Here we show that the Val602 variant of the non‐synonymous single nucleotide polymorphism (SNP) rs509749 in the SLAM family member CD229 (Ly9, SLAMF3) has a two‐fold lower affinity compared with the SLE‐associated Met602 variant for the small adaptor protein SAP. This evidence concerns the gene LY9 and systemic lupus erythematosus.