THU160 A Prospective Genetic Analysis Of Children With Idiopathic Short Stature (ISS) Using Whole-exome Sequencing (WES): First Results

Abstract

Abstract Disclosure: L.D. Cellin: None. N.L. Menezes De Andrade: None. R.C. Rezende: None. V. Souza: None. N.C. Dantas: None. E. Quedas: None. M.F. Funari: None. G. Vasques: None. R.D. Scalco: None. A.C. Malaquias: None. A. Jorge: Consulting Fee; Self; Novo Nordisk. Grant Recipient; Self; BioMarin. Introduction: Children classified as idiopathic short stature (ISS) may have a monogenic cause that can explain their growth disorder. In this context, genetic tests emerge as a new diagnostic tool. Objectives: To determine the usefulness of WES for the genetic investigation of children with ISS. Patients and Methods: We sequentially enrolled 95 children with ISS without previous genetic testing, except for karyotyping for girls. In WES analysis, we prioritized rare variants (MAF<0.001), classified as loss-of-function (LoF) or missense predicted to be deleterious on in silico predictions. All variants were categorized according to ACMG/AMP criteria. We analyzed genes previously associated with growth disorders. CNV analysis was performed based on WES data; additionally, MLPA for SHOX was performed to assess deletion in regulatory regions. In positive cases, we carry out segregation in the family. Results: Our cohort was characterized by male preponderance (67%), markedly short stature (height SDS -2.6±0.7, 20% with height SDS<-3), and in 48% of cases, at least one of the parents have short stature. We identified 12 pathogenic or likely pathogenic (P/LP) variants by WES, including two gene deletions (SHOX and PTHLH) and 10 point mutations in ACAN (2x), IHH, PRKG2, LTBP3, ERF, THRA, GHR, PTPN11, and NF1. Additionally, two deletions involving the regulatory region of the SHOX gene were identified by MLPA. One patient had two P/LP alterations, totaling a diagnostic yield of 13.7% (12.6% if only WES results were considered). It is noteworthy that in addition to genes already associated with ISS (ACAN, SHOX, IHH, GHR, PTPN11, NF1), we observed a greater diversity of genes, including resistance to thyroid hormones (THRA) and milder forms of skeletal dysplasia (LTBP3, PTHLH, PRKG2). All but one of the variants were in the heterozygous state, including two de novo variants and four inherited from a parent with short stature. Fifteen patients have variants of uncertain significance (VUS) in genes already associated with growth disorder: IHH (3x), FGFR3 (2x), NPR2 (2x), LZTR1 (2x), MMP13, COL11A1, COL11A2, EXT2, IGF1R, and WNT5. Furthermore, four patients have variants of interest in new candidate genes (MAU2, MAP3K4, NR2E1, C6ORF136). Conclusion: The diagnostic yield was similar to other studies in children with ISS, but a greater diversity of genetic causes was observed, with those involving growth-plate genes and the RAS-MAPK pathway being more frequent. The large number of VUS highlights the need for further studies and new tools to classify these variants definitively. Presentation: Thursday, June 15, 2023