TP53 mutations represent one of the strongest adverse prognostic factors in myelodysplastic neoplasms (MDS). While multi-hit TP53 (TP53multiHit) alterations uniformly lead to very poor outcomes, the prognostic relevance of monoallelic TP53 (TP53mono) mutations remains controversial. TP53 variants can cause loss-of-function, dominant-negative, or gain-of-function effects. We hypothesized that functional heterogeneity among TP53 variants contributes to the variable clinical behavior observed in monoallelic TP53-mutated MDS. Therefore, we analyzed pretreatment samples from 4,505 patients with MDS from two independent cohorts (IWG, n=3,173; J-MDS, n=1,332), including 271 patients with TP53mono and 499 with TP53multiHit. Functional annotation of TP53 variants was performed using a previously published phenotype score (PS) derived from saturation mutagenesis screens, capturing dominant-negative and loss-of-function effects.

Median overall survival (OS) differed significantly by TP53 allelic state (TP53 wild-type (TP53wt) 42.4 months; TP53mono 22.9 months; TP53multiHit 9.2 months; p < 0.001). Within the TP53mono subgroup, functional annotation identified marked heterogeneity. Patients with high PS (≥7) showed significantly inferior OS compared with those with low PS (median OS: 13.8 vs. 39.2 months; HR 1.68, 95% CI 1.16-2.42; p = 0.006), particularly for IPSS-R and IPSS-M low-risk cases. Combining PS and variant allele frequency (VAF) further improved risk stratification. TP53mono patients with PS ≥7 and VAF ≥22% had outcomes comparable to TP53multiHit (median OS: 8.8, p = 0.2), whereas those with PS <7 and VAF <22% exhibited survival similar to TP53wt(median OS: 49.7, p = 0.9).

Overall, functional annotation of TP53 variants refines prognostication in TP53mono-mutated MDS and may enhance individualized risk assessment.

The authors have declared no competing interest.

A.S. is a clinician scientist of the ICON program at the medical faculty Mannheim of Heidelberg University, DN is funded by the Deutsche Forschungsgemeinschaft (DFG), CRC1709 and was an endowed Professor of the German Jose-Carreras-Foundation (DJCLSH03/01). N.S. is supported by the Medical Faculty Mannheim of the Heidelberg University SEED and the Torsten Haferlach Leukemia Diagnostics Foundation. V.R. is funded by the Health + Life Science Alliance Heidelberg Mannheim and received state funds approved by the State Parliament of Baden-Wuerttemberg. This work was supported by grants from the Japan Agency for Medical Research and Development (AMED): nos. JP24tk0124003 to S.O, JP24ck0106791, JP25ck0106019, and JP25kk0305028 to Y.O., JP22ck0106691 and JP24ck0106875 to Y.O., Y.N., and S.O; the Moonshot Research and Development Program (no. JP24zf0127009) to S.O.; the Japan Society for the Promotion of Science (JSPS): KAKENHI (nos. JP24H00009 to S.O, JP24K19223 to Y.O.); the Japan Science and Technology Agency (JST): Fusion Oriented Research for disruptive Science and Technology (FOREST) Program (no. JPMJFR220L) to Y.O.

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

The Ethics Committee of Kyoto University Graduate School of Medicine gave ethical approval for this work. Data from the IWG cohort and TP53 phenotypic scores were obtained from previously published, publicly available sources. De-identified individual participant data from the Japanese cohort were obtained under a data transfer agreement.

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

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I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

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I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

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Data from the International Working Group (IWG) cohort is available as described in prior publications. Deidentified individual participant data from the Japanese J-MDS cohort are available upon reasonable request and subject to institutional approval and data transfer agreements.