BackgroundJuvenile Polyposis Syndrome (JPS) is an autosomal dominant condition with hamartomatous polyps in the gastrointestinal tract, associated with an increased risk of gastrointestinal malignancy. Disease causing variants (DCVs) inBMPR1aorSMAD4account for 45–60% of JPS cases, withBMPR1aDCVs accounting for 17–38% of JPS cases. Within those with either aBMPR1aorSMAD4DCV, there is phenotypic variability in location of polyps, risk of malignancy and extra-intestinal manifestations with limited published reports of gene-phenotype association or genotype–phenotype correlation.We aimed to identify any gene-phenotype association or genotype–phenotype correlation inBMPR1ato inform surveillance recommendations, and gene-specific modification to the ACMG classification of pathogenicity of DCVs.MethodsA literature search was performed through EMBASE, MEDLINE and PubMed. Studies that were included exploredBMPR1aDCV-related JPS or contiguous deletion ofPTENandBMPR1a. Data was also drawn from theBMPR1aspecific databases on LOVD and ClinVar.ResultsThere were 211 DCVs inBMPR1aidentified, 82 from patients with JPS in the literature, and 17 from LOVD and 112 from ClinVar classified as pathogenic or likely pathogenic. These included missense, nonsense and frameshift variants and large deletions, occurring across all functional domains of the gene.Unlike inSMAD4carriers, gastric polyposis and malignancy were not identified in our review inBMPR1acarriers, but colonic polyposis and malignancy occurred in carriers of eitherBMPR1aorSMAD4DCVs. Those with contiguous deletion ofPTENandBMPR1acan present with JPS of infancy, with a severe phenotype of GI bleeding, diarrhoea, exudative enteropathy and rectal prolapse.No specificBMPR1agenotype–phenotype correlation could be ascertained including by variant type or functional domain.ConclusionPhenotypic characteristics cannot be used to inform variant location inBMPR1a. However, the phenotypic characteristics ofBMPR1aDCV carriers, being almost exclusively related to the colon and rectum, can assist in pathogenicity assessment ofBMPR1avariants.Given these findings, we propose that carriers ofBMPR1aDCVs should only require surveillance for colorectal polyps and malignancy, and that surveillance for gastric polyps and malignancy may be unnecessary. However variant location withinBMPR1adoes not support differential surveillance recommendations.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13053-023-00255-3.