# WFS1 Wolframin — A126T Variant Card **Molecular Atlas Pilot · RareResearch.AI · Generated by wolfram-variant-card skill** *An alanine-to-threonine substitution inside wolframin's N-terminal cytoplasmic domain — a region that engages ATP6V1A (the V-ATPase regulatory partner) — and sits adjacent to a free cysteine that adds an unwanted disulfide-formation risk.* --- ## Identity | Field | Value | |---|---| | **Variant** | A126T (p.Alanine126Threonine) | | **DNA change** | c.376G>A | | **Gene · Protein** | WFS1 · Wolframin (890 aa) | | **UniProt** | O76024 · WFS1_HUMAN | | **ClinVar accession** | VCV000372583 | | **Amino acid change** | Alanine (small, hydrophobic, methyl side chain) to Threonine (small polar, beta-branched hydroxyl side chain) at position 126. The substitution introduces both a hydroxyl group and beta-branching where the wild-type contributed neither. | --- ## Structural Context | Field | Value | |---|---| | **AlphaFold model** | AF-O76024-F1, v6 | | **pLDDT at residue 126** | **93.00** — well-folded | | **Domain** | N-terminal cytoplasmic domain (87-313) | | **Position context** | Position 126 sits inside wolframin's N-terminal cytoplasmic domain (residues 87-313), which UniProt explicitly annotates as the Region of interaction with ATP6V1A (V-type proton ATPase catalytic subunit A) — residues 1-321. This is functional regulatory territory. pLDDT 93.0 marks the residue as exceptionally well-modeled. | | **IDR flag** | No — pLDDT above 50 threshold | **UniProt features at this position:** - Chain: 1-890 Wolframin - Region: 1-321 Interaction with ATP6V1A - Natural variant: 126-126 in WFS1; dbSNP:rs145639028 > A126 is held between Thr125 (2.45 Angstrom) and Val127 (2.46 Angstrom), with a tight through-space contact cluster: Asn122 (3.70 Angstrom), Ser123 (3.80 Angstrom), Tyr110 (3.85 Angstrom), Gly107 (4.06 Angstrom), Cys124 (4.22 Angstrom), and Asp128 (4.42 Angstrom). The local environment is polar-rich — three threonines and serines, a tyrosine, an aspartate, an asparagine, and a free cysteine within 4.5 Angstrom. This is a well-organized polar interface, almost certainly part of the ATP6V1A-binding surface. The wild-type alanine's methyl side chain occupies a single non-polar slot in the polar cluster. Threonine adds a hydroxyl and a beta-branched methyl group. The hydroxyl will look for a hydrogen-bond partner — and Asp128 at 4.42 Angstrom, Asn122 at 3.70 Angstrom, and Ser123 at 3.80 Angstrom all qualify. The result is a forced rearrangement of the local hydrogen-bond network: a contact the wild-type kept open (A126 contributed nothing) is now occupied by the threonine hydroxyl, and the polar partners reorganize accordingly. The Cys124 contact at 4.22 Angstrom is the second mechanistic concern. Free cytoplasmic cysteines are typically reduced, but local hydrogen-bond reorganization can alter the cysteine's pKa or its local solvation, raising the risk of inappropriate disulfide formation under oxidative stress — and ER-stressed cells in Wolfram syndrome are chronically oxidatively stressed. The threonine introduction at 126 thus has two failure modes: direct disruption of the ATP6V1A-binding surface, and secondary destabilization of Cys124 under cellular stress. DynaMut2 reports DeltaDeltaG = -1.76 kcal/mol — destabilising and the largest magnitude in this batch. AlphaMissense at 0.878 confirms strong functional constraint. The combination of high pLDDT, sizable destabilization, and functional-surface placement makes A126T mechanistically clear. --- ## Computational Predictions ### AlphaMissense | Field | Value | |---|---| | am_pathogenicity | **0.8776** | | am_class | **LPath** | | Interpretation | Likely pathogenic (threshold 0.564) | ### DynaMut2 | Field | Value | |---|---| | ΔΔG (kcal/mol) | **-1.76 (Destabilising)** | | Job ID | 177991406804 | | Result URL | https://biosig.lab.uq.edu.au/dynamut2/results_prediction/177991406804 | --- ## Clinical Evidence | Field | Value | |---|---| | Classification | **Pathogenic/Likely pathogenic** | | Review status | criteria provided, multiple submitters, no conflicts | | Last evaluated | 2026/01/19 00:00 | | Inheritance | Both autosomal dominant and autosomal recessive inheritance documented. | | WFS1 variant landscape | A126T is 1 of ~326 pathogenic-spectrum variants in WFS1 (out of 2,243 catalogued in ClinVar) | - Wolfram syndrome 1 - 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 2/3 borderline — pharmacological chaperone with site-directed elements. DeltaDeltaG of -1.76 kcal/mol is at the upper end of the small-magnitude bucket and approaching the chaperone-rescue threshold. The lesion is on a functional surface (ATP6V1A interaction zone), and the disruption is local — both pharmacological chaperone and site-directed small-molecule design are viable approaches. The Cys124 proximity warrants explicit modeling. Any compound designed against this site should be tested for cysteine reactivity, both to confirm no off-target covalent labeling and to verify that it does not inadvertently shift Cys124 toward disulfide-forming geometry. Conversely, antioxidant cofactors that preserve the reduced state of Cys124 may complement chaperone therapy in carriers under oxidative stress. **Why this card matters.** A126T is the first variant in this batch that sits on an explicitly annotated protein-protein interaction surface — wolframin's contact with ATP6V1A in V-ATPase regulation. Disrupting this interaction has functional consequences distinct from misfolding: it affects wolframin's role as a regulator of cellular acidification and calcium handling, not just its presence at the membrane. The therapeutic implication is that even if A126T-bearing wolframin reaches the membrane in normal abundance, it may functionally underperform. For the Atlas, A126T represents the cytoplasmic-domain Category 3 cluster — where the binding-surface-disruption variants live. These variants demand a different drug-design strategy than the lumenal Cat 3 cluster: stabilizers of the ATP6V1A-wolframin interaction rather than chaperones of wolframin folding alone. Mapping the cluster across the N-terminal cytoplasmic domain is a near-term Atlas deliverable. --- ## Files in this folder - `AF-O76024-F1-model_v6.pdb` — AlphaFold structure - `A126T_molstar_viewer.html` — interactive 3D viewer (auto-highlights position 126 with ball-and-stick + neighbors within 5Å) - `A126T_variant_card.md` — this card (source of truth) - `A126T_variant_card.html` — styled printable card - `A126T_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) - `A126T_wildtype_interactions.pse` / `A126T_mutant_interactions.pse` — PyMOL sessions --- *Generated by wolfram-variant-card skill · RareResearch.AI Molecular Atlas* *Every assumption documented. Every score sourced.*