# WFS1 Wolframin — R558H Variant Card

**Molecular Atlas Pilot · RareResearch.AI · Generated by wolfram-variant-card skill**

*Same residue as the Atlas's R558C pilot variant, different substitution — arginine retained as histidine, a partial charge swap that preserves the side chain's polar character but loses ~80% of the wild-type positive charge at physiological pH.*

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## Identity

| Field | Value |
|---|---|
| **Variant** | R558H (p.Arginine558Histidine) |
| **DNA change** | c.1673G>A |
| **Gene · Protein** | WFS1 · Wolframin (890 aa) |
| **UniProt** | O76024 · WFS1_HUMAN |
| **ClinVar accession** | VCV000427051 |
| **Amino acid change** | Arginine (large, positively charged, fully ionized guanidinium at physiological pH, pKa ~12.5) to Histidine (smaller, imidazole side chain with pKa ~6.0 — mostly neutral at physiological pH, partially positive in acidic compartments) at position 558. |

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## Structural Context

| Field | Value |
|---|---|
| **AlphaFold model** | AF-O76024-F1, v6 |
| **pLDDT at residue 558** | **84.56** — well-folded |
| **Domain** | Connecting loop |
| **Position context** | Position 558 sits in a cytoplasmic connecting loop between TM7 (residues 529-549) and TM8 (residues 563-583) — the same residue position as the Atlas's R558C pilot variant. pLDDT 84.56 (identical to R558C since they share the wild-type AlphaFold structure) confirms the position is well-modeled and not in an IDR. |
| **IDR flag** | No — pLDDT above 50 threshold |

**UniProt features at this position:**

  - Chain: 1-890 Wolframin
  - Natural variant: 558-558 in WFS1; dbSNP:rs199946797

> 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.

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## Computational Predictions

### AlphaMissense
| Field | Value |
|---|---|
| am_pathogenicity | **0.7602** |
| am_class | **LPath** |
| Interpretation | Likely pathogenic (threshold 0.564) |

### DynaMut2
| Field | Value |
|---|---|
| ΔΔG (kcal/mol) | **-1.31 (Destabilising)** |
| Job ID | 177991407167 |
| Result URL | https://biosig.lab.uq.edu.au/dynamut2/results_prediction/177991407167 |

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## Clinical Evidence

| Field | Value |
|---|---|
| Classification | **Pathogenic/Likely pathogenic** |
| Review status | criteria provided, multiple submitters, no conflicts |
| Last evaluated | 2025/11/23 00:00 |
| Inheritance | Both autosomal dominant and autosomal recessive forms documented. |
| WFS1 variant landscape | R558H is 1 of ~326 pathogenic-spectrum variants in WFS1 (out of 2,243 catalogued in ClinVar) |

- Wolfram syndrome 1
- Wolfram-like syndrome
- WFS1-related disorder
- Autosomal dominant nonsyndromic hearing loss 6
- Optic atrophy
- Cataract 41
- Type 2 diabetes mellitus
- Inborn genetic diseases

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## Research Path Decision Tree

```
ΔΔG < 2  + binding site affected   →  CATEGORY 3 — docking experiments
ΔΔG 2–4                            →  CATEGORY 2 — pharmacological chaperones
ΔΔG > 4                            →  CATEGORY 1 — gene therapy
pLDDT < 50                         →  CATEGORY 5 — IDR, experimental only
Stable fold + functional site hit  →  CATEGORY 4 — site-specific docking
```

## Final Schema Categorization

**Category 3/4 — Most Druggable**

Final classification: Category 3 — Most Druggable. The convergent evidence: pLDDT 84.56 (ordered, modelable), DeltaDeltaG magnitude 1.31 kcal/mol (mild-moderate, fold-intact), AlphaMissense 0.760 (pathogenic), and direct structural parallel to the R558C pilot. The therapeutic target is the same cytoplasmic anchor between TM7 and TM8.

A pharmacological chaperone designed against R558C should be directly tested against R558H — the two variants share the same loss-of-anchor mechanism, and any small molecule that restores the wild-type cytoplasmic loop geometry should rescue both. R558H is therefore a high-priority companion variant in any R558C-directed screening program. The shared chemistry argument is the kind of cross-variant leverage the Atlas exists to surface.

**Why this card matters.** R558H is the second variant in the Atlas at position 558 — the same locus that produces the Ashkenazi-Jewish founder mutation R558C. Both variants disrupt the same TM7-TM8 cytoplasmic anchor. This is exactly the cross-residue-substitution insight the Atlas was built to expose: position 558 is mechanistically a single therapeutic target, and a chaperone screen designed against the wild-type R558 geometry should produce hits useful for both R558C and R558H carriers.

The broader Atlas strategy implication is that variant clusters at the same residue position deserve unified druggability assessment. Position 558 is the first clear example. Similar logic should apply to other multi-substitution residues (e.g., G674 with at least four substitutions in the Atlas) — these are not three separate problems, they are one site with three failure modes.

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## Files in this folder

- `AF-O76024-F1-model_v6.pdb` — AlphaFold structure
- `R558H_molstar_viewer.html` — interactive 3D viewer (auto-highlights position 558 with ball-and-stick + neighbors within 5Å)
- `R558H_variant_card.md` — this card (source of truth)
- `R558H_variant_card.html` — styled printable card
- `R558H_dynamut2_summary.html` — clean offline DynaMut2 result card
- `dynamut2_result.json` — structured result data
- `dynamut2_result_page.html` — local snapshot of the Biosig result page (asset URLs absolutized)
- `R558H_wildtype_interactions.pse` / `R558H_mutant_interactions.pse` — PyMOL sessions

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*Generated by wolfram-variant-card skill · RareResearch.AI Molecular Atlas*
*Every assumption documented. Every score sourced.*