Paired box (PAX) genes encode a family of nine transcription factors that function as master regulators of embryogenesis, organogenesis, and lineage specification. Their tightly regulated spatial and temporal expression is essential for the development of multiple organ systems, including the central nervous system, eyes, kidneys, immune system, musculoskeletal system, and endocrine organs. Germline mutations of PAX genes result in a broad and often pleiotropic spectrum of human disease, reflecting the developmental programs governed by each family member. Pathogenic variants in PAX genes underlie diverse congenital disorders such as aniridia (PAX6), renal coloboma syndrome (PAX2), otofaciocervical syndrome with immunodeficiency (PAX1), Waardenburg syndrome (PAX3), maturity-onset diabetes of the young (PAX4), and tooth agenesis (PAX9). These conditions frequently demonstrate variable expressivity, incomplete penetrance, and overlapping phenotypes, which make it challenging to be clinically recognized. Beyond embryogenesis and embryologic development, emerging evidence indicates that several PAX proteins remain active in postnatal tissue maintenance, adult stem cell regulation, immune function, and regenerative responses (particularly PAX7 in skeletal muscle satellite cells and PAX5 in B-cell homeostasis), further expanding their clinical relevance. This review provides a synopsis of the major, clinically relevant, germline PAX gene mutations, emphasizing genotype-phenotype correlations, developmental mechanisms, and disease classification across the organ systems. By integrating molecular genetics with human pathology, we highlight the diagnostic implications of PAX genes as central determinants of congenital disease and provide a framework for understanding how alterations in the developmental transcriptional networks translate into human pathology.

Papillorenal syndrome (PAPRS), or renal coloboma syndrome, is a rare autosomal dominant disorder caused by PAX2 mutations. It classically manifests with renal hypodysplasia and optic nerve anomalies. However, recent literature suggests an expanding phenotypic spectrum. We report a 7-year-8-month-old boy born to consanguineous parents, presenting with stage 4 chronic kidney disease (CKD), nephrotic-range proteinuria, visual impairment, and ADHD. Renal biopsy revealed focal segmental glomerulosclerosis (FSGS), and ocular examination showed bilateral peripheral scalloped chorioretinal atrophy without optic nerve colobomas. Genetic testing confirmed a pathogenic heterozygous PAX2 frameshift mutation (c.69_70insG; p.Val26fs28*), establishing the diagnosis of PAPRS. This case illustrates an expanded phenotype of PAX2-related PAPRS, including FSGS, atypical retinal degeneration, cerebellar hypoplasia, and ADHD. Recognition of such atypical presentations is vital for early diagnosis and multidisciplinary management, especially in resource-limited settings where classic features may be absent.

PAX2-related disorders encompass renal coloboma syndrome (RCS) and hereditary focal segmental glomerulosclerosis (FSGS) type 7. We retrospectively analyzed 27 Korean patients with PAX2 pathogenic variants detected between 2004 and 2022 and conducted a literature review of 328 cases, including 301 previously reported. In our cohort, 19 had RCS, 4 had FSGS, and 4 had isolated congenital anomalies of the kidneys and urinary tract. Patients were classified by variant type into predicted loss of function (pLoF) and non-pLoF variant groups, and by variant location into paired domain and other sites group. pLoF variants were predominantly associated with RCS, observed in 82% of patients in both our data (18 of 22, P = 0.017) and the literature (140 of 171, P < 0.001). Kidney failure developed in 52% of Korean patients at a median age of 14.5 years, with no difference in kidney survival between variant types. However, the literature review indicated faster progression to kidney failure in patients with pLoF variants (11.0 vs. 24.0 years; pLoF, n = 138 vs. non-pLoF, n = 71; P = 0.002), with no significant difference by variant location. Ocular manifestations were more common, had earlier onset, and were more severe in the pLoF variants group in our cohort (P = 0.038). The literature confirmed a higher prevalence of ocular involvement in patients with pLoF variants (pLoF, n = 175 vs. non-pLoF, n = 88; P < 0.001) and in those with paired domain variants (P = 0.01). pLoF variants in PAX2 were associated with worse kidney and ocular outcomes. These findings support genotype-phenotype correlations, contributing to tailored management in patients with PAX2-related disorders.

Paired box 2 (PAX2)-related disorder, also known as renal coloboma syndrome, is a variably penetrant autosomal dominant condition, associated with renal and ophthalmological abnormalities. We report a child with PAX2-related disorder who presented atypically with acute ataxia on a background of stage 3 chronic kidney disease. Extensive biochemical, radiological and gene agnostic rapid trio exome sequencing was non-diagnostic. Identification of bilateral optic disc colobomas in the proband and his father raised the suspicion of an inherited PAX2-related disorder. No causative variants were identified on a focused review of the filtered genomic data. Given the strong suspicion of an inherited monogenic disorder, whole genome trio sequencing was requested. Analysis assuming incomplete penetrance identified a paternally inherited PAX2 microdeletion encompassing exon 4. This case adds to evidence of a broader PAX2-associated phenotype. It highlights the importance of a clinical genetics and mainstream interface when navigating and interpreting genetic testing.