# WFS1 Wolframin — Y669C Variant Card

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

*Tyrosine → Cysteine at position 669 in wolframin's C-terminal lumenal domain. ClinVar Likely pathogenic, associated with classical autosomal recessive Wolfram syndrome 1. AlphaMissense 0.998, DynaMut2 ΔΔG -0.41 kcal/mol (destabilising). One of the six pilot variants in the Atlas.*

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## Identity

| Field | Value |
|---|---|
| **Variant** | Y669C (p.Tyrosine669Cysteine) |
| **DNA change** | c.2006A>G |
| **Gene · Protein** | WFS1 · Wolframin (890 aa) |
| **UniProt** | O76024 · WFS1_HUMAN |
| **ClinVar accession** | VCV002576526 |
| **Amino acid change** | Tyrosine (Y) → Cysteine (C) — a large aromatic ring carrying a hydroxyl group replaced by a small thiol-bearing residue. Loss of aromatic packing and H-bond capacity; introduction of a reactive free thiol into the oxidizing ER lumen. |

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## Structural Context

| Field | Value |
|---|---|
| **AlphaFold model** | AF-O76024-F1, v6 |
| **pLDDT at residue 669** | **87.75** — well-folded |
| **Domain** | C-terminal lumenal domain (653-869) |
| **Position context** | C-terminal lumenal domain · position 669 sits in the ER lumen in a well-folded region (pLDDT 88). The oxidizing lumenal environment is structurally relevant: any newly-introduced cysteine here can participate in aberrant disulfide chemistry. |
| **IDR flag** | No — pLDDT above 50 threshold |

**UniProt features at this position:**

  - Chain: 1-890 Wolframin
  - Topological domain: 653-869 Lumenal
  - Natural variant: 669-669 in WFS1; dbSNP:rs1402999203
  - Natural variant: 669-669 in DFNA6

> Position 669 sits in wolframin's C-terminal lumenal domain (residues 653–869). The AlphaFold model places Y669 within 5 Å of GLN668 (2.5 Å), GLY670 (2.5 Å), TRP666 (3.8 Å), THR665 (4.0 Å), ALA671 (4.4 Å), and GLN667 (4.5 Å). The wild-type tyrosine ring sits in an aromatic-adjacent environment — TRP666 at 3.8 Å is consistent with edge-face π–π stacking between the Y669 phenol and the W666 indole. The hydroxyl group of the wild-type also makes plausible hydrogen-bonding contacts to GLN668 and THR665.

Replacing tyrosine with cysteine at this position has three layered effects. First, the aromatic ring is gone, eliminating the π-stacking with TRP666 and the hydrophobic surface contributed to the local fold. Second, the hydroxyl group is gone, removing two hydrogen-bond contacts. Third, a reactive free thiol is introduced into the oxidizing ER lumen — and the lumenal domain contains other cysteine residues (notably CYS673 at 3.8 Å from C690, a separate position) that could engage in aberrant disulfide formation. The new C669 is not directly in contact with another cysteine in the AlphaFold model, but disulfide chemistry in an oxidizing compartment is promiscuous.

DynaMut2 returns a modest |ΔΔG| of 0.41 kcal/mol. The fold survives the substitution. The damage is mechanistic — lost aromatic packing, lost H-bonding, plus the off-pathway disulfide risk that DynaMut2's structural prediction cannot fully capture.

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## Computational Predictions

### AlphaMissense
| Field | Value |
|---|---|
| am_pathogenicity | **0.9977** |
| am_class | **LPath** |
| Interpretation | Likely pathogenic (threshold 0.564) |

### DynaMut2
| Field | Value |
|---|---|
| ΔΔG (kcal/mol) | **-0.41 (Destabilising)** |
| Job ID | 177986259282 |
| Result URL | https://biosig.lab.uq.edu.au/dynamut2/results_prediction/177986259282 |

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## Clinical Evidence

| Field | Value |
|---|---|
| Classification | **Likely pathogenic** |
| Review status | criteria provided, single submitter |
| Last evaluated | 2023/08/15 00:00 |
| Inheritance | Autosomal recessive Wolfram syndrome 1 phenotype documented in ClinVar. |
| WFS1 variant landscape | Y669C 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**

<strong>Category 3/4 — Most Druggable.</strong> |ΔΔG| = 0.41 kcal/mol — fold intact. AlphaMissense 0.998 confirms severe functional consequence despite the modest structural cost.<br/><br/>The mechanism is layered: aromatic stacking with TRP666 broken, hydrogen bonding to GLN668/THR665 lost, and a new free thiol introduced into a compartment where it can form aberrant disulfides. Site-directed small molecules that occupy the lost aromatic packing footprint and/or block the introduced thiol are the rational therapeutic vector.<br/><br/>Compare with Y669H at the same position (Atlas card adjacent): Y669H preserves more of the aromatic character but introduces titratable basicity, and shows a stronger ΔΔG of -1.2 kcal/mol. The two variants together illustrate how substitution chemistry at a single position drives different mechanism and severity.

**Why this card matters.** Y669C is one of the six pilot variants the Atlas was built around (R558C, A716T, G695V, L543R, A48V, Y669C). It exemplifies the lumenal domain's vulnerability to substitutions that disrupt aromatic-aromatic π-stacking — a structural feature wolframin's lumenal fold appears to depend on heavily. Drug discovery aimed at this position should target the W666 aromatic environment as the rescue surface.

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## Files in this folder

- `AF-O76024-F1-model_v6.pdb` — AlphaFold structure
- `Y669C_molstar_viewer.html` — interactive 3D viewer (auto-highlights position 669 with ball-and-stick + neighbors within 5Å)
- `Y669C_variant_card.md` — this card (source of truth)
- `Y669C_variant_card.html` — styled printable card
- `Y669C_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)
- `Y669C_wildtype_interactions.pse` / `Y669C_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.*