# WFS1 Wolframin — T641K Variant Card

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

*Threonine → Lysine at position 641 inside wolframin's tenth transmembrane helix (TM10). ClinVar carries conflicting classifications — pathogenicity is documented but not universally confirmed. AlphaMissense 0.980, DynaMut2 ΔΔG -0.08 kcal/mol (essentially no destabilization). A near-zero-ΔΔG pathogenic variant with a striking mechanism.*

---

## Identity

| Field | Value |
|---|---|
| **Variant** | T641K (p.Threonine641Lysine) |
| **DNA change** | c.1922C>A |
| **Gene · Protein** | WFS1 · Wolframin (890 aa) |
| **UniProt** | O76024 · WFS1_HUMAN |
| **ClinVar accession** | VCV000166599 |
| **Amino acid change** | Threonine (T) → Lysine (K) — a small polar residue with a hydroxyl group replaced by a large, positively charged residue with a flexible alkyl chain and a primary amine. The chemistry shift inside a transmembrane helix is unusually severe. |

---

## Structural Context

| Field | Value |
|---|---|
| **AlphaFold model** | AF-O76024-F1, v6 |
| **pLDDT at residue 641** | **86.56** — well-folded |
| **Domain** | TM10 (632-652), helical transmembrane |
| **Position context** | TM10 (residues 632–652) · position 641 is bilayer-embedded, inside a helical transmembrane segment of wolframin. The lipid environment penalizes charged side chains heavily. |
| **IDR flag** | No — pLDDT above 50 threshold |

**UniProt features at this position:**

  - Chain: 1-890 Wolframin
  - Transmembrane: 632-652 Helical

> Position 641 sits inside TM10, one of wolframin's eleven transmembrane helices anchoring the protein in the ER membrane. The AlphaFold model places T641 within 5 Å of immediate sequence neighbors LEU640 (2.5 Å) and ALA642 (2.5 Å), and into a hydrophobic cluster with LEU637 (3.8 Å), VAL638 (4.0 Å), PHE414 (4.1 Å, from TM3 — indicating helix-helix contact), and ILE643 (4.5 Å). The wild-type threonine's small polar character fits well in this membrane-embedded helix — its hydroxyl can participate in a localized hydrogen bond pattern within the helix backbone.

Replacing threonine with lysine in this position is striking. Lysine's positively-charged primary amine and its long alkyl chain are exceptionally costly in a transmembrane context: charge buried in the bilayer hydrophobic core is thermodynamically unfavorable, and the larger volume cannot be accommodated without local rearrangement. Yet DynaMut2 returns a |ΔΔG| of only 0.08 kcal/mol — essentially no destabilization.

The explanation is geometric. The lysine side chain, despite being large and charged, is flexible and can extend outward toward the membrane-water interface where the charge can be partially satisfied by interaction with lipid headgroups or water. The fold can absorb the substitution. But — and this is the mechanistic insight — the functional integrity of TM10 depends on its packing against TM3 (the PHE414 contact at 4.1 Å). Introducing a charge into that interface, even if the fold accommodates it, disrupts the helix-helix geometry that the wild-type relied on. The result is a variant the protein can fold but cannot function correctly.

AlphaMissense's score of 0.980 reflects this functional severity even though the structural cost is near-zero. The variant is pathogenic by mechanism, not by misfolding.

---

## Computational Predictions

### AlphaMissense
| Field | Value |
|---|---|
| am_pathogenicity | **0.9803** |
| am_class | **LPath** |
| Interpretation | Likely pathogenic (threshold 0.564) |

### DynaMut2
| Field | Value |
|---|---|
| ΔΔG (kcal/mol) | **-0.08 (Destabilising)** |
| Job ID | 177992299153 |
| Result URL | https://biosig.lab.uq.edu.au/dynamut2/results_prediction/177992299153 |

---

## Clinical Evidence

| Field | Value |
|---|---|
| Classification | **Conflicting classifications of pathogenicity** |
| Review status | criteria provided, conflicting classifications |
| Last evaluated | 2025/02/27 00:00 |
| Inheritance | Documented in association with both Wolfram syndrome 1 (AR) and Wolfram-like syndrome (AD). ClinVar's conflicting classifications reflect that the variant's functional consequences depend on context — homozygous, compound heterozygous, or heterozygous with different penetrance. |
| WFS1 variant landscape | T641K is 1 of ~326 pathogenic-spectrum variants in WFS1 (out of 2,243 catalogued in ClinVar) |

- Wolfram syndrome 1
- Wolfram-like syndrome

---

## 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 4 — Stable Fold, Function Disrupted.</strong> |ΔΔG| = 0.08 kcal/mol — the fold is essentially unperturbed. But the variant is pathogenic by AlphaMissense and clinical evidence, which means the mechanism is functional disruption rather than fold instability.<br/><br/>The most likely mechanism is disrupted TM3-TM10 helix-helix packing: the introduced charge at the helix-helix interface (4.1 Å from PHE414 in TM3) is unfavorable in the bilayer hydrophobic core and would perturb the relative geometry of the two helices. The therapeutic strategy is site-specific: a small molecule that stabilizes the TM3-TM10 packing interface, occupying the geometric niche the wild-type threonine maintained.<br/><br/>This is a variant the Atlas captures particularly well — pre-atlas, the near-zero ΔΔG might have led screeners to deprioritize this position. The atlas tells you which interface to target.

**Why this card matters.** T641K illustrates why fold stability alone is not sufficient to identify therapeutic targets. The protein folds, the variant is pathogenic, and the mechanism is helix-helix interface disruption. Drug discovery here aims at the TM3-TM10 interface, not at the TM10 helix itself. The Atlas's neighbor analysis — surfacing the PHE414 contact across helices — is what makes that target visible.

---

## Files in this folder

- `AF-O76024-F1-model_v6.pdb` — AlphaFold structure
- `T641K_molstar_viewer.html` — interactive 3D viewer (auto-highlights position 641 with ball-and-stick + neighbors within 5Å)
- `T641K_variant_card.md` — this card (source of truth)
- `T641K_variant_card.html` — styled printable card
- `T641K_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)
- `T641K_wildtype_interactions.pse` / `T641K_mutant_interactions.pse` — PyMOL sessions

---

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