# A Case Report: Identification of a Pathogenic Microdeletion at Chromosome 21q21.3q22.13 Using Whole-Exome Sequencing and CNV Analysis in a Moroccan Child with Global Developmental Delay

## TL;DR

A Moroccan child with developmental delays was found to have a pathogenic microdeletion on chromosome 21q21.3–q22.13 using whole-exome sequencing and CNV analysis.

## Contribution

This case report highlights the use of integrated genomic and bioinformatic approaches to identify a rare microdeletion and its clinical implications.

## Key findings

- An 8.2 Mb de novo microdeletion in 21q21.3–q22.13 was identified in a child with global developmental delay and multiple anomalies.
- The deletion encompassed 124 clinically relevant genes, including dosage-sensitive genes like SON and RUNX1.
- Integrated analysis confirmed the deletion's pathogenicity and genotype–phenotype correlations.

## Abstract

Copy number variations (CNVs) affecting the chromosomal region 21q21.3–q22.13 are rare and have been increasingly associated with neurodevelopmental abnormalities and multisystemic manifestations. In this study, we aimed to characterize the clinical, genomic, and genotype–phenotype correlations of a Moroccan child carrying a de novo microdeletion in this region. Whole exome sequencing (WES) was performed using sequencing-by-synthesis technology on the GenoLab M platform, and CNV detection was achieved through the SeqOne platform. Variant interpretation was conducted using the Integrative Genomics Viewer (IGV), and a custom gene–phenotype heatmap was generated in R (ComplexHeatmap and pheatmap) based on OMIM, ClinVar, and DECIPHER databases to prioritize candidate genes within the deleted segment. The patient presented with global developmental delay, microcephaly, psychomotor and staturo-ponderal retardation, facial dysmorphism, epilepsy responsive to treatment, and cerebral anomalies, including passive biventricular hydrocephalus and diffuse cortical atrophy. WES-CNV analysis identified a heterozygous de novo microdeletion of approximately 8.2 Mb in 21q21.3–q22.13, encompassing 124 clinically relevant genes. Integrated analysis confirmed the pathogenicity of the deletion and highlighted genotype–phenotype correlations, particularly implicating dosage-sensitive genes such as SON and RUNX1. This case underlines the clinical utility of combining WES, CNV analysis, and phenotype-based bioinformatic tools for diagnosing complex microdeletion syndromes, contributes to understanding genotype–phenotype relationships in 21q21.3–q22.13 deletions, and supports improved clinical interpretation and patient management.