Heterozygous pathogenic variants in the gene cause impaired intellectual development and distinctive facial features with or without cardiac defects (MIM #616789). This complex neurodevelopmental disorder is characterised by various phenotypic features, including plagiocephaly, strabismus, clubfoot, poor speech, and developmental delay. The aim of this study was to evaluate the clinical significance and consequences of a novel heterozygous intragenic deletion in a proband with clinical features of a -related disorder through extensive clinical, molecular, and functional characterisation. Combined comparative genomic hybridisation and single-nucleotide polymorphism array (SNP-CGH) was used to identify the changes in the proband's gDNA sequence (DECIPHER #430183). Intragenic deletion was specified via quantitative polymerase chain reaction (qPCR) and Sanger sequencing of the proband's cDNA sample. Western blot and bioinformatics analyses were used to investigate the consequences of this copy number variant (CNV) at the protein level. CRISPR-Cas9 technology was used for a -gene-silencing experiment in a culture of the control individual's skin fibroblasts. After the -gene-editing experiment, subsequent functional fibroblast culture analyses were performed. The analysis of the proband's cDNA sample allowed for specifying the regions of the breakpoints and identifying the heterozygous deletion that spanned exons 3 to 10 of , which has not been reported previously. In silico, the deletion was predicted to result in a truncated protein NP_056150.1:p.(Val104Glyfs*5), partly altering the Med13_N domain and losing the MedPIWI and Med13_C domains. After gene editing was performed, reduced cell viability; an accelerated aging process; and inhibition of the , , and gene expression were found to exist. Based on these findings, heterozygous intragenic 12q24.21 deletion in the affected individual resulted in haploinsufficiency due to the premature termination of protein translation, therefore leading to haploinsufficiency syndrome.