# WFS1 Wolframin — P724S Variant Card

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

*Proline-to-serine substitution removes a backbone-locking residue from a tight lumenal stretch, releasing torsional constraint where the protein evolved to keep it.*

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## Identity

| Field | Value |
|---|---|
| **Variant** | P724S (p.Proline724Serine) |
| **DNA change** | c.2170C>T |
| **Gene · Protein** | WFS1 · Wolframin (890 aa) |
| **UniProt** | O76024 · WFS1_HUMAN |
| **ClinVar accession** | VCV000379865 |
| **Amino acid change** | Proline (cyclic, locks backbone phi near -60 degrees, no amide NH for hydrogen-bonding) to Serine (small polar, hydroxyl side chain, full backbone phi/psi flexibility, amide NH is now available as a hydrogen-bond donor) at position 724. |

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## Structural Context

| Field | Value |
|---|---|
| **AlphaFold model** | AF-O76024-F1, v6 |
| **pLDDT at residue 724** | **89.25** — well-folded |
| **Domain** | C-terminal lumenal domain (653-869) |
| **Position context** | Position 724 sits inside the C-terminal lumenal domain (residues 653-869), the large soluble ATF6-interacting module facing the ER lumen. pLDDT 89.25 places P724 in an ordered, well-modeled region. |
| **IDR flag** | No — pLDDT above 50 threshold |

**UniProt features at this position:**

  - Chain: 1-890 Wolframin
  - Topological domain: 653-869 Lumenal
  - Natural variant: 724-724 in WFS1; dbSNP:rs28937890

> P724 is tightly packed between Leu723 (2.46 Angstrom) and Phe725 (2.47 Angstrom), with downstream contacts to Phe726 (4.55 Angstrom) and Ile727 (4.99 Angstrom). The Leu-Pro-Phe sequence is structurally striking: a proline sandwiched between a hydrophobic aliphatic and an aromatic. This is a classical kink site — proline introduces a sharp backbone turn that allows the lumenal domain to redirect chain trajectory between two hydrophobic packing elements. The phenylalanine pair (Phe725, Phe726) one and two residues downstream likely participates in aromatic stacking that requires the proline-induced backbone orientation to maintain register.

Replacing P724 with serine eliminates the geometric constraint. Serine's backbone freedom allows the chain to relax out of the proline-enforced phi angle and into a more standard conformation. The structural consequence: the Phe725-Phe726 aromatic pair likely loses its packing register, and the entire local turn opens up. The newly available amide NH on serine may also form an unintended hydrogen bond with one of the nearby carbonyls, further pulling the backbone away from the wild-type trajectory.

DynaMut2's DeltaDeltaG of -0.81 kcal/mol is consistent with a mild but real destabilization — the protein survives but the turn geometry is degraded. AlphaMissense at 0.889 reads this as clearly pathogenic; the position is evolutionarily constrained for the precise reason the energy function partially captures: only proline holds this turn.

ClinVar documents P724S in Wolfram syndrome 1, with multiple-submitter no-conflict review. The phenotype is consistent with a lumenal-domain misfolding event that interferes with the ATF6-UPR axis.

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## Computational Predictions

### AlphaMissense
| Field | Value |
|---|---|
| am_pathogenicity | **0.8886** |
| am_class | **LPath** |
| Interpretation | Likely pathogenic (threshold 0.564) |

### DynaMut2
| Field | Value |
|---|---|
| ΔΔG (kcal/mol) | **-0.81 (Destabilising)** |
| Job ID | 177991405609 |
| Result URL | https://biosig.lab.uq.edu.au/dynamut2/results_prediction/177991405609 |

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## Clinical Evidence

| Field | Value |
|---|---|
| Classification | **Pathogenic/Likely pathogenic** |
| Review status | criteria provided, multiple submitters, no conflicts |
| Last evaluated | 2026/01/26 00:00 |
| Inheritance | Autosomal recessive (Wolfram syndrome 1). |
| WFS1 variant landscape | P724S is 1 of ~326 pathogenic-spectrum variants in WFS1 (out of 2,243 catalogued in ClinVar) |

- Wolfram syndrome 1

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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 combination — pLDDT 89.25 (ordered), DeltaDeltaG 0.81 kcal/mol (mild), AlphaMissense 0.889 (functionally constrained), lumenal location — places P724S squarely inside the pharmacological-chaperone window. The lesion is the loss of a single backbone constraint; a small molecule that recovers the wild-type turn geometry, either by hydrogen-bonding to the new serine hydroxyl in a way that mimics the proline kink or by stabilizing the Phe725-Phe726 stack independently, should rescue the phenotype.

For docking experiments, the Phe725-Phe726 stack is the obvious anchor: two aromatic rings within 4.5-5 Angstrom of P724 provide a built-in pharmacophore. Compounds that engage that stack and impose backbone constraint at residue 724 are the design target. P724S joins the lumenal-domain Category 3 cluster as a likely chaperone-rescuable variant.

**Why this card matters.** Proline-loss mutations are a recurring class in the Atlas — distinct from glycine-loss mutations in that the protein loses backbone restraint rather than backbone freedom, but mechanistically similar in being purely geometric. The Atlas should cross-reference all proline-substitution variants in the lumenal domain (P724S, P504L, P292S, etc.) because the same chaperone chemistry may rescue them.

Clinically, P724S contributes to the Wolfram syndrome 1 incidence in the documented carrier populations. Its membership in the lumenal-domain Category 3 cluster makes it a useful representative case: if a single chaperone screen produces hits against R558C, P724S, and one other lumenal Category 3 variant, the molecule warrants broader development.

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## Files in this folder

- `AF-O76024-F1-model_v6.pdb` — AlphaFold structure
- `P724S_molstar_viewer.html` — interactive 3D viewer (auto-highlights position 724 with ball-and-stick + neighbors within 5Å)
- `P724S_variant_card.md` — this card (source of truth)
- `P724S_variant_card.html` — styled printable card
- `P724S_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)
- `P724S_wildtype_interactions.pse` / `P724S_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.*