Application of genomic bioinformatic tools in clinical psychiatry and counseling

Genomic medicine has introduced transformative tools for psychiatric practice, facilitating the diagnosis of complex cases through the identification of genetic variants. The gene encodes a key component of the histone methyltransferase complex. Mutations in this gene have been linked to neurodevelopmental disorders and schizophrenia, particularly in cases with early onset and cognitive impairment. The aim of this article is to describe the application of genomic tools and international criteria for interpreting genetic pathogenicity in psychiatric clinical practice, using as a model. Based on an illustrative clinical case of a 13-year-old patient with psychotic symptoms, we conducted a comparative analysis of two single-nucleotide variants in (c.2209C>A and c.2209C>T). Genomic databases (Ensembl, ClinVar, gnomAD) and prediction tools (PolyPhen-2, MutationTaster, Align-GVGD) were used, following the American College of Medical Genetics and Genomics guidelines. The c.2209C>T (nonsense) variant was classified as pathogenic due to its truncating effect and prior reports. In contrast, the c.2209C>A (missense) variant, initially of uncertain significance, was reclassified as likely benign after a familial segregation study showed the variant was inherited from an unaffected parent. The integration of genomic tools allows for a precise approach to neuropsychiatric phenotypes. However, bioinformatic analysis must be complemented by clinical correlation and cosegregation studies. Finally, genetic counseling is emphasized as an essential process to integrate technical findings with the psychological and educational needs of the patient and their family.