The consequence of variants in SNRNP200, implicated in dominant retinitis pigmentosa (RP), remain unknown. SNRNP200 encodes for a component of the spliceosome complex. To investigate the effect of SNRNP200 variants, we generated human retinal organoids (ROs) from a patient with severe early-onset RP found to harbour compound heterozygous missense variants in SNRNP200; an unusual case of autosomal recessive inheritance. Computer-assisted pathogenicity programs and other tools were used to predict the pathogenicity of candidate variants. Control and patient-derived induced pluripotent stem cells (iPSCs) were differentiated into ROs for 350 days. Immunohistochemical, qRT-PCR, and transmission electron microscopic analysis was performed. iPSCs and ROs were also subjected to single cell RNA-Seq and bioinformatic analysis. Several morphological differences in patient ROs were identified including (1) reduced neuroepithelial integrity, (2) vacuole accumulation within photoreceptors, and (3) abnormal mitochondrial morphology. Transcriptomic analysis revealed multiple genes associated with immunologic signatures, and genes associated with cell coenzyme biosynthesis, were significantly differentially expressed. By generating a human RO-based model of RP we have identified patient-specific differences in gene, protein and transcriptomic expression, neuroepithelial integrity, photoreceptor morphology and ultrastructure. These data show the potential of using ROs to assess functional consequences in patients affected by variants of unknown significance.