M518I

Position 518 sits in a connecting loop. The AlphaFold model places M518 within 5 Å of ALA519 (2.5 Å), ARG517 (2.5 Å), PHE515 (3.7 Å), LEU514 (3.8 Å), LEU521 (3.9 Å), and GLN520 (4.4 Å). The wild-type methionine's flexible sulfur-containing side chain fits into the surrounding hydrophobic environment (LEU514, LEU521, PHE515) with comparable steric volume to an isoleucine.

Replacing methionine with isoleucine is among the most conservative substitutions chemically — both residues are medium-sized hydrophobic, and isoleucine's branched aliphatic side chain occupies similar volume to methionine's straight-chain thioether. The DynaMut2 |ΔΔG| of 0.29 kcal/mol reflects this conservatism: the fold barely notices the swap.

And yet AlphaMissense calls this pathogenic at 0.966. The mechanism is functional, not structural. Three plausible reasons: first, methionine sulfur can participate in specific protein chemistry that isoleucine cannot — oxidative regulation (Met can be oxidized to Met-sulfoxide as a redox switch), metal coordination, or specific S-mediated interactions; second, methionine residues in certain positions serve as translation initiation alternates or have post-translational modification roles that isoleucine cannot replace; third, the loop's role as a recognition surface depends on the precise methionine geometry, and isoleucine's branched structure presents a different surface even at comparable hydrophobic volume.

The conflicting ClinVar classifications make sense given this profile. Conservative substitutions whose pathogenicity depends on context-specific mechanisms get classified differently by different submitters with different evidence bases.