Novel CTNNB1 missense variant identified in child with spastic diplegia and visual defects

A 7-year-old boy with developmental delay, microcephaly, spasticity, limited speech, behavioral difficulties, strabismus and hypermetropia was found to carry a previously unreported missense variant in the CTNNB1 gene, according to a clinical case report from Iran. Whole-exome sequencing identified the heterozygous change c.2215A>C, designated p.Met739Leu, and testing of both parents showed that the variant was not inherited from either of them. Sanger sequencing confirmed the finding. The investigators classified the variant as likely pathogenic under American College of Medical Genetics and Genomics criteria, linking it to neurodevelopmental disorder with spastic diplegia and visual defects, or NEDSDV. The case adds a new candidate allele to the genetic causes of the condition, although functional experiments will be needed to establish its precise biological effects.

The child was born at 36 weeks of gestation after an uncomplicated pregnancy and vaginal delivery, with no reported perinatal problems. His birth measurements were a head circumference of 32 cm, weight of 3,200 g and length of 47 cm. After the neonatal period, his parents noticed truncal hypotonia, and his motor and language development was delayed. He walked independently at 18 months and produced only a few meaningful words by 5 years of age. At the age of 7, neurological examination showed microcephaly, with a head circumference of 48 cm below the third percentile, truncal hypotonia, peripheral spasticity, hyperactive deep-tendon reflexes and toe-toe walking. His weight and length were each two standard deviations below the expected values for age.

The assessment also identified several dysmorphic facial features, including epicanthal folds, a high-arched palate, a thin upper lip, a long smooth philtrum, an abnormal hairline and small alae nasi. The boy had moderate intellectual disability, required assistance with feeding, had not completed toilet training and could not form a sentence. Autistic behavior, restlessness and sleep disturbance were also present. Ophthalmological examination found strabismus and hypermetropia, for which he wore glasses. These features formed a clinical pattern consistent with CTNNB1-related neurodevelopmental disease: syndromic intellectual disability, global and motor delay, markedly limited speech, microcephaly, spasticity concentrated in the lower limbs, visual abnormalities and behavioral problems.

Initial evaluations for hereditary spastic paraplegia, including a complicated form, and leukodystrophy did not establish a diagnosis. Thyroid function, creatine phosphokinase, liver function, cholesterol and uric acid measurements were within normal limits, and an electrodiagnostic study was normal. Brain magnetic resonance imaging performed at 5 years of age was also reported as normal. The absence of abnormalities on metabolic testing and neuroimaging did not explain the combination of developmental impairment, hypotonia and spasticity, prompting the investigators to proceed with genetic analysis. The report emphasizes that CTNNB1-associated disease can remain in the differential diagnosis even when the perinatal history and initial neurological investigations are unremarkable.

For the molecular investigation, the researchers collected blood samples from the child and his parents and isolated genomic DNA using a salting-out method. Whole-exome sequencing was performed with the Agilent SureSelect Human All Exon V7 Target Enrichment kit, followed by sequencing on an Illumina NovaSeq 6000 platform to generate 150-base-pair paired-end reads. Reads were aligned to the GRCh37/hg19 reference genome with the Burrows-Wheeler Aligner, converted into sorted BAM files with SAMtools and assessed for raw-data quality with FastQC. The analysis set a mean depth-of-coverage threshold of at least 30-fold, and regions with insufficient coverage were addressed through supplementary sequencing. The resulting analysis identified a heterozygous A-to-C substitution at coding position 2215 in CTNNB1 as the most plausible pathogenic candidate.

Integrative visualization of the whole-exome data showed nearly balanced allelic reads at the variant site, with 58 adenine reads representing 51% of the sequence and 55 cytosine reads representing 49%, each with base-call quality above Q40. The finding was then validated using conventional Sanger sequencing on an ABI 3500 Genetic Analyzer. A 229-base-pair amplicon was amplified with primers 5′-TGGATGCCCTAACCTCAGTGT-3′ and 5′-CAGATCTGGCAGCCCATCAA-3′ at an annealing temperature of 60 °C. The proband’s chromatogram confirmed the heterozygous A>C change, while both parents showed wild-type sequences. The family segregation analysis therefore supported a de novo origin for the variant rather than inheritance from either parent.

At the DNA level, the change is designated NM_001904.4:c.2215A>C and converts the coding sequence ATG to CTG, producing the amino-acid substitution p.Met739Leu. Methionine and leucine are both nonpolar amino acids, but the substitution occurs near the C-terminal region of the coding sequence and maps to the armadillo-repeat domain of beta-catenin, the protein encoded by CTNNB1. The investigators applied ACMG guidelines and assigned a likely pathogenic classification using several pieces of evidence: PM2 for an extremely low or absent population frequency, PP4 for a highly characteristic phenotype, PM6 for the de novo occurrence in an affected individual and PP2 for a missense change in a gene with a low rate of benign missense variation and a known disease mechanism. The reported allele frequency in gnomAD was 0%, with no homozygous individuals observed.

CTNNB1 encodes beta-catenin, a protein involved in several processes relevant to neural development. It is central to the Wnt/beta-catenin signaling pathway and contributes to the formation of adherens junctions, cell adhesion, neural stem-cell proliferation, neurogenesis, neuronal survival and synaptic connections. The armadillo-repeat region containing the new variant is therefore of particular interest because beta-catenin coordinates mechanisms that influence neuronal architecture and synaptic function. Most previously established CTNNB1 disease variants associated with NEDSDV are loss-of-function changes, whereas pathogenic or likely pathogenic missense variants have been reported less often. The c.2215A>C change was not found in ClinVar or other publicly available disease databases, according to the report, making it a previously unreported candidate rather than an established disease-causing variant with extensive clinical precedent.

The case also fits the broader history and clinical distribution of CTNNB1-related neurodevelopmental disorder. The first cases were linked to de novo CTNNB1 variants through exome sequencing in 2012, and a later genomic and phenotypic study described 404 patients with CTNNB1-related neurodevelopmental disorders, describing a largely consistent set of neurological features. Subsequent reports have documented the disorder in Chinese, Iranian and Korean populations, supporting its occurrence across geographic and ethnic groups. Retinopathy and vitreoretinopathy have also been recognized in some affected individuals, while a previously described missense variant, c.1723G>A or p.Gly575Arg, was associated with significant vitreoretinopathy. The 7-year-old in the present report had strabismus and hypermetropia but no reported retinal disorder.

Overall, the report provides clinical and molecular evidence for a de novo CTNNB1 missense variant in a child whose presentation included developmental delay, microcephaly, truncal hypotonia, spasticity, intellectual disability, restricted speech, autistic behavior, sleep disturbance and visual defects. It illustrates a sequential diagnostic approach in which whole-exome sequencing identified the candidate change and Sanger sequencing established its presence in the child and its absence in both parents. The findings expand the reported allelic diversity of CTNNB1-related neurodevelopmental disorders and provide an additional case for evaluating the boundary between loss-of-function and missense mechanisms. The classification remains provisional in a strict mechanistic sense: no functional assays were reported to demonstrate how p.Met739Leu alters beta-catenin structure or Wnt signaling, and a single-patient case cannot establish prevalence, natural history or the full consequences of the variant. The boy was receiving outpatient physical, occupational and speech therapy, with regular multidisciplinary follow-up, and the report identifies no established disease-specific treatment.

Subject of Research: Clinical and molecular characterization of a de novo CTNNB1 p.Met739Leu variant in a child with neurodevelopmental disorder with spastic diplegia and visual defects.

Article Title: A Novel De Novo Heterozygous Missense Variant in CTNNB1 (c.2215A>C, p.Met739Leu) Underlying Neurodevelopmental Disorder With Spastic Diplegia and Visual Defects (NEDSDV): A Case Report

Article References: Ibrahim, O. J., Rajabi, A., Bonyadi, M., & Barzegar, M. (2026). A Novel De Novo Heterozygous Missense Variant in CTNNB1 (c. 2215A >C, p. Met739Leu ) Underlying Neurodevelopmental Disorder With Spastic Diplegia and Visual Defects ( NEDSDV ): A Case Report. Clinical Case Reports, 14(10), Article e73743. https://doi.org/10.1002/ccr3.73743

Image Credits: AI Generated

DOI: 10.1002/ccr3.73743

Keywords: CTNNB1, NEDSDV, missense variant, spastic diplegia, visual defects, whole-exome sequencing, Sanger sequencing, beta-catenin, Wnt signaling, case report, Novel, Novo