Clinical characteristics of patients with SALL1-related disorder

Abstract Background The Spalt-like transcription factor 1 (SALL1) gene is essential for kidney development. Pathogenic SALL1 variants cause Townes-Brocks syndrome 1 (TBS1), which typically presents with imperforate anus, dysplastic ears, and digital anomalies. However, clinical features vary widely. Some patients present only with dysplastic ears and hearing loss (HL) or with congenital anomalies of the kidney and urinary tract (CAKUT), resembling branchio-oto-renal syndrome (BORS), a presentation referred to as Townes-Brocks branchio-oto-renal-like (TBS BOR-like) syndrome. In this study, we aimed to describe the clinical characteristics of patients with SALL1-related disorders in the Japanese population. Methods We analyzed phenotypes of a nationwide cohort comprising 1108 families with chronic kidney disease (CKD) or mild urinary anomalies, using genetic testing conducted from 2010 to 2024. Results We identified SALL1 variants in 14 families (20 individuals): seven frameshift, four nonsense, one missense, one exon 2 deletion, and one whole-gene deletion. Ten variants were novel. The median age at diagnosis was 16 years (male:female = 13:7). Dysplastic ears were observed in 45%, HL in 40%, digital anomalies in 40%, and anorectal malformations in 25%. Based on clinical features, eight individuals were diagnosed with TBS1, four with TBS BOR-like syndrome, and seven with non-syndromic CAKUT. One case lacked detailed clinical data. Most variants were truncating and located in exon 2. Conclusions SALL1-related disorders exhibit broad phenotypic variability. Some cases present with atypical features overlapping with TBS BOR-like syndrome or isolated CAKUT, rather than with typical TBS1. These findings enhance the understanding and diagnosis of SALL1-related disorders.  Graphical abstract