A677T
Category 4 — Stable Fold, Function DisruptedUncertain significanceLumenal · predictedσ-1 candidateSource cardInteractive 3D Structure
Bond changes · DynaMut2 interaction analysis
| Interaction type | Wild-type partner | Mutant partner | Status |
|---|---|---|---|
| Hydrogen bond | A671 | A671 | Preserved |
| Hydrogen bond | — | L672 | Gained |
| Hydrogen bond | G674 | G674 | Preserved |
| Hydrogen bond | T681 | T681 | Preserved |
| Hydrogen bond | — | T686 | Gained |
| Polar contact | L672 | L672 | Preserved |
| Polar contact | G674 | G674 | Preserved |
| Polar contact | — | K679 | Gained |
| Polar contact | — | E680 | Gained |
| Polar contact | T681 | T681 | Preserved |
| Van der Waals | — | L672 | Gained |
| Van der Waals | — | G674 | Gained |
| Van der Waals | K679 | — | Lost |
| Hydrophobic | T686 | T686 | Preserved |
Lost / gained / preserved interatomic contacts at the variant residue, from the DynaMut2 (Arpeggio) interaction analysis of the wild-type and energy-minimized mutant structures.
Computational Predictions
Clinical Evidence
Observed at very low frequency in gnomAD.
Full Variant Card
WFS1 Wolframin — A677T Variant Card
Molecular Atlas Pilot · RareResearch.AI · Generated by wolfram-variant-card skill
Alanine → Threonine at position 677. C-terminal ER-lumenal (calcium binding. ClinVar Uncertain significance/Uncertain risk allele, AlphaMissense 0.488, DynaMut2 ΔΔG -1.70 kcal/mol (destabilising).
Identity
| Field | Value |
|---|---|
| Variant | A677T (p.Alanine677Threonine) |
| DNA change | c.2029G>A |
| Gene · Protein | WFS1 · Wolframin (890 aa) |
| UniProt | O76024 · WFS1_HUMAN |
| ClinVar accession | VCV000198834 |
| Amino acid change | Alanine (A) → Threonine (T) |
Structural Context
| Field | Value |
|---|---|
| AlphaFold model | AF-O76024-F1, v6 |
| pLDDT at residue 677 | 81.19 — well-folded |
| Domain | C-terminal ER-lumenal (calcium binding, calmodulin, chaperone) |
| Position context | C-terminal lumenal domain · position 677 projects into the ER lumen |
| IDR flag | No — pLDDT above 50 threshold |
UniProt features at this position:
(none catalogued)
Position 677 sits in the C-terminal lumenal domain (residues 653–869), wolframin's largest soluble region. This domain projects into the ER lumen and is implicated in calcium handling, ER stress sensing, and protein–protein interactions with ATF6 and Na+/K+ ATPase β1. The wild-type residue is small/hydrophobic (alanine — methyl sidechain); the mutant is small polar (threonine — hydroxyl). The chemistry shift implies altered local packing, hydrogen-bonding, and/or electrostatics at this site.
Computational Predictions
AlphaMissense
| Field | Value |
|---|---|
| am_pathogenicity | 0.4876 |
| am_class | ambiguous |
| Interpretation | Likely benign (threshold 0.564) |
DynaMut2
| Field | Value |
|---|---|
| ΔΔG (kcal/mol) | -1.7 (Destabilising) |
| Job ID | 178094717564 |
| Result URL | https://biosig.lab.uq.edu.au/dynamut2/results_prediction/178094717564 |
Clinical Evidence
| Field | Value |
|---|---|
| Classification | Uncertain significance/Uncertain risk allele |
| Review status | criteria provided, multiple submitters, no conflicts |
| Last evaluated | 2025/09/08 00:00 |
| Inheritance | Autosomal dominant pattern indicated by associated DFNA6/14/38 (WFS1 hearing loss 6). |
| WFS1 variant landscape | A677T is 1 of ~326 pathogenic-spectrum variants in WFS1 (out of 2,243 catalogued in ClinVar) |
- Retinal dystrophy
- Childhood onset hearing loss
- Cataract 41
- Wolfram syndrome 1
- Autosomal dominant nonsyndromic hearing loss 6
- Type 2 diabetes mellitus
- 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 4 — Stable Fold, Function Disrupted
<strong>Category 4 — Stable Fold, Function Disrupted</strong><br/><br/>|ΔΔG|=1.70 negligible. Likely site-specific functional disruption — docking strategy.
Why this card matters. Wolframin's fold survives this substitution (|ΔΔG|=1.70 kcal/mol). The pathogenic signal is real — AlphaMissense places it at 0.488. Protein still folds, but a specific local site is broken. Pharmacological chaperones and small-molecule binders are the rational therapeutic vector.
Files in this folder
AF-O76024-F1-model_v6.pdb— AlphaFold structureA677T_molstar_viewer.html— interactive 3D viewer (auto-highlights position 677 with ball-and-stick + neighbors within 5Å)A677T_variant_card.md— this card (source of truth)A677T_variant_card.html— styled printable cardA677T_dynamut2_summary.html— clean offline DynaMut2 result carddynamut2_result.json— structured result datadynamut2_result_page.html— local snapshot of the Biosig result page (asset URLs absolutized)A677T_wildtype_interactions.pse/A677T_mutant_interactions.pse— PyMOL sessions
Generated by wolfram-variant-card skill · RareResearch.AI Molecular Atlas Every assumption documented. Every score sourced.
Feed this card to Wolfram Intelligence
Download the A677T PDF below and upload it to Wolfram Intelligence to generate therapeutic-strategy proposals — guanidinium mimetics, sigma-1 agonist docking, NAC thiol-capping. NAC is already on the bench-testing list.