A106-21 Prevalence and Characterization of Protein-Changing PHOX2B Variants in the NIH-Funded All of Us Research Hub

Abstract Rationale Pathogenic variants in PHOX2B cause Congenital Central Hypoventilation Syndrome (CCHS), Hirschsprung disease, and neural crest tumors. Known PHOX2B disease-causing variants include heterozygous in-frame expansions of the 20-alanine repeat region (PARM) to between 24-33 repeats (denoted: 20/24-20/33), and non-PARM (NPARM) variants (frameshift, missense, nonsense) throughout the coding region. Prior case-reports and small-cohort studies have demonstrated variable expressivity and incomplete penetrance in many CCHS-causing PHOX2B variants. We hypothesized that examining PHOX2B protein-changing variants in the NIH-funded All of Us dataset might identify individuals with subclinical or variably expressed CCHS or autonomic dysregulation with unknown cause. Characterizing those variants may reveal previously unrecognized PHOX2B genotype-phenotype correlations. Methods The All of Us Research Hub is a NIH-funded program that aggregates participant data, including genomics, electronic health record (EHR), surveys, and physical measurements. PHOX2B variants analyzed included in-frame PARMs and polyalanine-repeat contractions (PARCs), and frameshift, missense, splice site, and nonsense NPARMs. Genomic data were used from individuals with short or long-read sequencing. Rare PHOX2B variants were defined as those with a population frequency of ≤ 0.1%, and common PHOX2B variants are 0.1%. Results Of 633,540 records in the All of Us dataset, 414,830 (65%) reported short or long-read genomic data. Among these, nearly 11,730 (3%) reported protein-changing PHOX2B variants. Seven unique heterozygous PARM variants (range 20/21-20/28; Table 1) were identified in ∼80 individuals, including 4 pathogenic CCHS-associated expansions. 13 unique heterozygous PARC variants (range 20/6 to 20/19) were identified in ∼9,570 individuals, along with 4 homozygous PARCs (genotypes 13/13, 14/14, 15/15, and 17/17) in ∼70 individuals. 192 unique NPARMs were identified, including six unique frameshift (≤20), 167 missense (in ∼1930 individuals), and 19 splice region variants (in ∼60 individuals). Among the 75% of our cohort with EHR data, none had a documented CCHS diagnosis, though 199 had autonomic nervous system disorders. Conclusion From the All of Us dataset, we identified 216 unique PHOX2B variants among ∼11,730 individuals, most with uncertain clinical significance, but some expected to be pathogenic and CCHS-related. Common PARCs were included given in-vitro work demonstrating a similar, but less severe impact on protein function compared with PARMs. These findings of protein-changing PHOX2B variants support our hypothesis and raise the possibility of undiagnosed CCHS or autonomic dysregulation with unknown cause. Moving forward, it is imperative to investigate the impact of these PHOX2B variants on unrecognized hypoventilation and broader autonomic dysregulation, including their potential for variable penetrance, expressivity and contribution to missed diagnoses of CCHS. This abstract is funded by: None