# WFS1 Wolframin — L804P Variant Card

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

*Leucine → Proline at position 804 in wolframin's C-terminal lumenal domain. ClinVar Likely pathogenic, associated with DFNA6 (WFS1-related hearing loss). AlphaMissense 0.999 (deep pathogenic signal), DynaMut2 ΔΔG -0.44 kcal/mol (destabilising). A fold-intact variant with severe local backbone disruption.*

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## Identity

| Field | Value |
|---|---|
| **Variant** | L804P (p.Leucine804Proline) |
| **DNA change** | c.2411T>C |
| **Gene · Protein** | WFS1 · Wolframin (890 aa) |
| **UniProt** | O76024 · WFS1_HUMAN |
| **ClinVar accession** | VCV000430096 |
| **Amino acid change** | Leucine (L) → Proline (P) — a flexible, medium-sized hydrophobic side chain replaced by a rigid, ring-locked amino acid that kinks the polypeptide backbone wherever it appears. |

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## Structural Context

| Field | Value |
|---|---|
| **AlphaFold model** | AF-O76024-F1, v6 |
| **pLDDT at residue 804** | **91.94** — well-folded |
| **Domain** | C-terminal lumenal domain (653-869) |
| **Position context** | C-terminal lumenal domain · position 804 sits inside the ER lumen at the heart of wolframin's largest soluble region, in a high-confidence local environment (pLDDT 92). |
| **IDR flag** | No — pLDDT above 50 threshold |

**UniProt features at this position:**

  - Chain: 1-890 Wolframin
  - Topological domain: 653-869 Lumenal

> Position 804 sits deep in wolframin's C-terminal lumenal domain (residues 653–869), the protein's largest soluble region and the documented interaction interface with ATF6 and the Na+/K+ ATPase β1 subunit. The AlphaFold model places L804 against immediate sequence neighbors ARG805 (2.4 Å) and VAL803 (2.5 Å), and into a hydrophobic pocket containing PHE840 (3.3 Å) and ILE777 (3.8 Å). The leucine side chain contributes branched hydrophobic packing into that pocket, supporting the local fold geometry of two distant segments of the lumenal domain.

Replacing leucine with proline at this position has a structural cost that DynaMut2's |ΔΔG| of 0.44 understates. Proline is the only amino acid whose backbone is locked into a ring — its phi angle is constrained, it cannot serve as a hydrogen-bond donor in the backbone, and it forces a kink at the position it occupies. When proline is introduced into a region with defined secondary structure, the local geometry has to rearrange to accommodate it, and the disruption propagates a few residues in either direction along the chain.

The ΔΔG value reflects the energetic cost of the global fold absorbing this disruption — modest, because the lumenal domain has flexibility to spare. But the local geometric perturbation around residues 803–805 will be substantial, and the lost packing against PHE840 and ILE777 is unrecoverable without further fold rearrangement. AlphaMissense's 0.999 score reflects this: the model recognizes the deep pathogenic signal of an introduced proline even when global stability is only modestly perturbed.

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## Computational Predictions

### AlphaMissense
| Field | Value |
|---|---|
| am_pathogenicity | **0.9989** |
| am_class | **LPath** |
| Interpretation | Likely pathogenic (threshold 0.564) |

### DynaMut2
| Field | Value |
|---|---|
| ΔΔG (kcal/mol) | **-0.44 (Destabilising)** |
| Job ID | 177991412243 |
| Result URL | https://biosig.lab.uq.edu.au/dynamut2/results_prediction/177991412243 |

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## Clinical Evidence

| Field | Value |
|---|---|
| Classification | **Likely pathogenic** |
| Review status | criteria provided, multiple submitters, no conflicts |
| Last evaluated | 2016/02/18 00:00 |
| Inheritance | Autosomal dominant pattern indicated by association with DFNA6 (WFS1-related hearing loss 6). Likely contributes to the WFS1-related dominant spectrum rather than classical AR Wolfram syndrome 1. |
| WFS1 variant landscape | L804P is 1 of ~326 pathogenic-spectrum variants in WFS1 (out of 2,243 catalogued in ClinVar) |

- Autosomal dominant nonsyndromic hearing loss 6 (DFNA6)

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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| = 0.44 kcal/mol — well below the fold-integrity threshold. The wolframin fold survives the substitution, but local geometry around position 804 is severely disrupted by the introduced proline.<br/><br/>The therapeutic strategy here is unusual for the Atlas: the lesion is geometric, not interaction-based. A small molecule that stabilizes the local α-helical geometry around residues 803–805 could compensate for the backbone kink introduced by proline. Alternative: a chaperone that biases the fold toward the wild-type local geometry during synthesis would shift the population toward functional protein.<br/><br/>AlphaMissense's near-maximum score (0.999) confirms that the field's clinical observation of pathogenicity matches the structural prediction — this is a real lesion despite the small ΔΔG. The variant illustrates a category of pathogenicity the Atlas captures well: severe local geometric disruption with mild global energetic cost.

**Why this card matters.** L804P is one of several proline-introduction variants in the Atlas (L543P, L402P, P504L is the inverse). When proline appears or disappears from a position with defined secondary structure, the structural cost is qualitatively different from a typical amino acid swap. The Atlas's |ΔΔG| < 2 framing applies, but the therapeutic vector shifts subtly — chaperones that stabilize local geometry become as relevant as site-directed binders.

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## Files in this folder

- `AF-O76024-F1-model_v6.pdb` — AlphaFold structure
- `L804P_molstar_viewer.html` — interactive 3D viewer (auto-highlights position 804 with ball-and-stick + neighbors within 5Å)
- `L804P_variant_card.md` — this card (source of truth)
- `L804P_variant_card.html` — styled printable card
- `L804P_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)
- `L804P_wildtype_interactions.pse` / `L804P_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.*