The medical literature does not currently report a case of co-occurring congenital thumb aplasia, radioulnar synostosis (RUS), and Chiari malformation with scoliosis. Furthermore, there is an overlap of clinical features with other documented syndromes and associations that have potential cardiac, gastrointestinal, hematologic, and nephrological implications, thus contributing to increased morbidity and mortality if left undetected. We describe an interesting case of congenital thumb aplasia, RUS, and Chiari malformation with scoliosis in the absence of non-musculoskeletal abnormalities. These findings prompted further investigation to determine whether this is a unique presentation of a previously described syndrome, due to teratogenic exposure in utero, or a syndromic association yet to be adequately identified by the scientific community. We also identified several candidate genes that may guide genetic testing in the future.