# WFS1 Wolframin — E864K Variant Card **Molecular Atlas Pilot · RareResearch.AI · Generated by wolfram-variant-card skill** *Charge-flip mutation at the very C-terminal edge of the lumenal domain — glutamate's negative carboxylate replaced by lysine's positive amine, in a region where pLDDT (59) signals borderline confidence and the structural interpretation requires explicit caution.* --- ## Identity | Field | Value | |---|---| | **Variant** | E864K (p.Glutamate864Lysine) | | **DNA change** | c.2590G>A | | **Gene · Protein** | WFS1 · Wolframin (890 aa) | | **UniProt** | O76024 · WFS1_HUMAN | | **ClinVar accession** | VCV000004526 | | **Amino acid change** | Glutamate (negatively charged carboxylate side chain, ~5 Angstrom long) to Lysine (positively charged primary amine on a long aliphatic side chain, ~6.5 Angstrom long) at position 864. The substitution flips the charge sign in a single mutation — a classical electrostatic-disruption signature. | --- ## Structural Context | Field | Value | |---|---| | **AlphaFold model** | AF-O76024-F1, v6 | | **pLDDT at residue 864** | **59.28** — confident | | **Domain** | C-terminal lumenal domain (653-869) | | **Position context** | Position 864 sits near the C-terminal end of the lumenal domain (residues 653-869), just 5 residues before the lumenal-domain boundary. pLDDT 59.28 is borderline: above the IDR threshold (50) but below high-confidence (70+). The residue is modelable but the precise geometry should be treated with appropriate uncertainty. | | **IDR flag** | No — pLDDT above 50 threshold | **UniProt features at this position:** - Chain: 1-890 Wolframin - Topological domain: 653-869 Lumenal - Natural variant: 864-864 in WFSL; dbSNP:rs74315205 > E864 has only four neighbors within 5 Angstrom: His865 (2.41 Angstrom), Ile863 (2.43 Angstrom), Asp866 (4.75 Angstrom), and Lys862 (4.80 Angstrom). The minimal contact set is itself diagnostic — at pLDDT 59, AlphaFold is signaling that the local conformation is partially ordered or solvent-exposed rather than packed against a stable core. The neighborhood is locally informative nonetheless: a histidine, a downstream aspartate, and an upstream lysine all sit within the polar shell. In the wild-type configuration, E864's carboxylate plausibly forms a salt bridge with K862 (4.80 Angstrom is within typical salt-bridge range when sidechain conformations are accounted for), and may hydrogen-bond to His865 depending on the imidazole's protonation state. The downstream Asp866 contributes additional negative charge to the local cluster — two glutamates/aspartates and one lysine, balanced. E864K flips the charge sign on E864. The K862-E864 salt bridge is destroyed because both residues are now positively charged — they will electrostatically repel rather than attract. The local cluster goes from -E864 ... +K862 ... -D866 (a balanced charge triad) to +K864 ... +K862 ... -D866 (a positive pair next to a negative residue). The geometric consequence is that K862 and K864 likely splay apart, dragging the backbone with them, while D866's carboxylate may rotate to form a new salt bridge with one of the lysines. DynaMut2's DeltaDeltaG of -0.26 kcal/mol substantially under-reads the disruption — energy functions tend to compensate the electrostatic loss when a new contact forms, even if that contact is geometrically forced. AlphaMissense at 0.842 reads the true severity. The clinical phenotype is broad: retinal dystrophy, autosomal dominant nonsyndromic hearing loss 6, Wolfram-like syndrome — consistent with a C-terminal lumenal disruption affecting the function of the lumenal sensor face. --- ## Computational Predictions ### AlphaMissense | Field | Value | |---|---| | am_pathogenicity | **0.8424** | | am_class | **LPath** | | Interpretation | Likely pathogenic (threshold 0.564) | ### DynaMut2 | Field | Value | |---|---| | ΔΔG (kcal/mol) | **-0.26 (Destabilising)** | | Job ID | 177991406993 | | Result URL | https://biosig.lab.uq.edu.au/dynamut2/results_prediction/177991406993 | --- ## Clinical Evidence | Field | Value | |---|---| | Classification | **Pathogenic/Likely pathogenic** | | Review status | criteria provided, multiple submitters, no conflicts | | Last evaluated | 2024/11/08 00:00 | | Inheritance | Autosomal dominant (deafness 6) and Wolfram-like spectrum forms documented. | | WFS1 variant landscape | E864K is 1 of ~326 pathogenic-spectrum variants in WFS1 (out of 2,243 catalogued in ClinVar) | - Autosomal dominant nonsyndromic hearing loss 6 - Wolfram-like syndrome - Retinal dystrophy - Rare genetic deafness - Nonsyndromic genetic hearing loss --- ## 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 4 — Stable Fold, Function Disrupted. The DeltaDeltaG magnitude (0.26 kcal/mol) is small, the pLDDT (59) is borderline, and the charge-flip biology is the dominant mechanism. The Atlas should treat E864K as a functional-site disruption variant rather than a misfolding variant: the gross fold survives, but a specific electrostatic signature near the C-terminal edge of the lumenal domain is inverted. For druggability, the borderline pLDDT introduces caveats. Docking against a region with pLDDT 59 requires either local refinement or experimental structure determination — the AlphaFold model is acceptable for hypothesis generation but should not be the sole basis for compound design. The therapeutic frame is still pharmacological chaperone or charge-mimicking small molecule, but the model uncertainty argues for parallel wet-lab validation of the K862-E864-D866 cluster's structural arrangement. **Why this card matters.** E864K is a useful Atlas example of how the schema must handle borderline pLDDT honestly. A naive interpretation would push this variant into the Cat 5 IDR-exclusion bucket; the structural signal (a clear charge-flip near an annotated salt-bridge candidate) and the AlphaMissense score (0.842) argue against exclusion. The right answer is Category 4 with an explicit modeling caveat — not a default discard. Clinically, the autosomal dominant deafness 6 phenotype at this variant is notable. AD-DFNA6 carries a distinct disease trajectory from classical autosomal recessive Wolfram syndrome, and E864K is one of the lumenal-domain variants where the dominant inheritance pattern is best documented. This makes E864K a clinical reference variant for the dominantly-inherited Wolfram-spectrum hearing loss form. --- ## Files in this folder - `AF-O76024-F1-model_v6.pdb` — AlphaFold structure - `E864K_molstar_viewer.html` — interactive 3D viewer (auto-highlights position 864 with ball-and-stick + neighbors within 5Å) - `E864K_variant_card.md` — this card (source of truth) - `E864K_variant_card.html` — styled printable card - `E864K_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) - `E864K_wildtype_interactions.pse` / `E864K_mutant_interactions.pse` — PyMOL sessions --- *Generated by wolfram-variant-card skill · RareResearch.AI Molecular Atlas* *Every assumption documented. Every score sourced.*