# WFS1 Wolframin — P428R Variant Card

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

*Proline → Arginine at position 428 inside wolframin's fourth transmembrane helix (TM4). ClinVar Pathogenic. AlphaMissense 0.920, DynaMut2 ΔΔG -0.22 kcal/mol (destabilising). A proline-removal variant in a TM helix — opposite mechanism to L543P-type variants.*

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## Identity

| Field | Value |
|---|---|
| **Variant** | P428R (p.Proline428Arginine) |
| **DNA change** | c.1283C>G |
| **Gene · Protein** | WFS1 · Wolframin (890 aa) |
| **UniProt** | O76024 · WFS1_HUMAN |
| **ClinVar accession** | VCV002203517 |
| **Amino acid change** | Proline (P) → Arginine (R) — rigid helix-breaking residue replaced by a large positively-charged residue. Loss of backbone constraint plus introduction of charge into the bilayer. |

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## Structural Context

| Field | Value |
|---|---|
| **AlphaFold model** | AF-O76024-F1, v6 |
| **pLDDT at residue 428** | **89.00** — well-folded |
| **Domain** | TM4 (427-447), helical transmembrane |
| **Position context** | TM4 (residues 427–447) · position 428 is at the very start of TM4, in the membrane-water interface region (pLDDT 89). |
| **IDR flag** | No — pLDDT above 50 threshold |

**UniProt features at this position:**

  - Chain: 1-890 Wolframin
  - Transmembrane: 427-447 Helical

> Position 428 sits at the start of TM4. The AlphaFold model places P428 within 5 Å of ILE427 (2.5 Å), CYS429 (2.5 Å), SER430 (4.5 Å), and GLU431 (4.9 Å). The wild-type proline at 428 likely defines the helix-initiation geometry of TM4, providing a controlled bend or break at the start of the membrane-spanning segment.

Replacing proline with arginine has the same backbone-flexibility-gain as P504L (removed proline kink) but with a substantial added complication: a positive charge is introduced near the membrane-water interface. At position 428 — right at the start of TM4 — the arginine side chain can extend toward the lumenal interface where its charge is favorable, but the lost helix-initiation geometry remains a structural problem.

The |ΔΔG| of 0.22 indicates the fold absorbs the substitution. AlphaMissense's 0.920 score captures the functional consequence — TM4's insertion register shifts, the C429 immediately downstream (a possible disulfide-capable residue) is now in a different local geometry, and the E431 contact (4.9 Å) is perturbed.

Notably, the same E431 residue appears as a neighbor in the A559D atlas card — E431 sits between the connecting loop containing R558 and TM4 containing P428. The position is structurally connective in the lumenal-facing region.

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## Computational Predictions

### AlphaMissense
| Field | Value |
|---|---|
| am_pathogenicity | **0.9197** |
| am_class | **LPath** |
| Interpretation | Likely pathogenic (threshold 0.564) |

### DynaMut2
| Field | Value |
|---|---|
| ΔΔG (kcal/mol) | **-0.22 (Destabilising)** |
| Job ID | 177990265297 |
| Result URL | https://biosig.lab.uq.edu.au/dynamut2/results_prediction/177990265297 |

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## Clinical Evidence

| Field | Value |
|---|---|
| Classification | **Pathogenic** |
| Review status | criteria provided, single submitter |
| Last evaluated | 2024/02/23 00:00 |
| Inheritance | Inheritance not specified. ClinVar Pathogenic. |
| WFS1 variant landscape | P428R is 1 of ~326 pathogenic-spectrum variants in WFS1 (out of 2,243 catalogued in ClinVar) |

- (no specific conditions catalogued for P428R — ClinVar Pathogenic by review evidence)

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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**

<strong>Category 3/4 — Most Druggable.</strong> |ΔΔG| = 0.22 kcal/mol — fold survives. AlphaMissense 0.920 confirms severe functional consequence.<br/><br/>The mechanism combines loss of proline-defined helix-initiation geometry plus charge introduction at the membrane-water interface. Therapeutic strategy: site-directed small molecules at the TM4 N-terminal region.<br/><br/>The E431 contact suggests this position may be structurally connected to the R558-E431 microregion that A559D perturbs. Combined drug discovery in both regions has overlapping targets.

**Why this card matters.** P428R is the proline-removal complement to the L→P variants elsewhere in the Atlas. The Atlas's mechanism vocabulary handles both proline introduction (helix break created) and proline removal (helix break eliminated) as distinct but related target categories.

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## Files in this folder

- `AF-O76024-F1-model_v6.pdb` — AlphaFold structure
- `P428R_molstar_viewer.html` — interactive 3D viewer (auto-highlights position 428 with ball-and-stick + neighbors within 5Å)
- `P428R_variant_card.md` — this card (source of truth)
- `P428R_variant_card.html` — styled printable card
- `P428R_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)
- `P428R_wildtype_interactions.pse` / `P428R_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.*