Prevalence and characterization of germline RAS pathway variants in children with chronic myeloid leukemia

Leukemia LETTER www.nature.com/leu OPEN Prevalence and characterization of germline RAS pathway variants in children with chronic myeloid leukemia © The Author(s) 2026 1234567890();,: Leukemia; https://doi.org/10.1038/s41375-026-02952-z INTRODUCTION Genetic predisposition to chronic myeloid leukemia (CML) is not extensively defined, since CML predominantly affects older adults and leukemogenesis is facilitated by age-related accumulation of secondary mutations. Pediatric cases are rare, but studies show that 10% of pediatric patients with CML carry pathogenic germline variants [1], similar to that observed in myelodysplastic syndrome [2]. Moreover, myeloproliferative disorders can be associated with RASopathies [3], but the role of variants within the RAS/RAF/MAPK pathway in CML remains insufficiently understood. The molecular pathogenesis in CML differs from that in myelodysplastic neoplasm or juvenile myelomonocytic leukemia (JMML), because, in CML, BCR::ABL1 is generally the mandatory, driving oncogene. However, it is not sufficient for the development of CML in all cells [4]. One patient with a pathogenic SOS1 variant had a clinical diagnosis of Noonan syndrome (NS) and developed CML at an exceptionally young age with a complicated clinical course. This led us to specifically examine the variants within the RAS/RAF/ MAPK pathway present in pediatric patients with CML. Through this analysis, germline variants were identified in the genes encoding proteins involved in RAS activation (SOS1 and PTPN11) [5, 6] and in genes encoding negative regulators of RAS (NF1 and NF2) [7, 8]. We hypothesize that germline variants in RAS pathway genes predispose cells to excessive proliferation in combination with the BCR::ABL1 fusion protein, enabling earlier CML onset. To estimate their potential contribution to leukemogenesis pending experimental validation, we classified variants using several in silico tools. Furthermore, we compared them with similar germline variants within the RAS pathway that had previously been reported in individuals with hematological malignancies and/or with RASopathies. MATERIAL AND METHODS Whole-exome sequencing and targeted enrichment sequencing were performed on diagnosis and follow-up samples from pediatric patients with BCR::ABL1-positive CML from the German pediatric CMLpaed II trial (n = 145; EudraCT 2007-001339-69; Supplementary Methods). All participants or legal guardians provided informed consent in accordance with the Declaration of Helsinki (EK282 122 006, EK 236_18 B). To contextualize the CML variants within the RAS pathway, we compared them with published germline missense variants (“external cohort”) across three groups: hematological malignancies, syndromic hematological malignancies, and syndromic cases (Supplementary Table 1). Overall, 215 variants were identified in SOS1 (n = 61), PTPN11 (n = 73), NF1 (n = 67), and NF2 (n = 14), distributed among hematological malignancies (n = 19), syndromic hematological malignancies (n = 26), and syndromic cases (n = 171). Germline variants in pediatric patients with CML were characterized according to the American College of Medical Genetics and Genomics (ACMG) classification system [9], and their prevalence was evaluated using the reference population (gnomAD™ version 2.1.1, non-cancer) [10]. Additionally, in silico prediction tools were applied to quantify the potential effect of the germline variant on the protein structure and function (Supplementary Methods). RESULTS Within our cohort, one patient was diagnosed with NS at birth and developed CML in blast phase (CML-BP) at 1.4 years of age (Table 1). Clinical features included short stature, motor delay, and valvular and supravalvular pulmonary stenosis, with a germline SOS1 R552S variant identified as the underlying genetic cause. No mutations were detected in JMML-associated genes. At presentation, the patient had severe anemia (hemoglobin 6.1 g/dl) and lymphoid blasts in blood. Bone marrow morphology revealed 30–40% lymphoid blasts in a markedly hypocellular marrow. Detection of a BCR::ABL1 fusion with a major breakpoint and the presence of BCR::ABL1 in 42% of myeloid interphase nuclei after cytoreductive therapy, confirmed the diagnosis of CML-BP. Treatment included reduced induction chemotherapy (two doses of vincristine and prednisolone) and tyrosine kinase inhibitor treatment. Due to refractory chylothorax, dasatinib was replaced by ponatinib after 15 months. On ponatinib, the patient achieved a major molecular response (BCR::ABL1/ABL1 ratio ≤1%), but no deeper molecular remission. Allogeneic hematopoietic stem cell transplantation was performed 3.3 years after diagnosis. Two years post-transplantation, the patient remains BCR::ABL1-negative despite subsequent graft failure. The R552S variant resides in a strictly conserved codon and disrupts the autoinhibitory function of the protein through the lack of interaction with the side chains of D140 and D169 in the histone domain (Fig. 1A). SOS1 R552S was classified as pathogenic by ACMG and in silico predictors (mean score 0.823). In addition, the OncoVI tool for oncogenicity classification [11] labeled the variant as likely oncogenic. R552S belongs to a spectrum of known SOS1 variants in individuals with NS, with mean scores ranging from 0.086 to 0.969 (median 0.753; Supplementary Table 1). Within the specific context of NS-associated leukemia, R552S scored similarly to previously identified variants in pediatric patients with NS and acquired leukemia (M269R and M269T with a score of 0.898 and 0.871, respectively). While the SOS1 variants in CML are located in similar domains to those in acute leukemia, no cluster between the two cohorts can be defined (Fig. 1B). Received: 17 December 2025 Revised: 5 March 2026 Accepted: 27 March 2026 Letter 2 Table 1. Germline variants in RAS signaling pathway in pediatric patients from CMLpaed II registry (reference genome GRCh37). The reference population was obtained from gnomAD™ v2.1.1 non-cancer (1). Gene CML Phase SOS1 de novo BP SOS1 SOS1 Age at VAF Gender diagnoisis (%) (years) Ref. Sequence Chr. Chr. Posion REVEL (5) Mean Score gnomAD v2.1.1 non-cancer (1) AF (%) Allele number ACMG Classificaon (6) Ref. Time to achieve BCR::ABL1 0.01% Post- HSCT 0.997 0.447 0.863 0.823 / 0 Pathogenic (PS2, PS3, PS4, PM1_str, PP2, PP3_mod, PM2_sup) (7) G A 0.682 0.304 0.463 0.426 0.469 / 0 VUS (PM2_sup) / 8 months A G 0.368 0.375 0.387 0.339 0.367 / 0 VUS (PM2_sup) / 32 months R722K C T 0.060 0.108 0.178 0.052 0.100 0.01 267 214 Likely benign (BP4_str, PM2_sup) / 59 months 39 281 876 T200S G C 0.092 0.067 0.108 0.263 0.133 0.002 268 084 VUS (PM2_sup, BP4) / Post-HSCT 12 112 888 246 L88I T A 0.755 0.965 0.601 0.555 0.719 0 VUS (PM2_sup, PP2, PP3) (8) 82 months ENST00000358273 17 29 664 529 S2191P T C 0.396 0.174 0.363 0.350 0.321 0.0004 236 896 VUS (PM2_sup, PP2) (...truncated)