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S. E. Boonen

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Sep 2026

Phenotypic manifestations and variant reclassification of germline PTEN variants: a nationwide Danish study.

BACKGROUND Classification of heterozygous germline PTEN variants in patients with, or suspected of having, PTEN hamartoma tumour syndrome (PHTS) remains challenging. Accurate classification is essential as these patients require lifelong cancer surveillance. METHODS We identified all patients with a PTEN variant previously classified as a variant of uncertain significance (VUS), likely pathogenic (LP) or pathogenic (P), collected clinical data and reclassified all variants using the latest PTEN gene-specific American College of Medical Genetics (ACMG) guidelines. Moreover, genotype-phenotype correlations were assessed. RESULTS 167 patients from 112 families were enrolled. Eighty-seven unique PTEN variants were identified, including 20 novel variants. After applying the PTEN gene-specific ACMG guidelines, 32 variants (36.8%) were reclassified, resulting in 60 PTEN variants classified as LP/P (69.0%), 18 variants classified as VUS (20.7%), while 9 variants were classified as LB/B (10.3%). Genotype-phenotype correlation was performed among 104 patients with LP/P variants: 51 cancer cases were recorded in 41 patients and a distinct PHTS phenotype was observed in 25% of patients, with macrocephaly being present in 99% of patients with a known head circumference. Twenty-three patients had neurodevelopmental delay and/or autism, and we observed an increased prevalence of missense variants in these patients. CONCLUSION We identified 87 different PTEN variants, and application of PTEN gene-specific ACMG guidelines led to reclassification of 32 variants (36.8%), underscoring the importance of regular variant reassessment using the most recent gene-specific guidelines, ensuring optimal patient management and surveillance.

Annette Lyngholm Sandsdalen, A. M. Jelsig, B. Bertelsen et al. · 0 citations
Review Open access Sep 2026

Variants in the Imprinted IGF2 Gene: A Review and Phasing of De Novo Variants Using Long-Read Sequencing.

Pathogenic variants on the paternal allele of IGF2 are linked to Silver-Russell syndrome (SRS). This report describes two unrelated individuals-a 5-year-old girl and an adult female-with de novo IGF2 missense variants, both diagnosed with SRS. While one exhibited normal development, the other had intellectual disability, highlighting phenotypic variability. A review of 20 individuals with IGF2 variants revealed that SRS features, as defined by the Netchine-Harbison Clinical Scoring System, were most common. Additional recurrent traits included delayed speech and motor development, under-masculinized male genitalia, hand/foot anomalies, and congenital heart defects. Growth faltering patterns varied, and intellectual disability was seen in some. We also demonstrated that long-read sequencing can determine the allelic origin of de novo IGF2 variants using differentially methylated regions, eliminating the need for parental samples. This approach confirms long-read sequencing as a powerful tool for identifying de novo variant origins in imprinted genes like IGF2.

T. Juul, S. E. Boonen, K. V. Pedersen et al. · 0 citations

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