Systematic Approach To Define Clinically Significant Variants of Unknown Significance (VUS) in Children With Short Stature

Annalisa Deodati; Giulia Mirra; Valentina Pampanini; Francesca Fausti; Rosario Ruta; Mafalda Mucciolo; Graziamaria Ubertini; Antonio Novelli; Stefano Cianfarani

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ESPE Abstracts (2024) 98 P1-160

ESPE2024 Poster Category 1 GH and IGFs 2 (11 abstracts)

Systematic Approach To Define Clinically Significant Variants of Unknown Significance (VUS) in Children With Short Stature

Annalisa Deodati ^1,2 , Giulia Mirra ¹ , Valentina Pampanini ¹ , Francesca Fausti ² , Rosario Ruta ³ , Mafalda Mucciolo ³ , Graziamaria Ubertini ¹ , Antonio Novelli ³ & Stefano Cianfarani ^1,2,4

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¹Unit of Endocrinology and Diabetology, Rome, Italy. ²Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy. ³Translational cytogenomics research unit, Laboratory of Medical Genetica, Bambino Gesù Children's Hospital, Rome, Italy. ⁴Affiliated Researcher, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden

Background: Next generation sequencing (NGS) has recently been proposed as a primary diagnostic tool in the work-up of children with idiopathic short stature (ISS) and born small for gestational age (SGA). The main limitation of a multi-gene approach is represented by the difficulty in the interpretation of VUS clinical significance.

Aim: To identify and characterize genetic variants in a cohort of children born SGA and ISS through advanced and systematic genetic testing.

Patients and Methods: A cohort of 144 children with SS (height < -2.5 SD) without major syndromic/dysmorphic features was recruited: 65 SGA and 79 ISS. All patients underwent to SNP array and WES. We developed customized targeted panel sequencing, including over 40 genes involved both in growth plate and GH-IGF1 axis. Targeted genetic testing was applied based on known disease frequencies and phenotypic characteristics. To assess potential impact on protein function we performed in VUS class 3 in silico analysis using several bioinformatic predictors or in vitro functional study.

Results: In SGA (n = 65) patients we found: in 35% of cases (23 pts) no genetic variants; in 25% (16 pts) SNP array or chromosomal abnormalities; in 10% (7 pts) known pathogenic genetic variants syndromes; in 30% (43 pts), NGS panel showed 21 point mutations: 2 likely pathogenic (class 4) and 19 VUS (class 3). In ISS (n = 79) patients we found: in 34% (31 pts) no genetic variants; in 6% (5 pts) SNP array or chromosomal abnormalities; in 5% (4 pts) variants associated with known syndromes; in 55% (43 pts) 64 point mutations: 3 likely pathogenic (class 4) and 54 VUS (class 3). To define the role of these point mutations we reanalyzed all variants using a systematic approach combined including clinical and hormonal assessment, in silico predictor scores and in vitro functional studies. In more than 50 % of SGA and 23% of the ISS patients we found new clinically significant variants in the following genes: IGF1R (n = 5), ACAN (n = 3), XRCC4 (n = 1), COL27A1 (n = 1), FLNB (n = 2), FGFR3 (n = 1), OBSL1 (n = 1)

Conclusion: A combined approach of detailed phenotyping, targeted genetic testing and bioinformatic analysis allows the identification of the underlying cause of short stature in at least 23% of ISS patients and more than 50% of SGA children, enabling the pediatric endocrinologist to make a diagnosis, decide the appropriate treatment and management and provide genetic counseling.