R558H

R558 sits at the cytoplasmic edge of the membrane interface, 5 residues before the start of TM8. The structural neighbors here are: Ala559 (2.45 Angstrom), Leu557 (2.47 Angstrom), Gly555 (3.63 Angstrom), Leu554 (3.82 Angstrom), Leu556 (4.50 Angstrom), Ser560 (4.61 Angstrom), Ile561 (4.81 Angstrom), and Gly562 (4.90 Angstrom). The cluster is dominated by hydrophobic residues — three leucines, one alanine, one isoleucine, two glycines — and a single polar serine. The wild-type arginine's guanidinium therefore projects outward into solvent or toward an anionic phospholipid headgroup, while its long aliphatic stem packs against the surrounding leucine/alanine cluster.

Replacing arginine with histidine removes the full positive charge but retains a polar imidazole. At cytoplasmic pH (~7.2), histidine is predominantly neutral (~10% protonated). The electrostatic anchor to anionic lipid headgroups is lost. The long aliphatic stem of arginine, which contributes hydrophobic packing against the surrounding leucines, is also lost — histidine's side chain is much shorter (~4 Angstrom vs ~6 Angstrom). The combined effect is geometric: histidine cannot reach the same packing partners as arginine, and the local cluster loses both an electrostatic and a hydrophobic contribution.

DynaMut2's DeltaDeltaG of -1.31 kcal/mol is a clean read of this combined loss — somewhat larger than R558C's -0.5 kcal/mol, consistent with histidine being a more conservative substitution chemically but geometrically more disruptive because of the side-chain length mismatch. AlphaMissense scores R558H at 0.760 (LPath) — pathogenic but notably lower than R558C's 0.849, reflecting the imidazole's partial retention of polar character.

Cross-reference to the R558C pilot card: both variants disrupt the same anchor at the TM7-TM8 cytoplasmic loop. R558C loses the positive charge and adds a free thiol with potential disulfide-formation risk. R558H loses ~90% of the positive charge but adds no covalent-modification liability. The two variants therefore share most of their molecular phenotype but diverge in one respect — R558C carries an additional oxidative-stress vulnerability that R558H does not. Clinically, the consequence is that R558H may present with somewhat milder disease, though both are classified Pathogenic/Likely pathogenic.