanger sequencing (Fig. 1A). The c.308+1G>A variant is located in the canonical splice site of KIF11 and is predicted to significantly affect RNA splicing (SpliceAI score of 0.99). Following the guidelines for variant interpretation [6, 7], this variant is classified as pathogenic based on one very strong piece of evidence (PVS1), one strong piece of evidence (PS2), two moderate pieces of evidence (PM2 and PS4_moderate), and one supportive piece of evidence (PS1_supporting). ACGS (The Association for Clinical Genomic Science) recommendations were applied to one moderate piece of evidence (PS4_moderate) based on previous reports in multiple unrelated affected individuals [8-10]. Recommendations from the ClinGen SVI splicing subgroup were applied to one very strong piece of evidence (PVS1) and one supporting piece of evidence (PS1_supporting), based on splicing prediction data (SpliceAI donor loss delta score 0.99) and a pathogenic variant at this nucleotide position (c.308+1G>T) with the same predicted impact (SpliceAI donor loss delta score of 1.00) [7].

This study was approved by the institutional review board of Samsung Medical Center (SMC 2020-10-042), and informed consent was obtained for molecular testing and research use of biological and related clinical data. Informed written consent was obtained from the parents of the underage patient.

MLCRD (OMIM #152950) is an autosomal dominant disease with variable expression, first described in 1992 [3]. It encompasses a broad spectrum of ocular diseases, often associated with KIF11 mutations in familial exudative vitreoretinopathy (FEVR). The KIF11 c.308+1G>A variant identified in this case has been previously reported in two Chinese families diagnosed with FEVR [8, 10]. It was also observed in a Mexican boy with microcephaly, seizures, and intellectual disability (Table 1) [9]. However, lymphedema and ocular abnormalities were not noted, and the variant was classified as a variant of uncertain significance [9]. In a study of RNA from the previously reported c.308+1G>T mutation, exon 3 of KIF11 is skipped (r.211_308del), resulting in a frameshift that leads to protein loss via nonsense-mediated mRNA decay (p. Thr71Argfs*8) [11]. Given that the pathogenic variant identified in our case, c.308+1G>A, is located at the same splice site as the c.308+1G>T mutation [11], and in silico predictions show similar SpliceAI scores of 1.00 and 0.99, respectively, we hypothesized that the c.308+1G>A variant may also affect RNA splicing. To date, two cases of KIF11-related retinopathy have been reported in Korea: one with a nonsense variant (c.2220_2221del; p.Cys740*) and the other with a frameshift variant (c.2304_2305del; p.His768Glnfs*7) [12] (Fig. 1B). Both reported Korean cases presented with ocular abnormalities, microcephaly, and developmental delay, but the history of lymphedema was unclear.

In conclusion, we report the first case of a KIF11 pathogenic variant (c.308+1G>A) in a Korean patient with MLCRD. For patients with congenital microcephaly and a wide range of ocular abnormalities, with or without lymphedema, we recommend genetic testing, including KIF11. This report will contribute to a better understanding of the genetic background of Korean patients with MLCRD.