A continuum of inherited telomere dysfunction links TERT rare variants to age-related diseases

Abstract Background Telomere biology disorders (TBDs) are caused by pathogenic variants in telomerase reverse transcriptase (TERT) and other telomere-related genes and are defined by premature telomere shortening and multiorgan manifestations, including bone marrow failure, pulmonary fibrosis, liver disease, osteoporosis, and cancer. Although TBDs are clinically rare, TERT rare missense variants occur in ~1% of the population with 90% classified as variants of uncertain significance. This disparity suggests that classical TBDs represent the extreme end of a broader continuum of telomere dysfunction. To quantify this latent potential, we generated a population-scale functional atlas of TERT missense variants in the UK Biobank and assessed their association with telomere length (TL), clonal hematopoiesis (CH), and clinical phenotypes. Methods We identified TERT rare variants (max population allele frequency 0.001) in 462,666 UK Biobank participants. To define their functional impact, we developed a cell-based assay to quantify telomere extension relative to wild-type (WT) TERT. We performed molecular simulations and free energy (ΔΔG) calculations using the cryo-EM structure of telomerase bound to TPP1. Functional scores were integrated with a common variant-derived TL polygenic risk score (PRS) to define their impact on TL, hematologic traits, CH, and clinical phenotypes. Results To establish functional thresholds, we benchmarked our assay using 9 common variants and 120 TBD-associated variants. Common variants did not impact telomere extension, while all TBD-associated variants were impaired: 62% showed no extension ('severe') and 38% had reduced extension ('intermediate'). Among 601TERT missense variants, 69% were impaired (13% severe, 56% intermediate) in 1297 UK Biobank participants. Severe variants clustered in domains that form the active site (C-terminal extension domain, CTE: 29%; reverse transcriptase domain, RTD: 18%) or bind to TPP1 (telomerase-essential N-terminal domain, TEN: 25%). Variants in the telomerase RNA binding domain (TRBD) had fewer severe (7%) but more intermediate variants, yielding similar impairment rates (69% vs 74%, p=0.28). No severe variants occurred in the linker domain. To investigate mechanisms of impairment, we modeled 14 variants across five multiallelic positions (TEN:G135, TRBD:R358, RTD:R669/R756, CTE:R962) that had variants with divergent functional scores. Functional impairment correlated with increased ΔΔG (3 kcal/mol, r = -0.75, p=0.007) and reduced side-chain contacts with TPP1, TERC, or the RNA:DNA duplex. Severe variants showed disrupted interactions and intermediate variants showed partial contact loss or altered flexibility, indicating domain-specific mechanisms of dysfunction and a gradient of severity across alleles. To determine whether TERT functional impairment correlated with in vivo telomere shortening, we analyzed leukocyte TL in UK Biobank participants. Severe variants were associated with shorter TL compared to controls (β = -1.55, p0.0001), similar to protein-truncating variants (β= -1.27). Intermediate variants had a moderate effect (β = -0.55, p0.0001), while preserved variants had minimal impact (β = -0.09). TL effects were strongest for variants in the TEN, RTD, and CTE domains. The PRS modified TL across functional groups, but its effect was attenuated with increasing TERT variant impairment (standardized interaction coefficients: preserved 1.7, intermediate 0.9, severe 0.3). Among intermediate carriers, TL ranged from preserved-like to severe-like across PRS quartiles. We examined whether TERT functional impairment was associated with clinical phenotypes. Intermediate and severe, but not preserved, variants were associated with bone marrow dysfunction (higher MCV, lower RBC count, lower platelet mass), TBD-related CH with somatic PPM1D or TERT promoter mutations (OR=22 and 118, both p0.0001), interstitial lung disease (OR=7.9 and 66.1, both p0.0001). Severe variants were associated with aplastic anemia (OR=10.4, p=0.012) and osteoporosis (OR=29.5, p0.0001). Conclusion Most germline TERT rare missense variants are functionally impaired (69%) with domain-specific effects linked to shorter TL and manifestations of telomere dysfunction including TBD-related CH and clinical phenotypes. Polygenic background modulates – but does not offset – the effects of impaired TERT variants, revealing a continuum of inherited telomere dysfunction shaped by rare and common variants.