Poster Presentation ESA-SRB-ANZOS 2025 in conjunction with ENSA

A Clinical Approach to MEN1 Variants of Uncertain Significance: Application of In Silico Tools to Upgrade Variants   (128424)

Jessica Bindra 1 2 3 , Luke Ephraums 4 , Michael Field 5 , Sunita De Sousa 4 6 7 , Roderick Clifton-Bligh 1 2 3
  1. Department of Endocrinology, Royal North Shore Hospital, Sydney, NSW, Australia
  2. Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
  3. Cancer Genetics and Diagnostics Laboratory, Kolling Institute, Sydney, NSW, Australia
  4. Endocrine & Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
  5. Familial Cancer Service, Royal North Shore Hospital, Sydney, NSW, Australia
  6. Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
  7. South Australian Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia

Aims
Multiple Endocrine Neoplasia Type 1 (MEN1) is an autosomal dominant hereditary tumour syndrome characterised by high penetrance and phenotypic heterogeneity (1). Variants of uncertain significance (VUS) in the MEN1 gene, encoding menin, present a significant challenge for clinical diagnosis, risk stratification, and genetic counselling. This study aimed to assess the potential utility of advanced in silico prediction tools, AlphaMissense and REVEL, in supporting the reclassification of MEN1 VUS in individuals with a clinical MEN1 phenotype.

Methods
A retrospective review was conducted across three Australian tertiary centres, identifying six individuals with clinical features of MEN1 and MEN1 VUS. Detailed clinical, familial, and genetic data were analysed. Variant pathogenicity was reassessed using the ACMG/AMP framework (2), incorporating in silico predictions from AlphaMissense (3) and REVEL scores (4). Structural implications were evaluated through AlphaFold-based protein modelling and visualised with PyMOL to assess variant localisation within conserved and functionally critical menin domains (5).

Results
The cohort of six individuals comprised four missense, one frameshift, and one in-frame deletion variant. All missense variants demonstrated strong pathogenic predictions via AlphaMissense (score >0.99), supported by high REVEL scores (>0.89) and localisation to structurally constrained or functionally essential regions of the menin protein. Structural modelling indicated disruptions affecting domains integral to menin’s tumour suppressor activity.

Conclusion
This study highlights the clinical applicability of computational predictive tools such as AlphaMissense and REVEL in the interpretation of MEN1 VUS. When integrated with protein structural modelling and clinical phenotyping, these tools offer a practical and scalable strategy for variant reclassification. This has meaningful clinical implications, including more precise risk assessment, tailored surveillance protocols, informed reproductive decision-making, and appropriate cascade genetic testing for affected families.

  1. Brandi ML, Pieterman CRC, English KA, Lines KE, Shariq OA, Marini F, et al. Multiple endocrine neoplasia type 1 (MEN1): recommendations and guidelines for best practice. Lancet Diabetes Endocrinol. 2025 Jun.
  2. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genetics in Medicine. 2015 May;17(5):405–24.
  3. Cheng J, Novati G, Pan J, Bycroft C, Žemgulytė A, Applebaum T, et al. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science (1979). 2023 Sep 22;381(6664).
  4. Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, et al. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. The American Journal of Human Genetics. 2016 Oct;99(4):877–85.
  5. Schrödinger LLC. The PyMOL Molecular Graphics System, version 2.0. Schrödinger LLC; 2015.