NM_000330.4(RS1):c.177T>G (p.Cys59Trp) is a missense variant encoding the substitution of cysteine with tryptophan at amino acid 59, which is a critical amino acid residue involved in disulfide bridge formation as defined by the ClinGen X-linked IRD VCEP (PMID: 26812435, PM1_Strong). Another missense variant in the same codon, NM_000330.4(RS1):c.175T>A (p.Cys59Ser), (PMIDs: 31174210, 10450864, 17987333, 9618178) has been classified as pathogenic for X-linked retinoschisis by the ClinGen X-linked IRD VCEP, while no benign missense variants have been identified in this codon. The present variant has a higher Grantham’s distance (215) than the comparison variant (112), and SpliceAI has been used to confirm that neither variant has a predicted impact on RS1 splicing (PM5). This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.724, which is within the ClinGen X-linked IRD VCEP range of 0.772 to 0.644 and predicts a damaging effect on RS1 function. The PM1_strong code is ineligible to be used in combination with the PP3 code, and therefore, this code was not met. The computational splicing predictor SpliceAI gives a delta score of 0.00 for all predictive splice changes, which is below the ClinGen X-linked IRD VCEP threshold of >0.2 and does not predict that the variant disrupts RS1 splicing. In summary, this variant is classified as likely pathogenic for X-linked retinoschisis based on the ClinGen X-linked Inherited Retinal Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RS1 Version 1.0.0: PM2_Supporting, PM1_Strong, and PM5.