# WFS1 Wolframin — A433P Variant Card **Molecular Atlas Pilot · RareResearch.AI · Generated by wolfram-variant-card skill** *Alanine-to-proline mutation inside transmembrane helix TM4 — a classical helix-breaking substitution that introduces a backbone kink into a structural element that must remain alpha-helical to function as a membrane anchor.* --- ## Identity | Field | Value | |---|---| | **Variant** | A433P (p.Alanine433Proline) | | **DNA change** | c.1297G>C | | **Gene · Protein** | WFS1 · Wolframin (890 aa) | | **UniProt** | O76024 · WFS1_HUMAN | | **ClinVar accession** | VCV003250063 | | **Amino acid change** | Alanine (small, hydrophobic, helix-promoting — alanine has one of the highest alpha-helix propensities of any amino acid) to Proline (cyclic side chain, locks backbone phi near -60 degrees, lacks the amide NH needed for the alpha-helix hydrogen-bond network, the canonical helix-breaker) at position 433. | --- ## Structural Context | Field | Value | |---|---| | **AlphaFold model** | AF-O76024-F1, v6 | | **pLDDT at residue 433** | **91.31** — well-folded | | **Domain** | TM4 (427-447), helical transmembrane | | **Position context** | Position 433 sits inside transmembrane helix TM4 (residues 427-447) — one of wolframin's eleven membrane-spanning helices. The residue is buried in the ER bilayer interior and contributes to inter-helix packing. pLDDT 91.31 confirms a confidently modeled position. | | **IDR flag** | No — pLDDT above 50 threshold | **UniProt features at this position:** - Chain: 1-890 Wolframin - Transmembrane: 427-447 Helical > A433 is held between Val434 (2.47 Angstrom) and Leu432 (2.48 Angstrom), with through-space contacts to Thr436 (3.30 Angstrom), Cys429 (3.61 Angstrom), Ile547 (4.04 Angstrom — note: this is far in sequence, indicating an inter-helix contact, likely with TM5), Ser430 (4.10 Angstrom), Glu431 (4.35 Angstrom), and Ile435 (4.42 Angstrom). The contact set tells two stories: a hydrophobic packing core within TM4 itself (Val434, Leu432, Ile435), and an inter-helix interaction with TM5 (Ile547 at 4.04 Angstrom). The wild-type alanine's compact methyl fits cleanly into both contexts. The Cys429 contact at 3.61 Angstrom is mechanistically important. A free cysteine inside a transmembrane helix at close distance to A433 suggests the wild-type geometry holds the cysteine in a defined orientation. If A433P perturbs that geometry, the cysteine's local environment changes — and a TM-buried cysteine that becomes solvent-accessible or shifts toward an oxidative environment becomes a disulfide-formation liability. Replacing A433 with proline is one of the most disruptive single-residue substitutions possible inside an alpha-helix. Proline's pyrrolidine ring forces phi near -60 degrees (incompatible with the standard alpha-helix phi of -60 to -65 degrees only when its other constraints are also satisfied — typically not in the middle of an extended helix) and eliminates the backbone amide NH needed for the i-to-i+4 hydrogen bond that defines the alpha-helix structure. Proline insertions in the middle of TM helices reliably introduce 20-30 degree kinks in the helix axis. The consequence for TM4 is a kink at residue 433 that propagates upward and downward through the helix, shifting the inter-helix register with TM5 (the Ile547 contact at 4.04 Angstrom). The Cys429 environment is also disturbed. DynaMut2 reports DeltaDeltaG = -0.05 kcal/mol — essentially zero. This is a known limitation of energy functions for proline introductions: the local van der Waals improvement from proline's rigid ring partially compensates the lost hydrogen-bonding capacity, and the energy function under-weighs the structural propagation cost. AlphaMissense at 0.990 reads the true severity: A433P is essentially a TM4 disruption, predicted to be near-fully pathogenic. --- ## Computational Predictions ### AlphaMissense | Field | Value | |---|---| | am_pathogenicity | **0.9902** | | am_class | **LPath** | | Interpretation | Likely pathogenic (threshold 0.564) | ### DynaMut2 | Field | Value | |---|---| | ΔΔG (kcal/mol) | **-0.05 (Destabilising)** | | Job ID | 177991410826 | | Result URL | https://biosig.lab.uq.edu.au/dynamut2/results_prediction/177991410826 | --- ## Clinical Evidence | Field | Value | |---|---| | Classification | **Likely pathogenic** | | Review status | no assertion criteria provided | | Last evaluated | 2019/01/01 00:00 | | Inheritance | Inheritance pattern documented: optic atrophy. | | WFS1 variant landscape | A433P is 1 of ~326 pathogenic-spectrum variants in WFS1 (out of 2,243 catalogued in ClinVar) | - Optic atrophy --- ## 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 per the schema's DeltaDeltaG-magnitude rule, but with a strong structural-chemistry override note. A proline introduction in a TM helix is mechanistically severe regardless of what the energy function reports. The variant likely behaves more like Category 2 (chaperone-rescuable) or even Category 1 (gene therapy candidate) in practice, depending on how cleanly TM4 inserts into the bilayer with the proline-induced kink. For druggability, pharmacological chaperones that stabilize TM4 packing during co-translational membrane insertion are the most plausible therapeutic route. The Cys429 disulfide-formation risk should be modeled explicitly. Site-directed compound design against TM4 from the lumenal or cytoplasmic face is challenging given the buried geometry, but the helix-helix interface with TM5 (the Ile547 contact) is a potential anchor for stabilizing molecules. **Why this card matters.** A433P is the second buried-TM proline introduction in the Atlas batch this week (alongside A806P, which is in the lumenal domain rather than a TM helix). The Atlas's treatment of TM proline introductions is a recurring pattern: the energy function under-reads, AlphaMissense correctly flags, and the structural chemistry argues for an override to a more serious category. This pattern matters because TM helix mutations are mechanistically tractable in a way the lumenal-domain mutations are not — pharmacological chaperone screening has a long history of rescuing TM-folding defects in proteins like CFTR, rhodopsin, and the V2 vasopressin receptor. If the wolframin program adopts the same chaperone-screening strategy, TM helix variants like A433P and G437R are the highest-priority candidates. --- ## Files in this folder - `AF-O76024-F1-model_v6.pdb` — AlphaFold structure - `A433P_molstar_viewer.html` — interactive 3D viewer (auto-highlights position 433 with ball-and-stick + neighbors within 5Å) - `A433P_variant_card.md` — this card (source of truth) - `A433P_variant_card.html` — styled printable card - `A433P_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) - `A433P_wildtype_interactions.pse` / `A433P_mutant_interactions.pse` — PyMOL sessions --- *Generated by wolfram-variant-card skill · RareResearch.AI Molecular Atlas* *Every assumption documented. Every score sourced.*